Starting phenix.real_space_refine on Wed Feb 4 05:57:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ko4_62469/02_2026/9ko4_62469.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ko4_62469/02_2026/9ko4_62469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ko4_62469/02_2026/9ko4_62469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ko4_62469/02_2026/9ko4_62469.map" model { file = "/net/cci-nas-00/data/ceres_data/9ko4_62469/02_2026/9ko4_62469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ko4_62469/02_2026/9ko4_62469.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.035 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 64 5.16 5 C 5716 2.51 5 N 1486 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8908 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 531 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 65} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "R" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2437 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 6, 'TRANS': 309} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "A" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1712 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2256 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 298} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "G" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 242 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 30} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1730 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 1.99, per 1000 atoms: 0.22 Number of scatterers: 8908 At special positions: 0 Unit cell: (104, 113.36, 144.56, 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 64 16.00 O 1642 8.00 N 1486 7.00 C 5716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS L 8 " - pdb=" SG CYS L 34 " distance=2.03 Simple disulfide: pdb=" SG CYS L 9 " - pdb=" SG CYS L 52 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 298 " distance=2.03 Simple disulfide: pdb=" SG CYS R 129 " - pdb=" SG CYS R 210 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 246.5 milliseconds 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 36.9% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'L' and resid 18 through 20 No H-bonds generated for 'chain 'L' and resid 18 through 20' Processing helix chain 'L' and resid 57 through 67 Processing helix chain 'R' and resid 40 through 44 Processing helix chain 'R' and resid 50 through 87 Proline residue: R 62 - end of helix removed outlier: 3.564A pdb=" N ILE R 67 " --> pdb=" O ILE R 63 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU R 74 " --> pdb=" O PHE R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 120 removed outlier: 3.555A pdb=" N THR R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) Proline residue: R 112 - end of helix Processing helix chain 'R' and resid 125 through 159 Processing helix chain 'R' and resid 160 through 165 Processing helix chain 'R' and resid 167 through 190 removed outlier: 3.993A pdb=" N VAL R 180 " --> pdb=" O LYS R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 197 Processing helix chain 'R' and resid 216 through 230 removed outlier: 4.237A pdb=" N PHE R 220 " --> pdb=" O HIS R 216 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE R 221 " --> pdb=" O VAL R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 251 removed outlier: 4.150A pdb=" N LEU R 244 " --> pdb=" O SER R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 292 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 297 through 326 removed outlier: 3.546A pdb=" N SER R 301 " --> pdb=" O THR R 297 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS R 302 " --> pdb=" O CYS R 298 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 343 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.991A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 53 removed outlier: 4.414A pdb=" N GLY A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.240A 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 256 Processing helix chain 'A' and resid 257 through 260 removed outlier: 3.569A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.088A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.897A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.603A pdb=" N VAL A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 44 removed outlier: 4.016A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.605A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.889A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 22 through 25 removed outlier: 4.408A pdb=" N SER L 24 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 198 through 202 removed outlier: 4.952A pdb=" N SER R 202 " --> pdb=" O ALA R 207 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ALA R 207 " --> pdb=" O SER R 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.212A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 50 removed outlier: 3.821A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.805A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.141A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 148 through 153 removed outlier: 6.517A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.862A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.451A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.794A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 286 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.625A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.379A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB6, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.750A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1266 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: 1.30 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2839 1.34 - 1.46: 2294 1.46 - 1.59: 3879 