Starting phenix.real_space_refine on Sun Dec 29 12:35:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y66_33635/12_2024/7y66_33635_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y66_33635/12_2024/7y66_33635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y66_33635/12_2024/7y66_33635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y66_33635/12_2024/7y66_33635.map" model { file = "/net/cci-nas-00/data/ceres_data/7y66_33635/12_2024/7y66_33635_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y66_33635/12_2024/7y66_33635_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2097 atoms to isotropic. 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 59 5.16 5 C 5693 2.51 5 N 1517 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8917 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1795 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "D" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2231 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 13, 'TRANS': 267} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 48 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 4} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Classifications: {'peptide': 2} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 1} Time building chain proxies: 5.72, per 1000 atoms: 0.64 Number of scatterers: 8917 At special positions: 0 Unit cell: (88.4, 119.85, 127.5, 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 59 16.00 O 1648 8.00 N 1517 7.00 C 5693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 188 " 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 Links applied TRANS " DAL E 7 " - " ALA E 6 " Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL E 7 " Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 37.1% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 8 through 28 Processing helix chain 'A' and resid 29 through 33 removed outlier: 3.686A pdb=" N GLU A 33 " --> pdb=" O ALA A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.675A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.626A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.521A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.826A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.612A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.680A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.584A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 66 removed outlier: 4.159A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE D 64 " --> pdb=" O TRP D 60 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 88 removed outlier: 3.746A pdb=" N PHE D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU D 78 " --> pdb=" O TRP D 74 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 removed outlier: 4.064A pdb=" N LEU D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 139 removed outlier: 3.735A pdb=" N CYS D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) Proline residue: D 113 - end of helix removed outlier: 3.636A pdb=" N MET D 120 " --> pdb=" O ILE D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 150 through 174 removed outlier: 3.504A pdb=" N TRP D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Proline residue: D 170 - end of helix removed outlier: 3.789A pdb=" N LEU D 173 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR D 174 " --> pdb=" O PRO D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 211 removed outlier: 3.754A pdb=" N GLU D 199 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 232 removed outlier: 4.238A pdb=" N ARG D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 268 removed outlier: 3.672A pdb=" N LYS D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) Proline residue: D 257 - end of helix Processing helix chain 'D' and resid 272 through 280 Processing helix chain 'D' and resid 281 through 303 removed outlier: 3.540A pdb=" N CYS D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS D 294 " --> pdb=" O TYR D 290 " (cutoff:3.500A) Proline residue: D 297 - end of helix removed outlier: 4.155A pdb=" N TYR D 300 " --> pdb=" O ASN D 296 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 301 " --> pdb=" O PRO D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 314 removed outlier: 3.506A pdb=" N SER D 314 " --> pdb=" O ARG D 310 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.712A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.956A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.522A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.719A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.986A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.770A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.868A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.896A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.571A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.721A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.045A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.636A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 