1.59 - 1.71: 0 1.71 - 1.83: 88 Bond restraints: 9100 Sorted by residual: bond pdb=" N ASP L 2 " pdb=" CA ASP L 2 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.44e+00 bond pdb=" C SER B 67 " pdb=" N ARG B 68 " ideal model delta sigma weight residual 1.332 1.303 0.029 1.40e-02 5.10e+03 4.31e+00 bond pdb=" N GLN L 48 " pdb=" CA GLN L 48 " ideal model delta sigma weight residual 1.453 1.481 -0.028 1.37e-02 5.33e+03 4.03e+00 bond pdb=" C THR L 70 " pdb=" N PRO L 71 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.85e+00 bond pdb=" C SER R 49 " pdb=" N LYS R 50 " ideal model delta sigma weight residual 1.333 1.309 0.025 1.56e-02 4.11e+03 2.47e+00 ... (remaining 9095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 12100 1.68 - 3.36: 235 3.36 - 5.04: 27 5.04 - 6.73: 9 6.73 - 8.41: 3 Bond angle restraints: 12374 Sorted by residual: angle pdb=" N GLN R 286 " pdb=" CA GLN R 286 " pdb=" C GLN R 286 " ideal model delta sigma weight residual 111.07 106.86 4.21 1.07e+00 8.73e-01 1.55e+01 angle pdb=" N ASP L 2 " pdb=" CA ASP L 2 " pdb=" C ASP L 2 " ideal model delta sigma weight residual 110.80 103.20 7.60 2.13e+00 2.20e-01 1.27e+01 angle pdb=" C ALA R 157 " pdb=" N ILE R 158 " pdb=" CA ILE R 158 " ideal model delta sigma weight residual 122.97 119.74 3.23 9.80e-01 1.04e+00 1.09e+01 angle pdb=" CA ASP L 2 " pdb=" CB ASP L 2 " pdb=" CG ASP L 2 " ideal model delta sigma weight residual 112.60 115.66 -3.06 1.00e+00 1.00e+00 9.39e+00 angle pdb=" N ILE R 293 " pdb=" CA ILE R 293 " pdb=" C ILE R 293 " ideal model delta sigma weight residual 113.07 108.99 4.08 1.36e+00 5.41e-01 9.02e+00 ... (remaining 12369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.60: 4753 12.60 - 25.19: 416 25.19 - 37.79: 120 37.79 - 50.39: 50 50.39 - 62.98: 14 Dihedral angle restraints: 5353 sinusoidal: 1934 harmonic: 3419 Sorted by residual: dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 298 " pdb=" CB CYS R 298 " ideal model delta sinusoidal sigma weight residual -86.00 -136.00 50.00 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 140.05 -47.05 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CA ILE R 230 " pdb=" C ILE R 230 " pdb=" N GLY R 231 " pdb=" CA GLY R 231 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 792 0.027 - 0.055: 395 0.055 - 0.082: 164 0.082 - 0.109: 69 0.109 - 0.137: 25 Chirality restraints: 1445 Sorted by residual: chirality pdb=" CB ILE R 223 " pdb=" CA ILE R 223 " pdb=" CG1 ILE R 223 " pdb=" CG2 ILE R 223 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE L 36 " pdb=" N ILE L 36 " pdb=" C ILE L 36 " pdb=" CB ILE L 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 1442 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 230 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C ILE R 230 " -0.037 2.00e-02 2.50e+03 pdb=" O ILE R 230 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY R 231 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L 70 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.33e+00 pdb=" N PRO L 71 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO L 71 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 71 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 234 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO R 235 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO R 235 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 235 " -0.025 5.00e-02 4.00e+02 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3206 2.85 - 3.37: 8886 3.37 - 3.88: 15363 3.88 - 4.39: 17583 4.39 - 4.90: 29668 Nonbonded interactions: 74706 Sorted by model distance: nonbonded pdb=" O SER L 1 " pdb=" N GLY L 3 " model vdw 2.343 3.120 nonbonded pdb=" O LYS R 50 " pdb=" N VAL R 53 " model vdw 2.452 3.120 nonbonded pdb=" N ASP L 2 " pdb=" OD1 ASP L 2 " model vdw 2.494 3.120 nonbonded pdb=" C THR H 215 " pdb=" OG1 THR H 215 " model vdw 2.526 2.616 nonbonded pdb=" O SER R 49 " pdb=" CA LYS R 50 " model vdw 2.579 2.776 ... (remaining 74701 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.130 Find NCS groups from input model: 0.030 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 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 : 0.005 0.041 9107 Z= 0.223 Angle : 0.612 8.407 12388 Z= 0.336 Chirality : 0.042 0.137 1445 Planarity : 0.004 0.052 1554 Dihedral : 11.813 62.982 3126 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 5.79 % Allowed : 8.80 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.25), residues: 1159 helix: 0.91 (0.28), residues: 370 sheet: -0.36 (0.29), residues: 289 loop : -0.92 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.021 0.002 TYR R 136 PHE 0.016 0.002 PHE B 151 TRP 0.013 0.002 TRP B 99 HIS 0.002 0.001 HIS R 127 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9100) covalent geometry : angle 0.61113 (12374) SS BOND : bond 0.00440 ( 7) SS BOND : angle 1.17658 ( 14) hydrogen bonds : bond 0.12316 ( 450) hydrogen bonds : angle 6.33158 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 302 time to evaluate : 0.224 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: L 2 ASP cc_start: 0.6847 (OUTLIER) cc_final: 0.6017 (p0) REVERT: R 50 LYS cc_start: 0.7944 (mmmm) cc_final: 0.7741 (mtmm) REVERT: R 92 MET cc_start: 0.8321 (ttp) cc_final: 0.8076 (ttt) REVERT: R 177 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7401 (mt) REVERT: R 329 ILE cc_start: 0.7684 (tp) cc_final: 0.7442 (tp) REVERT: A 197 LYS cc_start: 0.7890 (pttt) cc_final: 0.7393 (pttt) REVERT: A 247 MET cc_start: 0.7471 (ttm) cc_final: 0.7223 (ttm) REVERT: A 256 ASN cc_start: 0.8283 (m-40) cc_final: 0.8053 (m-40) REVERT: A 321 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.7913 (p) REVERT: A 345 LYS cc_start: 0.7909 (tttt) cc_final: 0.7531 (tttt) REVERT: A 349 LYS cc_start: 0.8385 (ttmm) cc_final: 0.8185 (mtmm) REVERT: A 351 CYS cc_start: 0.6409 (m) cc_final: 0.6123 (m) REVERT: B 54 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.7355 (m-70) REVERT: B 105 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.7007 (t80) REVERT: B 235 PHE cc_start: 0.5661 (OUTLIER) cc_final: 0.5421 (t80) REVERT: H 30 SER cc_start: 0.8840 (p) cc_final: 0.8532 (m) REVERT: H 145 SER cc_start: 0.8444 (t) cc_final: 0.8139 (p) REVERT: H 186 GLN cc_start: 0.7542 (tt0) cc_final: 0.7333 (tt0) outliers start: 54 outliers final: 21 residues processed: 338 average time/residue: 0.0808 time to fit residues: 37.2084 Evaluate side-chains 297 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 286 GLN Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 343 ASP Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 48 GLN R 216 HIS R 286 GLN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** H 231 GLN ** 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 = 0.3923 r_free = 0.3923 target = 0.124378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.108912 restraints weight = 16476.851| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.11 r_work: 0.3570 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9107 Z= 0.158 Angle : 0.636 7.701 12388 Z= 0.327 Chirality : 0.043 0.158 1445 Planarity : 0.004 0.053 1554 Dihedral : 7.997 63.290 1313 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.94 % Allowed : 18.24 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.25), residues: 1159 helix: 1.24 (0.27), residues: 372 sheet: -0.10 (0.31), residues: 268 loop : -0.93 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 52 TYR 0.028 0.002 TYR R 279 PHE 0.019 0.002 PHE R 241 TRP 0.013 0.002 TRP H 111 HIS 0.006 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9100) covalent geometry : angle 0.63365 (12374) SS BOND : bond 0.00687 ( 7) SS BOND : angle 1.62424 ( 14) hydrogen bonds : bond 0.04219 ( 450) hydrogen bonds : angle 5.04936 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 274 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 ILE cc_start: 0.8711 (mt) cc_final: 0.8291 (mt) REVERT: R 42 THR cc_start: 0.8663 (m) cc_final: 0.8218 (m) REVERT: R 49 SER cc_start: 0.8677 (t) cc_final: 0.8438 (p) REVERT: R 73 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8203 (mt) REVERT: R 92 MET cc_start: 0.8281 (ttp) cc_final: 0.7964 (ttt) REVERT: R 136 TYR cc_start: 0.5738 (OUTLIER) cc_final: 0.5246 (t80) REVERT: R 160 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7646 (mt0) REVERT: R 177 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7479 (mt) REVERT: R 236 LEU cc_start: 0.7445 (tt) cc_final: 0.7181 (tp) REVERT: R 247 ILE cc_start: 0.6870 (mm) cc_final: 0.6564 (mm) REVERT: R 279 TYR cc_start: 0.6794 (t80) cc_final: 0.6055 (t80) REVERT: R 308 TYR cc_start: 0.6973 (t80) cc_final: 0.6264 (t80) REVERT: R 312 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.7091 (t80) REVERT: A 32 ARG cc_start: 0.8696 (ttm170) cc_final: 0.8456 (ttm110) REVERT: A 197 LYS cc_start: 0.7933 (pttt) cc_final: 0.7402 (pttt) REVERT: A 219 THR cc_start: 0.8419 (m) cc_final: 0.8160 (t) REVERT: A 279 LYS cc_start: 0.9063 (mmtp) cc_final: 0.8823 (mmtp) REVERT: A 308 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7931 (mt-10) REVERT: A 345 LYS cc_start: 0.8098 (tttt) cc_final: 0.7652 (tttt) REVERT: A 349 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8277 (mtmm) REVERT: A 351 CYS cc_start: 0.6085 (m) cc_final: 0.5741 (m) REVERT: B 45 MET cc_start: 0.7949 (mtt) cc_final: 0.7604 (mtp) REVERT: B 52 ARG cc_start: 0.8374 (ttm110) cc_final: 0.8007 (mtt-85) REVERT: B 217 MET cc_start: 0.7161 (mtm) cc_final: 0.6910 (ptp) REVERT: B 235 PHE cc_start: 0.5645 (OUTLIER) cc_final: 0.5436 (t80) REVERT: B 247 ASP cc_start: 0.6507 (t70) cc_final: 0.6305 (t0) REVERT: H 145 SER cc_start: 0.8513 (t) cc_final: 0.8164 (p) REVERT: H 186 GLN cc_start: 0.8007 (tt0) cc_final: 0.7707 (tt0) outliers start: 46 outliers final: 34 residues processed: 300 average time/residue: 0.0786 time to fit residues: 32.4553 Evaluate side-chains 302 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 312 TYR Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 324 PHE Chi-restraints excluded: chain R residue 343 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 62 GLN R 216 HIS R 224 GLN R 255 ASN R 280 ASN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.122238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.107870 restraints weight = 17157.041| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.07 r_work: 0.3501 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 9107 Z= 0.262 Angle : 0.707 8.505 12388 Z= 0.365 Chirality : 0.046 0.162 1445 Planarity : 0.005 0.051 1554 Dihedral : 7.719 60.185 1298 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 7.19 % Allowed : 18.67 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.24), residues: 1159 helix: 0.80 (0.27), residues: 371 sheet: -0.25 (0.31), residues: 273 loop : -1.14 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 314 TYR 0.031 0.003 TYR R 136 PHE 0.020 0.002 PHE R 272 TRP 0.022 0.002 TRP L 59 HIS 0.004 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 9100) covalent geometry : angle 0.70332 (12374) SS BOND : bond 0.00608 ( 7) SS BOND : angle 2.22527 ( 14) hydrogen bonds : bond 0.04443 ( 450) hydrogen bonds : angle 5.15518 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 278 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 TYR cc_start: 0.8079 (p90) cc_final: 0.7829 (p90) REVERT: R 49 SER cc_start: 0.8706 (t) cc_final: 0.8473 (p) REVERT: R 73 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8147 (mt) REVERT: R 177 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7536 (mt) REVERT: R 236 LEU cc_start: 0.7561 (tt) cc_final: 0.7338 (tp) REVERT: R 247 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6813 (mm) REVERT: R 248 ARG cc_start: 0.8360 (tmm-80) cc_final: 0.8140 (ttt180) REVERT: R 260 LYS cc_start: 0.7527 (tttm) cc_final: 0.7248 (tttp) REVERT: R 279 TYR cc_start: 0.6889 (t80) cc_final: 0.6073 (t80) REVERT: R 329 ILE cc_start: 0.7657 (tt) cc_final: 0.6388 (tt) REVERT: R 334 ARG cc_start: 0.7793 (ttm110) cc_final: 0.7330 (mtt180) REVERT: A 8 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6872 (mt-10) REVERT: A 32 ARG cc_start: 0.8785 (ttm170) cc_final: 0.8570 (ttm110) REVERT: A 197 LYS cc_start: 0.7907 (pttt) cc_final: 0.7452 (pttt) REVERT: A 219 THR cc_start: 0.8583 (m) cc_final: 0.8335 (t) REVERT: A 266 LEU cc_start: 0.7238 (mt) cc_final: 0.6993 (mp) REVERT: A 275 GLU cc_start: 0.6284 (tp30) cc_final: 0.6047 (tp30) REVERT: A 279 LYS cc_start: 0.9116 (mmtp) cc_final: 0.8786 (mmtp) REVERT: A 302 TYR cc_start: 0.8228 (t80) cc_final: 0.7845 (t80) REVERT: A 308 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8100 (mt-10) REVERT: A 345 LYS cc_start: 0.8203 (tttt) cc_final: 0.7785 (tttt) REVERT: A 349 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8357 (mtmm) REVERT: A 351 CYS cc_start: 0.6314 (m) cc_final: 0.6068 (m) REVERT: B 45 MET cc_start: 0.7990 (mtt) cc_final: 0.7788 (mtp) REVERT: B 52 ARG cc_start: 0.8423 (ttm110) cc_final: 0.8077 (mtt-85) REVERT: B 105 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.7130 (t80) REVERT: B 217 MET cc_start: 0.7096 (mtm) cc_final: 0.6878 (ptp) REVERT: B 228 ASP cc_start: 0.6740 (OUTLIER) cc_final: 0.5440 (p0) REVERT: B 247 ASP cc_start: 0.6855 (t70) cc_final: 0.6562 (t0) REVERT: B 278 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7773 (m-80) REVERT: B 284 LEU cc_start: 0.7491 (mm) cc_final: 0.7237 (tp) REVERT: B 333 ASP cc_start: 0.6677 (m-30) cc_final: 0.6086 (m-30) REVERT: H 145 SER cc_start: 0.8644 (t) cc_final: 0.8316 (p) REVERT: H 173 TYR cc_start: 0.6988 (m-10) cc_final: 0.6093 (m-80) REVERT: H 186 GLN cc_start: 0.8050 (tt0) cc_final: 0.7800 (tt0) REVERT: H 220 GLU cc_start: 0.7672 (mp0) cc_final: 0.7377 (mp0) REVERT: H 223 ASP cc_start: 0.8198 (m-30) cc_final: 0.7997 (m-30) outliers start: 67 outliers final: 47 residues processed: 318 average time/residue: 0.0786 time to fit residues: 34.0663 Evaluate side-chains 324 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 270 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 255 ASN Chi-restraints excluded: chain R residue 256 PHE Chi-restraints excluded: chain R residue 266 ILE Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 324 PHE Chi-restraints excluded: chain R residue 343 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 110 optimal weight: 0.0050 chunk 42 optimal weight: 0.8980 chunk 3 optimal weight: 0.0000 chunk 114 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 105 optimal weight: 5.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 HIS ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** 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 = 0.3944 r_free = 0.3944 target = 0.126610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.112057 restraints weight = 17167.842| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.15 r_work: 0.3572 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9107 Z= 0.128 Angle : 0.628 8.329 12388 Z= 0.320 Chirality : 0.042 0.196 1445 Planarity : 0.004 0.051 1554 Dihedral : 6.864 58.410 1289 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.04 % Allowed : 22.21 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.25), residues: 1159 helix: 1.01 (0.27), residues: 374 sheet: -0.21 (0.31), residues: 270 loop : -1.02 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 314 TYR 0.025 0.002 TYR R 136 PHE 0.021 0.002 PHE R 241 TRP 0.032 0.002 TRP L 59 HIS 0.002 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9100) covalent geometry : angle 0.62420 (12374) SS BOND : bond 0.00396 ( 7) SS BOND : angle 2.04951 ( 14) hydrogen bonds : bond 0.03820 ( 450) hydrogen bonds : angle 4.85608 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 275 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 62 GLN cc_start: 0.8492 (pt0) cc_final: 0.8289 (pt0) REVERT: R 50 LYS cc_start: 0.8636 (mmmm) cc_final: 0.8364 (mmtm) REVERT: R 136 TYR cc_start: 0.5747 (OUTLIER) cc_final: 0.5312 (t80) REVERT: R 177 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7520 (mt) REVERT: R 247 ILE cc_start: 0.7028 (mm) cc_final: 0.6702 (mm) REVERT: R 279 TYR cc_start: 0.6822 (t80) cc_final: 0.6076 (t80) REVERT: R 312 TYR cc_start: 0.7347 (t80) cc_final: 0.7122 (t80) REVERT: R 329 ILE cc_start: 0.7722 (tt) cc_final: 0.6641 (tt) REVERT: R 334 ARG cc_start: 0.7653 (ttm110) cc_final: 0.7182 (mtm180) REVERT: A 32 ARG cc_start: 0.8777 (ttm170) cc_final: 0.8561 (ttm110) REVERT: A 197 LYS cc_start: 0.7841 (pttt) cc_final: 0.7511 (pttt) REVERT: A 219 THR cc_start: 0.8536 (m) cc_final: 0.8234 (t) REVERT: A 275 GLU cc_start: 0.6276 (tp30) cc_final: 0.6036 (tp30) REVERT: A 279 LYS cc_start: 0.9149 (mmtp) cc_final: 0.8839 (mmtp) REVERT: A 308 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: A 345 LYS cc_start: 0.8193 (tttt) cc_final: 0.7759 (tttt) REVERT: A 348 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7579 (tp) REVERT: A 349 LYS cc_start: 0.8676 (ttmm) cc_final: 0.8340 (mtmm) REVERT: A 351 CYS cc_start: 0.6099 (m) cc_final: 0.5859 (m) REVERT: B 52 ARG cc_start: 0.8389 (ttm110) cc_final: 0.8047 (mtt-85) REVERT: B 111 TYR cc_start: 0.7429 (m-80) cc_final: 0.7229 (m-80) REVERT: B 247 ASP cc_start: 0.6817 (t70) cc_final: 0.6483 (t0) REVERT: B 284 LEU cc_start: 0.7221 (mm) cc_final: 0.7002 (tp) REVERT: B 291 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6647 (p0) REVERT: H 145 SER cc_start: 0.8564 (t) cc_final: 0.8202 (p) REVERT: H 186 GLN cc_start: 0.8011 (tt0) cc_final: 0.7719 (tt0) REVERT: H 223 ASP cc_start: 0.8236 (m-30) cc_final: 0.7950 (m-30) outliers start: 47 outliers final: 25 residues processed: 300 average time/residue: 0.0843 time to fit