175 through 180 removed outlier: 3.650A pdb=" N VAL D 176 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS D 185 " --> pdb=" O GLU D 180 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2873 1.35 - 1.47: 2248 1.47 - 1.59: 3903 1.59 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 9107 Sorted by residual: bond pdb=" C ACE E 0 " pdb=" O ACE E 0 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C THR D 168 " pdb=" N ILE D 169 " ideal model delta sigma weight residual 1.329 1.341 -0.012 1.13e-02 7.83e+03 1.13e+00 bond pdb=" CA THR S 243 " pdb=" CB THR S 243 " ideal model delta sigma weight residual 1.528 1.555 -0.027 2.61e-02 1.47e+03 1.06e+00 bond pdb=" N ILE D 169 " pdb=" CA ILE D 169 " ideal model delta sigma weight residual 1.461 1.474 -0.012 1.23e-02 6.61e+03 1.02e+00 bond pdb=" CA THR B 164 " pdb=" C THR B 164 " ideal model delta sigma weight residual 1.523 1.536 -0.013 1.34e-02 5.57e+03 9.45e-01 ... (remaining 9102 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 12060 1.57 - 3.15: 224 3.15 - 4.72: 41 4.72 - 6.29: 12 6.29 - 7.87: 3 Bond angle restraints: 12340 Sorted by residual: angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N ILE D 169 " pdb=" CA ILE D 169 " pdb=" C ILE D 169 " ideal model delta sigma weight residual 108.88 114.36 -5.48 2.16e+00 2.14e-01 6.45e+00 angle pdb=" N ASP B 118 " pdb=" CA ASP B 118 " pdb=" C ASP B 118 " ideal model delta sigma weight residual 114.39 110.73 3.66 1.45e+00 4.76e-01 6.37e+00 angle pdb=" CA LEU S 178 " pdb=" CB LEU S 178 " pdb=" CG LEU S 178 " ideal model delta sigma weight residual 116.30 124.17 -7.87 3.50e+00 8.16e-02 5.05e+00 angle pdb=" CA MET S 192 " pdb=" CB MET S 192 " pdb=" CG MET S 192 " ideal model delta sigma weight residual 114.10 118.54 -4.44 2.00e+00 2.50e-01 4.93e+00 ... (remaining 12335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 4976 17.49 - 34.97: 360 34.97 - 52.46: 45 52.46 - 69.95: 9 69.95 - 87.44: 8 Dihedral angle restraints: 5398 sinusoidal: 2101 harmonic: 3297 Sorted by residual: dihedral pdb=" CB CYS D 109 " pdb=" SG CYS D 109 " pdb=" SG CYS D 188 " pdb=" CB CYS D 188 " ideal model delta sinusoidal sigma weight residual -86.00 -171.79 85.79 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CA PRO D 183 " pdb=" C PRO D 183 " pdb=" N PRO D 184 " pdb=" CA PRO D 184 " ideal model delta harmonic sigma weight residual -180.00 -155.13 -24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA TYR D 181 " pdb=" C TYR D 181 " pdb=" N PHE D 182 " pdb=" CA PHE D 182 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1062 0.045 - 0.090: 268 0.090 - 0.134: 65 0.134 - 0.179: 6 0.179 - 0.224: 1 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CB ILE D 169 " pdb=" CA ILE D 169 " pdb=" CG1 ILE D 169 " pdb=" CG2 ILE D 169 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB THR S 91 " pdb=" CA THR S 91 " pdb=" OG1 THR S 91 " pdb=" CG2 THR S 91 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 1399 not shown) Planarity restraints: 1559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 89 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO D 90 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 90 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 90 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN S 13 " -0.032 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO S 14 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO S 14 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO S 14 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 2 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO E 3 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 3 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 3 " -0.023 5.00e-02 4.00e+02 ... (remaining 1556 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 147 2.70 - 3.25: 8172 3.25 - 3.80: 13054 3.80 - 4.35: 16817 4.35 - 4.90: 29290 Nonbonded interactions: 67480 Sorted by model distance: nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.144 3.040 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.169 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.228 3.040 nonbonded pdb=" OD1 ASP D 282 " pdb=" NH1 ARG E 8 " model vdw 2.265 3.120 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.266 3.040 ... (remaining 67475 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.410 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 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 : 0.002 0.035 9107 Z= 0.161 Angle : 0.585 7.865 12340 Z= 0.328 Chirality : 0.042 0.224 1402 Planarity : 0.004 0.050 1558 Dihedral : 12.304 87.435 3261 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1122 helix: 2.05 (0.27), residues: 377 sheet: 0.00 (0.30), residues: 287 loop : -1.66 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.005 0.001 HIS S 167 PHE 0.013 0.001 PHE B 199 