residues: 34.2626 Evaluate side-chains 294 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 324 PHE Chi-restraints excluded: chain R residue 343 ASP Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 60 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 HIS R 255 ASN ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 231 GLN ** 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 = 0.3930 r_free = 0.3930 target = 0.125382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.110210 restraints weight = 17169.310| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.29 r_work: 0.3540 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9107 Z= 0.157 Angle : 0.643 9.693 12388 Z= 0.328 Chirality : 0.043 0.204 1445 Planarity : 0.004 0.050 1554 Dihedral : 6.488 59.936 1283 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.69 % Allowed : 22.53 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.25), residues: 1159 helix: 0.98 (0.27), residues: 374 sheet: -0.23 (0.31), residues: 270 loop : -0.94 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 314 TYR 0.025 0.002 TYR R 136 PHE 0.017 0.002 PHE R 241 TRP 0.016 0.002 TRP L 59 HIS 0.003 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9100) covalent geometry : angle 0.64101 (12374) SS BOND : bond 0.00295 ( 7) SS BOND : angle 1.72084 ( 14) hydrogen bonds : bond 0.03929 ( 450) hydrogen bonds : angle 4.83728 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 274 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 TYR cc_start: 0.7857 (p90) cc_final: 0.7614 (p90) REVERT: L 62 GLN cc_start: 0.8552 (pt0) cc_final: 0.8333 (pt0) REVERT: R 51 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8295 (tppt) REVERT: R 136 TYR cc_start: 0.5817 (OUTLIER) cc_final: 0.5541 (t80) REVERT: R 177 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7479 (mt) REVERT: R 247 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6681 (mm) REVERT: R 248 ARG cc_start: 0.8440 (tmm-80) cc_final: 0.8237 (ttt180) REVERT: R 260 LYS cc_start: 0.7281 (tttp) cc_final: 0.7045 (tttm) REVERT: R 279 TYR cc_start: 0.6998 (t80) cc_final: 0.6213 (t80) REVERT: R 312 TYR cc_start: 0.7269 (t80) cc_final: 0.6824 (t80) REVERT: R 329 ILE cc_start: 0.7664 (tt) cc_final: 0.6477 (tt) REVERT: R 334 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7188 (mtm180) REVERT: A 197 LYS cc_start: 0.7808 (pttt) cc_final: 0.7459 (pttt) REVERT: A 219 THR cc_start: 0.8534 (m) cc_final: 0.8236 (t) REVERT: A 275 GLU cc_start: 0.6314 (tp30) cc_final: 0.6072 (tp30) REVERT: A 279 LYS cc_start: 0.9143 (mmtp) cc_final: 0.8843 (mmtp) REVERT: A 345 LYS cc_start: 0.8135 (tttt) cc_final: 0.7706 (tttt) REVERT: A 348 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7537 (tp) REVERT: A 349 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8341 (mtmm) REVERT: A 351 CYS cc_start: 0.5971 (m) cc_final: 0.5745 (m) REVERT: B 52 ARG cc_start: 0.8397 (ttm110) cc_final: 0.8048 (mtt-85) REVERT: B 124 TYR cc_start: 0.7419 (m-80) cc_final: 0.6896 (m-80) REVERT: B 220 GLN cc_start: 0.7924 (mp10) cc_final: 0.7580 (mp10) REVERT: B 247 ASP cc_start: 0.6895 (t70) cc_final: 0.6532 (t0) REVERT: B 284 LEU cc_start: 0.7310 (mm) cc_final: 0.7031 (tp) REVERT: B 291 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6651 (p0) REVERT: H 18 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6446 (ttm170) REVERT: H 145 SER cc_start: 0.8562 (t) cc_final: 0.8200 (m) REVERT: H 186 GLN cc_start: 0.8036 (tt0) cc_final: 0.7732 (tt0) REVERT: H 223 ASP cc_start: 0.8214 (m-30) cc_final: 0.8005 (m-30) outliers start: 53 outliers final: 39 residues processed: 304 average time/residue: 0.0803 time to fit residues: 33.0794 Evaluate side-chains 311 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 324 PHE Chi-restraints excluded: chain R residue 343 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 44 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 104 optimal weight: 0.0370 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 69 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 HIS ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 231 GLN ** 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 = 0.3861 r_free = 0.3861 target = 0.119856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105426 restraints weight = 17213.329| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.01 r_work: 0.3526 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9107 Z= 0.211 Angle : 0.701 10.737 12388 Z= 0.356 Chirality : 0.045 0.245 1445 Planarity : 0.004 0.052 1554 Dihedral : 6.557 59.526 1283 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.90 % Allowed : 23.50 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.39 (0.25), residues: 1159 helix: 0.81 (0.26), residues: 374 sheet: -0.32 (0.31), residues: 270 loop : -0.97 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 314 TYR 0.028 0.002 TYR R 136 PHE 0.018 0.002 PHE A 250 TRP 0.018 0.002 TRP L 59 HIS 0.003 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9100) covalent geometry : angle 0.69000 (12374) SS BOND : bond 0.00350 ( 7) SS BOND : angle 3.67714 ( 14) hydrogen bonds : bond 0.04145 ( 450) hydrogen bonds : angle 4.92808 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 267 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 TYR cc_start: 0.7600 (p90) cc_final: 0.7392 (p90) REVERT: L 64 MET cc_start: 0.8060 (mmm) cc_final: 0.7753 (mmm) REVERT: R 136 TYR cc_start: 0.5815 (OUTLIER) cc_final: 0.5521 (t80) REVERT: R 177 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7497 (mt) REVERT: R 247 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6749 (mm) REVERT: R 260 LYS cc_start: 0.7466 (tttp) cc_final: 0.7246 (tttp) REVERT: R 279 TYR cc_start: 0.6963 (t80) cc_final: 0.6360 (t80) REVERT: R 312 TYR cc_start: 0.7270 (t80) cc_final: 0.6842 (t80) REVERT: R 329 ILE cc_start: 0.7714 (tt) cc_final: 0.6682 (tt) REVERT: R 334 ARG cc_start: 0.7766 (ttm110) cc_final: 0.7257 (mtm180) REVERT: A 188 HIS cc_start: 0.7887 (m-70) cc_final: 0.7594 (m-70) REVERT: A 197 LYS cc_start: 0.7951 (pttt) cc_final: 0.7580 (pttt) REVERT: A 219 THR cc_start: 0.8549 (m) cc_final: 0.8289 (t) REVERT: A 243 MET cc_start: 0.8127 (mmm) cc_final: 0.7920 (mmm) REVERT: A 275 GLU cc_start: 0.6308 (tp30) cc_final: 0.6055 (tp30) REVERT: A 279 LYS cc_start: 0.9153 (mmtp) cc_final: 0.8795 (mmtp) REVERT: A 345 LYS cc_start: 0.8158 (tttt) cc_final: 0.7697 (tttt) REVERT: A 349 LYS cc_start: 0.8724 (ttmm) cc_final: 0.8312 (mtmm) REVERT: A 351 CYS cc_start: 0.5944 (m) cc_final: 0.5735 (m) REVERT: B 52 ARG cc_start: 0.8422 (ttm110) cc_final: 0.8081 (mtt-85) REVERT: B 124 TYR cc_start: 0.7547 (m-80) cc_final: 0.7126 (m-80) REVERT: B 220 GLN cc_start: 0.7863 (mp10) cc_final: 0.7493 (mp10) REVERT: B 247 ASP cc_start: 0.6957 (t70) cc_final: 0.6581 (t0) REVERT: B 284 LEU cc_start: 0.7398 (mm) cc_final: 0.7111 (tp) REVERT: B 291 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6888 (p0) REVERT: B 332 TRP cc_start: 0.7857 (m100) cc_final: 0.7143 (m-10) REVERT: H 18 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6782 (tpt170) REVERT: H 145 SER cc_start: 0.8573 (t) cc_final: 0.8202 (m) REVERT: H 186 GLN cc_start: 0.8060 (tt0) cc_final: 0.7785 (tt0) REVERT: H 220 GLU cc_start: 0.7399 (mp0) cc_final: 0.7170 (mp0) outliers start: 55 outliers final: 42 residues processed: 295 average time/residue: 0.0795 time to fit residues: 31.9716 Evaluate side-chains 310 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 TYR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 266 ILE Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 343 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 HIS ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 231 GLN ** 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 = 0.3913 r_free = 0.3913 target = 0.124697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.109355 restraints weight = 17181.827| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.31 r_work: 0.3519 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9107 Z= 0.189 Angle : 0.687 10.222 12388 Z= 0.350 Chirality : 0.044 0.235 1445 Planarity : 0.004 0.053 1554 Dihedral : 6.428 59.318 1280 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.58 % Allowed : 25.00 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.39 (0.25), residues: 1159 helix: 0.79 (0.26), residues: 375 sheet: -0.31 (0.31), residues: 276 loop : -0.96 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 314 TYR 0.026 0.002 TYR R 136 PHE 0.018 0.002 PHE A 250 TRP 0.020 0.002 TRP L 59 HIS 0.003 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 9100) covalent geometry : angle 0.68132 (12374) SS BOND : bond 0.00418 ( 7) SS BOND : angle 2.78253 ( 14) hydrogen bonds : bond 0.04108 ( 450) hydrogen bonds : angle 4.95574 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 266 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 136 TYR cc_start: 0.5781 (OUTLIER) cc_final: 0.5469 (t80) REVERT: R 177 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7472 (mt) REVERT: R 247 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6769 (mm) REVERT: R 279 TYR cc_start: 0.7036 (t80) cc_final: 0.6408 (t80) REVERT: R 302 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7317 (ptmm) REVERT: R 312 TYR cc_start: 0.7275 (t80) cc_final: 0.6827 (t80) REVERT: R 329 ILE cc_start: 0.7639 (tt) cc_final: 0.6638 (tt) REVERT: R 334 ARG cc_start: 0.7815 (ttm110) cc_final: 0.7282 (mtm180) REVERT: A 188 HIS cc_start: 0.7904 (m-70) cc_final: 0.7585 (m-70) REVERT: A 197 LYS cc_start: 0.7919 (pttt) cc_final: 0.7565 (pttt) REVERT: A 219 THR cc_start: 0.8527 (m) cc_final: 0.8249 (t) REVERT: A 250 PHE cc_start: 0.6716 (t80) cc_final: 0.6339 (t80) REVERT: A 275 GLU cc_start: 0.6332 (tp30) cc_final: 0.6082 (tp30) REVERT: A 279 LYS cc_start: 0.9151 (mmtp) cc_final: 0.8843 (mmtp) REVERT: A 298 GLU cc_start: 0.8152 (tp30) cc_final: 0.7410 (tp30) REVERT: A 345 LYS cc_start: 0.8120 (tttt) cc_final: 0.7666 (tttt) REVERT: A 349 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8312 (mtmm) REVERT: A 351 CYS cc_start: 0.6015 (m) cc_final: 0.5795 (m) REVERT: B 52 ARG cc_start: 0.8438 (ttm110) cc_final: 0.8076 (mtt-85) REVERT: B 54 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.7271 (m170) REVERT: B 124 TYR cc_start: 0.7497 (m-80) cc_final: 0.7085 (m-80) REVERT: B 228 ASP cc_start: 0.6829 (OUTLIER) cc_final: 0.5927 (p0) REVERT: B 247 ASP cc_start: 0.6991 (t70) cc_final: 0.6629 (t0) REVERT: B 291 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6989 (p0) REVERT: H 18 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6457 (ttm170) REVERT: H 145 SER cc_start: 0.8483 (t) cc_final: 0.8116 (m) REVERT: H 186 GLN cc_start: 0.8089 (tt0) cc_final: 0.7800 (tt0) outliers start: 52 outliers final: 42 residues processed: 293 average time/residue: 0.0835 time to fit residues: 33.2556 Evaluate side-chains 309 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 TYR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 257 GLU Chi-restraints excluded: chain R residue 266 ILE Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 302 LYS Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 343 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 29 optimal weight: 0.0040 chunk 59 optimal weight: 0.0970 chunk 26 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 43 optimal weight: 0.0020 chunk 67 optimal weight: 0.9980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 62 GLN R 216 HIS ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 231 GLN ** 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 = 0.3949 r_free = 0.3949 target = 0.127291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.111796 restraints weight = 