TYR 0.022 0.001 TYR D 222 ARG 0.011 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.970 Fit side-chains REVERT: A 25 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7227 (tm-30) REVERT: A 198 MET cc_start: 0.7757 (ttt) cc_final: 0.7485 (ttp) REVERT: A 248 LYS cc_start: 0.7387 (mtmt) cc_final: 0.7106 (mtmm) REVERT: A 289 GLU cc_start: 0.7373 (mp0) cc_final: 0.7072 (mp0) REVERT: B 215 GLU cc_start: 0.6330 (tm-30) cc_final: 0.5596 (tm-30) REVERT: B 228 ASP cc_start: 0.7103 (m-30) cc_final: 0.6710 (m-30) REVERT: S 83 MET cc_start: 0.7344 (mmt) cc_final: 0.6724 (mmt) REVERT: S 192 MET cc_start: 0.7636 (ppp) cc_final: 0.7228 (pp-130) outliers start: 0 outliers final: 2 residues processed: 234 average time/residue: 1.0496 time to fit residues: 265.9570 Evaluate side-chains 199 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain D residue 43 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9107 Z= 0.393 Angle : 0.665 9.117 12340 Z= 0.347 Chirality : 0.047 0.169 1402 Planarity : 0.005 0.051 1558 Dihedral : 4.752 38.644 1238 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.79 % Allowed : 13.65 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.24), residues: 1122 helix: 2.01 (0.26), residues: 379 sheet: -0.03 (0.29), residues: 303 loop : -1.73 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.006 0.002 HIS S 232 PHE 0.021 0.003 PHE D 75 TYR 0.028 0.002 TYR D 258 ARG 0.011 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7234 (tm-30) REVERT: A 197 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7579 (ttmm) REVERT: A 248 LYS cc_start: 0.7570 (mtmt) cc_final: 0.7352 (mtpp) REVERT: A 289 GLU cc_start: 0.7568 (mp0) cc_final: 0.7243 (mp0) REVERT: A 308 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: B 16 ASN cc_start: 0.8012 (m110) cc_final: 0.7626 (m110) REVERT: B 164 THR cc_start: 0.8463 (m) cc_final: 0.8146 (m) REVERT: S 192 MET cc_start: 0.7697 (ppp) cc_final: 0.7310 (pp-130) REVERT: D 266 SER cc_start: 0.7949 (OUTLIER) cc_final: 0.7657 (t) outliers start: 27 outliers final: 15 residues processed: 219 average time/residue: 1.0534 time to fit residues: 248.3786 Evaluate side-chains 215 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 0.0870 chunk 100 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 155 ASN B 183 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9107 Z= 0.190 Angle : 0.565 8.653 12340 Z= 0.294 Chirality : 0.042 0.150 1402 Planarity : 0.004 0.048 1558 Dihedral : 4.412 32.858 1236 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.69 % Allowed : 17.58 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1122 helix: 2.36 (0.27), residues: 373 sheet: 0.13 (0.29), residues: 304 loop : -1.66 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.004 0.001 HIS S 167 PHE 0.031 0.002 PHE D 182 TYR 0.016 0.001 TYR D 258 ARG 0.009 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7210 (tm-30) REVERT: A 197 LYS cc_start: 0.7789 (ttmm) cc_final: 0.7581 (ttmm) REVERT: A 289 GLU cc_start: 0.7547 (mp0) cc_final: 0.7232 (mp0) REVERT: A 308 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: B 16 ASN cc_start: 0.7955 (m110) cc_final: 0.7580 (m110) REVERT: B 164 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8020 (m) REVERT: B 246 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: S 192 MET cc_start: 0.7705 (ppp) cc_final: 0.7254 (pp-130) REVERT: S 245 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7851 (mp) outliers start: 26 outliers final: 12 residues processed: 195 average time/residue: 0.9815 time to fit residues: 207.0509 Evaluate side-chains 203 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 9107 Z= 0.471 Angle : 0.671 9.237 12340 Z= 0.353 Chirality : 0.048 0.171 1402 Planarity : 0.005 0.051 1558 Dihedral : 4.815 33.413 1236 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.14 % Allowed : 17.58 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.24), residues: 1122 helix: 1.93 (0.26), residues: 382 sheet: 0.32 (0.29), residues: 298 loop : -1.82 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 63 HIS 0.005 0.001 HIS B 62 PHE 0.035 0.003 PHE D 182 TYR 0.028 0.003 TYR D 258 ARG 0.009 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 1.006 Fit side-chains REVERT: A 25 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7237 (tm-30) REVERT: A 289 GLU cc_start: 0.7617 (mp0) cc_final: 0.7268 (mp0) REVERT: B 16 ASN cc_start: 0.8078 (m110) cc_final: 0.7670 (m110) REVERT: B 164 THR cc_start: 0.8477 (m) cc_final: 0.8150 (m) REVERT: B 228 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6512 (m-30) REVERT: S 192 MET cc_start: 0.7632 (ppp) cc_final: 0.7352 (pp-130) REVERT: S 245 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7908 (tp) REVERT: D 266 SER cc_start: 0.7883 (OUTLIER) cc_final: 0.7624 (t) REVERT: D 271 SER cc_start: 0.8295 (t) cc_final: 0.7915 (p) REVERT: D 291 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8472 (mt) outliers start: 