17091.695| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.36 r_work: 0.3572 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9107 Z= 0.128 Angle : 0.667 11.162 12388 Z= 0.337 Chirality : 0.043 0.214 1445 Planarity : 0.004 0.055 1554 Dihedral : 6.106 58.051 1280 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.61 % Allowed : 26.39 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.25), residues: 1159 helix: 0.97 (0.26), residues: 375 sheet: -0.39 (0.31), residues: 270 loop : -0.86 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 314 TYR 0.032 0.002 TYR H 50 PHE 0.017 0.001 PHE A 250 TRP 0.024 0.002 TRP L 59 HIS 0.004 0.001 HIS H 167 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9100) covalent geometry : angle 0.66493 (12374) SS BOND : bond 0.00284 ( 7) SS BOND : angle 1.58739 ( 14) hydrogen bonds : bond 0.03830 ( 450) hydrogen bonds : angle 4.89452 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 265 time to evaluate : 0.192 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: L 25 TYR cc_start: 0.7499 (p90) cc_final: 0.7156 (p90) REVERT: R 51 LYS cc_start: 0.8661 (mmmt) cc_final: 0.8383 (mmmt) REVERT: R 177 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7440 (mt) REVERT: R 247 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6744 (mm) REVERT: R 248 ARG cc_start: 0.8435 (ttp-170) cc_final: 0.8225 (tmm-80) REVERT: R 260 LYS cc_start: 0.7220 (tttp) cc_final: 0.6955 (tttm) REVERT: R 279 TYR cc_start: 0.7012 (t80) cc_final: 0.6480 (t80) REVERT: R 302 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7122 (ptpp) REVERT: R 329 ILE cc_start: 0.7623 (tt) cc_final: 0.6747 (tt) REVERT: R 334 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7573 (mtt180) REVERT: A 32 ARG cc_start: 0.8722 (ttm-80) cc_final: 0.8424 (ttm-80) REVERT: A 197 LYS cc_start: 0.7817 (pttt) cc_final: 0.7602 (pttt) REVERT: A 219 THR cc_start: 0.8548 (m) cc_final: 0.8232 (t) REVERT: A 230 TYR cc_start: 0.6993 (p90) cc_final: 0.6714 (p90) REVERT: A 275 GLU cc_start: 0.6387 (tp30) cc_final: 0.6142 (tp30) REVERT: A 279 LYS cc_start: 0.9141 (mmtp) cc_final: 0.8850 (mmtp) REVERT: A 345 LYS cc_start: 0.8091 (tttt) cc_final: 0.7586 (tttt) REVERT: A 349 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8274 (mtmm) REVERT: B 54 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.7143 (m170) REVERT: B 124 TYR cc_start: 0.7404 (m-80) cc_final: 0.6962 (m-80) REVERT: B 247 ASP cc_start: 0.6939 (t70) cc_final: 0.6630 (t0) REVERT: H 18 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6296 (ttm170) REVERT: H 59 TYR cc_start: 0.8233 (m-10) cc_final: 0.8025 (m-10) REVERT: H 186 GLN cc_start: 0.8048 (tt0) cc_final: 0.7736 (tt0) outliers start: 43 outliers final: 34 residues processed: 287 average time/residue: 0.0742 time to fit residues: 29.1031 Evaluate side-chains 299 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 260 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 TYR Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 302 LYS Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 343 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 HIS ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 231 GLN ** 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 = 0.3920 r_free = 0.3920 target = 0.125441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.110442 restraints weight = 16989.604| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.18 r_work: 0.3543 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9107 Z= 0.184 Angle : 0.710 10.764 12388 Z= 0.362 Chirality : 0.045 0.183 1445 Planarity : 0.004 0.057 1554 Dihedral : 6.070 57.048 1275 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.61 % Allowed : 26.72 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.25), residues: 1159 helix: 0.80 (0.26), residues: 377 sheet: -0.48 (0.31), residues: 270 loop : -0.96 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 314 TYR 0.029 0.003 TYR R 136 PHE 0.025 0.002 PHE R 86 TRP 0.034 0.002 TRP H 111 HIS 0.004 0.001 HIS H 232 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9100) covalent geometry : angle 0.70844 (12374) SS BOND : bond 0.00346 ( 7) SS BOND : angle 1.61886 ( 14) hydrogen bonds : bond 0.04130 ( 450) hydrogen bonds : angle 4.96915 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 0.237 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: L 25 TYR cc_start: 0.7344 (p90) cc_final: 0.7070 (p90) REVERT: R 51 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8376 (tppt) REVERT: R 129 CYS cc_start: 0.5044 (OUTLIER) cc_final: 0.4633 (t) REVERT: R 135 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6782 (tt) REVERT: R 138 MET cc_start: 0.6313 (mmt) cc_final: 0.5694 (mmt) REVERT: R 177 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7493 (mt) REVERT: R 247 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6832 (mm) REVERT: R 279 TYR cc_start: 0.7031 (t80) cc_final: 0.6582 (t80) REVERT: R 302 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7231 (ptpp) REVERT: R 329 ILE cc_start: 0.7611 (tt) cc_final: 0.7285 (tt) REVERT: R 334 ARG cc_start: 0.7753 (ttm110) cc_final: 0.7539 (mtm180) REVERT: A 188 HIS cc_start: 0.7847 (m-70) cc_final: 0.7511 (m-70) REVERT: A 197 LYS cc_start: 0.7943 (pttt) cc_final: 0.7630 (pttt) REVERT: A 219 THR cc_start: 0.8622 (m) cc_final: 0.8328 (t) REVERT: A 243 MET cc_start: 0.8239 (mmm) cc_final: 0.7968 (mmm) REVERT: A 275 GLU cc_start: 0.6309 (tp30) cc_final: 0.6070 (tp30) REVERT: A 279 LYS cc_start: 0.9103 (mmtp) cc_final: 0.8778 (mmtp) REVERT: A 345 LYS cc_start: 0.8143 (tttt) cc_final: 0.7694 (tttt) REVERT: A 349 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8363 (mtmm) REVERT: B 54 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.7172 (m170) REVERT: B 124 TYR cc_start: 0.7502 (m-80) cc_final: 0.7113 (m-80) REVERT: B 247 ASP cc_start: 0.7004 (t70) cc_final: 0.6619 (t0) REVERT: H 18 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6433 (ttm170) REVERT: H 100 ILE cc_start: 0.8226 (tt) cc_final: 0.7943 (tt) REVERT: H 173 TYR cc_start: 0.6379 (m-80) cc_final: 0.6009 (t80) REVERT: H 186 GLN cc_start: 0.8050 (tt0) cc_final: 0.7782 (tt0) outliers start: 43 outliers final: 34 residues processed: 284 average time/residue: 0.0861 time to fit residues: 33.1186 Evaluate side-chains 296 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 TYR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 129 CYS Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 302 LYS Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 343 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 68 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 62 GLN R 160 GLN R 216 HIS ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 231 GLN ** 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 = 0.3942 r_free = 0.3942 target = 0.126711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.111079 restraints weight = 16982.239| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.34 r_work: 0.3548 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9107 Z= 0.175 Angle : 0.722 10.589 12388 Z= 0.367 Chirality : 0.045 0.231 1445 Planarity : 0.004 0.058 1554 Dihedral : 6.073 56.811 1275 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.61 % Allowed : 27.47 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.25), residues: 1159 helix: 0.76 (0.26), residues: 375 sheet: -0.41 (0.31), residues: 276 loop : -0.99 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 314 TYR 0.029 0.002 TYR H 50 PHE 0.038 0.002 PHE R 86 TRP 0.031 0.002 TRP H 111 HIS 0.003 0.001 HIS H 232 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9100) covalent geometry : angle 0.72039 (12374) SS BOND : bond 0.00351 ( 7) SS BOND : angle 1.41026 ( 14) hydrogen bonds : bond 0.04074 ( 450) hydrogen bonds : angle 4.98430 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2318 Ramachandran restraints generated. 1159 Oldfield, 0 Emsley, 1159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 25 TYR cc_start: 0.7291 (p90) cc_final: 0.7070 (p90) REVERT: R 51 LYS cc_start: 0.8775 (mmmt) cc_final: 0.8521 (tppt) REVERT: R 135 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.6643 (tt) REVERT: R 138 MET cc_start: 0.6254 (mmt) cc_final: 0.5668 (mmt) REVERT: R 177 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7468 (mt) REVERT: R 247 ILE cc_start: 0.7135 (OUTLIER) cc_final: 0.6636 (tp) REVERT: R 279 TYR cc_start: 0.6978 (t80) cc_final: 0.6618 (t80) REVERT: R 302 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7263 (ptpp) REVERT: R 334 ARG cc_start: 0.7720 (ttm110) cc_final: 0.7453 (ttp-110) REVERT: R 343 ASP cc_start: 0.2116 (OUTLIER) cc_final: 0.1605 (t70) REVERT: A 188 HIS cc_start: 0.7852 (m-70) cc_final: 0.7552 (m-70) REVERT: A 197 LYS cc_start: 0.7884 (pttt) cc_final: 0.7587 (pttt) REVERT: A 219 THR cc_start: 0.8559 (m) cc_final: 0.8242 (t) REVERT: A 242 ARG cc_start: 0.8040 (mtt90) cc_final: 0.7358 (mtt90) REVERT: A 243 MET cc_start: 0.8214 (mmm) cc_final: 0.7821 (mmm) REVERT: A 275 GLU cc_start: 0.6341 (tp30) cc_final: 0.6064 (tp30) REVERT: A 279 LYS cc_start: 0.9115 (mmtp) cc_final: 0.8818 (mmtp) REVERT: A 345 LYS cc_start: 0.8084 (tttt) cc_final: 0.7601 (tttt) REVERT: A 349 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8289 (mtmm) REVERT: B 52 ARG cc_start: 0.8306 (ttm110) cc_final: 0.7974 (mtt-85) REVERT: B 54 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7170 (m170) REVERT: B 124 TYR cc_start: 0.7477 (m-80) cc_final: 0.7089 (m-80) REVERT: B 187 VAL cc_start: 0.7329 (OUTLIER) cc_final: 0.6977 (p) REVERT: B 247 ASP cc_start: 0.6977 (t70) cc_final: 0.6606 (t0) REVERT: H 18 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6296 (ttm170) REVERT: H 100 ILE cc_start: 0.8179 (tt) cc_final: 0.7942 (tt) REVERT: H 173 TYR cc_start: 0.6163 (m-80) cc_final: 0.5725 (t80) REVERT: H 186 GLN cc_start: 0.8110 (tt0) cc_final: 0.7813 (tt0) outliers start: 43 outliers final: 33 residues processed: 280 average time/residue: 0.0871 time to fit residues: 33.1535 Evaluate side-chains 293 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 TYR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain R residue 46 SER Chi-restraints excluded: chain R residue 91 THR Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 302 LYS Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 343 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 18 ARG Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 78 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 HIS ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 231 GLN ** 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 = 0.3947 r_free = 0.3947 target = 0.126993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.111276 restraints weight = 16732.299| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.33 r_work: 0.3551 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9107 Z= 0.174 Angle : 0.746 14.734 12388 Z= 0.375 Chirality : 0.044 0.219 1445 Planarity : 0.004 0.058 1554 Dihedral : 6.116 56.515 1275 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.04 % Allowed : 27.25 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.25), residues: 1159 helix: 0.74 (0.26), residues: 378 sheet: -0.45 (0.31), residues: 277 loop : -1.00 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 314 TYR 0.029 0.002 TYR H 50 PHE 0.034 0.002 PHE R 86 TRP 0.031 0.002 TRP H 111 HIS 0.003 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9100) covalent geometry : angle 0.74540 (12374) SS BOND : bond 0.00333 ( 7) SS BOND : angle 1.15691 ( 14) hydrogen bonds : bond 0.04090 ( 450) hydrogen bonds : angle 5.01462 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2088.00 seconds wall clock time: 36 minutes 29.41 seconds (2189.41 seconds total)