40 outliers final: 20 residues processed: 223 average time/residue: 1.0269 time to fit residues: 248.0416 Evaluate side-chains 215 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 0.0570 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9107 Z= 0.189 Angle : 0.572 8.361 12340 Z= 0.299 Chirality : 0.043 0.135 1402 Planarity : 0.004 0.048 1558 Dihedral : 4.515 37.741 1236 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.21 % Allowed : 20.17 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1122 helix: 2.36 (0.27), residues: 376 sheet: 0.42 (0.29), residues: 295 loop : -1.66 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.003 0.001 HIS B 183 PHE 0.027 0.002 PHE D 182 TYR 0.016 0.001 TYR S 190 ARG 0.010 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.966 Fit side-chains REVERT: A 25 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7214 (tm-30) REVERT: A 289 GLU cc_start: 0.7620 (mp0) cc_final: 0.7260 (mp0) REVERT: A 308 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7279 (mt-10) REVERT: B 16 ASN cc_start: 0.8032 (m110) cc_final: 0.7641 (m110) REVERT: B 164 THR cc_start: 0.8323 (m) cc_final: 0.7978 (m) REVERT: B 198 LEU cc_start: 0.8118 (mt) cc_final: 0.7879 (mt) REVERT: S 192 MET cc_start: 0.7552 (ppp) cc_final: 0.7303 (pp-130) REVERT: S 245 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7923 (mp) REVERT: D 266 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7608 (t) REVERT: D 271 SER cc_start: 0.8184 (t) cc_final: 0.7825 (p) outliers start: 31 outliers final: 18 residues processed: 201 average time/residue: 0.9866 time to fit residues: 215.1310 Evaluate side-chains 205 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.0670 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 104 optimal weight: 0.0970 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9107 Z= 0.161 Angle : 0.541 8.650 12340 Z= 0.281 Chirality : 0.042 0.138 1402 Planarity : 0.004 0.047 1558 Dihedral : 4.338 36.007 1236 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.21 % Allowed : 20.89 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1122 helix: 2.48 (0.27), residues: 376 sheet: 0.43 (0.29), residues: 299 loop : -1.57 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS A 188 PHE 0.044 0.001 PHE D 182 TYR 0.019 0.001 TYR S 190 ARG 0.011 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 1.072 Fit side-chains REVERT: A 308 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: B 16 ASN cc_start: 0.8032 (m110) cc_final: 0.7622 (m110) REVERT: B 164 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7946 (m) REVERT: B 217 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7117 (pmt) REVERT: S 192 MET cc_start: 0.7550 (ppp) cc_final: 0.7316 (pp-130) REVERT: S 245 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7949 (mp) outliers start: 31 outliers final: 20 residues processed: 202 average time/residue: 1.0334 time to fit residues: 226.8353 Evaluate side-chains 207 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 0.0980 chunk 91 optimal weight: 0.0570 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9107 Z= 0.148 Angle : 0.539 8.692 12340 Z= 0.278 Chirality : 0.041 0.136 1402 Planarity : 0.004 0.045 1558 Dihedral : 4.194 35.771 1234 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.00 % Allowed : 20.99 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1122 helix: 2.52 (0.27), residues: 376 sheet: 0.53 (0.29), residues: 297 loop : -1.51 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS A 188 PHE 0.041 0.001 PHE D 182 TYR 0.019 0.001 TYR S 190 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.900 Fit side-chains REVERT: A 289 GLU cc_start: 0.7585 (mp0) cc_final: 0.7106 (mp0) REVERT: B 16 ASN cc_start: 0.8031 (m110) cc_final: 0.7626 (m110) REVERT: B 164 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7862 (m) REVERT: B 188 MET cc_start: 0.7978 (mmp) cc_final: 0.7774 (mmt) REVERT: B 217 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7115 (pmt) REVERT: B 314 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7551 (ttt180) REVERT: B 336 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8534 (mt) REVERT: S 93 MET cc_start: 0.7336 (ttm) cc_final: 0.7084 (ttm) REVERT: S 245 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7937 (mp) REVERT: D 266 SER cc_start: 0.7928 (OUTLIER) cc_final: 0.7677 (t) REVERT: D 291 ILE cc_start: 0.8633 (mt) cc_final: 0.8385 (tt) outliers start: 29 outliers final: 20 residues processed: 201 average time/residue: 1.1506 time to fit residues: 249.3263 Evaluate side-chains 204 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 0.0170 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9107 Z= 0.189 Angle : 0.547 9.220 12340 Z= 0.284 Chirality : 0.042 0.163 1402 Planarity : 0.004 0.049 1558 Dihedral : 4.199 35.268 1234 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.00 % Allowed : 22.13 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1122 helix: 2.57 (0.27), residues: 374 sheet: 0.57 (0.29), residues: 299 loop : -1.52 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.004 0.001 HIS A 188 PHE 0.045 0.002 PHE D 182 TYR 0.019 0.001 TYR S 190 ARG 0.012 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.125 Fit side-chains REVERT: A 289 GLU cc_start: 0.7631 (mp0) cc_final: 0.7141 (mp0) REVERT: B 16 ASN cc_start: 0.8046 (m110) cc_final: 0.7637 (m110) REVERT: B 164 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7904 (m) REVERT: B 198 LEU cc_start: 0.8208 (mt) cc_final: 0.8004 (mt) REVERT: B 217 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7111 (pmt) REVERT: B 336 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8528 (mt) REVERT: S 93 MET cc_start: 0.7335 (ttm) cc_final: 0.7075 (ttm) REVERT: S 245 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7930 (mp) outliers start: 29 outliers final: 21 residues processed: 199 average time/residue: 0.9682 time to fit residues: 209.3794 Evaluate side-chains 206 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 0.0030 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.0270 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.4048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9107 Z= 0.152 Angle : 0.534 9.291 12340 Z= 0.276 Chirality : 0.041 0.146 1402 Planarity : 0.004 0.057 1558 Dihedral : 4.102 34.906 1234 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.69 % Allowed : 22.54 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1122 helix: 2.61 (0.27), residues: 374 sheet: 0.59 (0.29), residues: 296 loop : -1.46 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.003 0.001 HIS A 188 PHE 0.046 0.001 PHE D 182 TYR 0.021 0.001 TYR S 190 ARG 0.013 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.929 Fit side-chains REVERT: A 289 GLU cc_start: 0.7651 (mp0) cc_final: 0.7154 (mp0) REVERT: B 16 ASN cc_start: 0.8087 (m110) cc_final: 0.7681 (m110) REVERT: B 82 TRP cc_start: 0.8424 (m100) cc_final: 0.8127 (m100) REVERT: B 164 THR cc_start: 0.8152 (OUTLIER) cc_final: 0.7831 (m) REVERT: B 217 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7110 (pmt) REVERT: B 336 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8519 (mt) REVERT: S 93 MET cc_start: 0.7323 (ttm) cc_final: 0.7074 (ttm) REVERT: S 245 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7940 (mp) REVERT: D 291 ILE cc_start: 0.8598 (mt) cc_final: 0.8351 (tt) outliers start: 26 outliers final: 19 residues processed: 200 average time/residue: 1.0001 time to fit residues: 216.0965 Evaluate side-chains 202 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 0.0070 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9107 Z= 0.157 Angle : 0.540 9.612 12340 Z= 0.277 Chirality : 0.041 0.163 1402 Planarity : 0.004 0.059 1558 Dihedral : 4.065 34.995 1234 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.69 % Allowed : 23.37 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1122 helix: 2.62 (0.26), residues: 374 sheet: 0.63 (0.29), residues: 297 loop : -1.41 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.004 0.001 HIS A 188 PHE 0.046 0.001 PHE D 182 TYR 0.021 0.001 TYR S 190 ARG 0.013 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.993 Fit side-chains REVERT: A 289 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: B 16 ASN cc_start: 0.8090 (m110) cc_final: 0.7688 (m110) REVERT: B 82 TRP cc_start: 0.8426 (m100) cc_final: 0.8137 (m100) REVERT: B 164 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7833 (m) REVERT: B 217 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7106 (pmt) REVERT: S 93 MET cc_start: 0.7321 (ttm) cc_final: 0.7079 (ttm) REVERT: S 245 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7916 (mp) REVERT: D 291 ILE cc_start: 0.8582 (mt) cc_final: 0.8338 (tt) outliers start: 26 outliers final: 19 residues processed: 202 average time/residue: 0.9101 time to fit residues: 200.1129 Evaluate side-chains 208 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 294 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.0050 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.133283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.114875 restraints weight = 12875.087| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.06 r_work: 0.3435 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9107 Z= 0.176 Angle : 0.556 9.622 12340 Z= 0.286 Chirality : 0.042 0.165 1402 Planarity : 0.004 0.057 1558 Dihedral : 4.088 35.560 1234 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.48 % Allowed : 23.47 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1122 helix: 2.63 (0.26), residues: 374 sheet: 0.63 (0.29), residues: 297 loop : -1.40 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.006 0.001 HIS S 167 PHE 0.049 0.002 PHE D 182 TYR 0.021 0.001 TYR S 190 ARG 0.014 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3912.54 seconds wall clock time: 71 minutes 20.60 seconds (4280.60 seconds total)