Starting phenix.real_space_refine on Fri Mar 14 07:08:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9grc_51520/03_2025/9grc_51520.cif Found real_map, /net/cci-nas-00/data/ceres_data/9grc_51520/03_2025/9grc_51520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9grc_51520/03_2025/9grc_51520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9grc_51520/03_2025/9grc_51520.map" model { file = "/net/cci-nas-00/data/ceres_data/9grc_51520/03_2025/9grc_51520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9grc_51520/03_2025/9grc_51520.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 56 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 52 5.16 5 C 6195 2.51 5 N 1703 2.21 5 O 1767 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9717 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2969 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Chain: "E" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3159 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 14, 'TRANS': 394} Chain: "F" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1730 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 8, 'TRANS': 217} Chain: "D" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1730 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 8, 'TRANS': 217} Chain: "V" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 73 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "V" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'PLM': 1, 'Z41': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.71, per 1000 atoms: 0.59 Number of scatterers: 9717 At special positions: 0 Unit cell: (99.84, 146.88, 118.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1767 8.00 N 1703 7.00 C 6195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.1 seconds 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 46.1% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'C' and resid 5 through 13 removed outlier: 3.506A pdb=" N GLY C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 28 removed outlier: 3.976A pdb=" N SER C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP C 28 " --> pdb=" O ARG C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 59 removed outlier: 3.580A pdb=" N THR C 43 " --> pdb=" O MET C 39 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 63 removed outlier: 3.576A pdb=" N MET C 63 " --> pdb=" O LEU C 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 60 through 63' Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.605A pdb=" N VAL C 85 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 148 through 155 removed outlier: 3.788A pdb=" N GLN C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 198 removed outlier: 3.886A pdb=" N ASP C 197 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY C 198 " --> pdb=" O GLU C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 198' Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 255 through 293 removed outlier: 3.851A pdb=" N LEU C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 304 Processing helix chain 'C' and resid 306 through 337 removed outlier: 3.679A pdb=" N MET C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 314 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 379 Processing helix chain 'C' and resid 380 through 390 removed outlier: 3.689A pdb=" N ALA C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR C 390 " --> pdb=" O ARG C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.786A pdb=" N ALA C 395 " --> pdb=" O GLN C 391 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU C 396 " --> pdb=" O PRO C 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 391 through 396' Processing helix chain 'E' and resid 11 through 16 Processing helix chain 'E' and resid 22 through 59 removed outlier: 3.803A pdb=" N ILE E 26 " --> pdb=" O MET E 22 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY E 37 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 87 removed outlier: 3.938A pdb=" N LYS E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 3.635A pdb=" N VAL E 133 " --> pdb=" O PRO E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 159 Processing helix chain 'E' and resid 199 through 202 Processing helix chain 'E' and resid 208 through 215 Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 233 through 242 removed outlier: 3.544A pdb=" N VAL E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG E 239 " --> pdb=" O ASN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 298 removed outlier: 6.088A pdb=" N TYR E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N MET E 261 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET E 267 " --> pdb=" O ARG E 263 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE E 268 " --> pdb=" O ASP E 264 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 309 Processing helix chain 'E' and resid 311 through 344 removed outlier: 4.045A pdb=" N PHE E 319 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL E 320 " --> pdb=" O ARG E 316 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA E 326 " --> pdb=" O TYR E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 357 Processing helix chain 'E' and resid 378 through 395 Processing helix chain 'E' and resid 396 through 403 Processing helix chain 'F' and resid 47 through 56 removed outlier: 3.713A pdb=" N LEU F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N HIS F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU F 54 " --> pdb=" O THR F 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 89 removed outlier: 3.574A pdb=" N LEU F 89 " --> pdb=" O ARG F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 109 removed outlier: 3.735A pdb=" N VAL F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 115 Processing helix chain 'F' and resid 125 through 134 Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 150 through 160 removed outlier: 4.165A pdb=" N VAL F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU F 160 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 195 removed outlier: 4.413A pdb=" N LEU F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU F 188 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN F 192 " --> pdb=" O LEU F 188 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.914A pdb=" N LEU D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 54 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 103 through 116 removed outlier: 3.698A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 121 through 134 removed outlier: 3.837A pdb=" N ALA D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU D 127 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.960A pdb=" N ALA D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU D 160 " --> pdb=" O ILE D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.385A pdb=" N LEU D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU D 188 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 161 through 162 removed outlier: 6.989A pdb=" N VAL C 144 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N PHE C 190 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU C 146 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ASN C 143 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN C 204 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY C 147 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLU C 200 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY C 99 " --> pdb=" O MET C 114 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG C 92 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C 66 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 165 through 166 removed outlier: 4.136A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 165 through 170 removed outlier: 3.659A pdb=" N ILE E 168 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL E 185 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE E 148 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE E 192 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE E 150 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLN E 147 " --> pdb=" O PRO E 207 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS E 116 " --> pdb=" O ILE E 206 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS E 252 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 104 through 105 removed outlier: 3.754A pdb=" N VAL E 104 " --> pdb=" O ARG E 111 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG E 111 " --> pdb=" O VAL E 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 31 through 32 removed outlier: 3.517A pdb=" N VAL F 32 " --> pdb=" O LEU F 6 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP F 9 " --> pdb=" O ASP F 65 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP F 65 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 14 through 16 Processing sheet with id=AA7, first strand: chain 'F' and resid 38 through 41 removed outlier: 3.924A pdb=" N MET F 38 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL F 201 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL F 167 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL F 202 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA F 169 " --> pdb=" O VAL F 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 31 through 32 removed outlier: 3.669A pdb=" N VAL D 32 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP D 9 " --> pdb=" O ASP D 65 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP D 65 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 14 through 16 Processing sheet with id=AB1, first strand: chain 'D' and resid 38 through 41 removed outlier: 3.961A pdb=" N MET D 38 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D 201 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL D 167 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL D 202 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA D 169 " --> pdb=" O VAL D 202 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1131 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: 2.57 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3244 1.34 - 1.46: 1815 1.46 - 1.58: 4716 1.58 - 1.69: 0 1.69 - 1.81: 97 Bond restraints: 9872 Sorted by residual: bond pdb=" C17 Z41 V 101 " pdb=" C18 Z41 V 101 " ideal model delta sigma weight residual 1.512 1.550 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" CA LEU F 223 " pdb=" CB LEU F 223 " ideal model delta sigma weight residual 1.526 1.555 -0.029 1.70e-02 3.46e+03 2.94e+00 bond pdb=" CA LEU D 223 " pdb=" CB LEU D 223 " ideal model delta sigma weight residual 1.526 1.555 -0.029 1.70e-02 3.46e+03 2.93e+00 bond pdb=" C19 Z41 V 101 " pdb=" O3 Z41 V 101 " ideal model delta sigma weight residual 1.333 1.366 -0.033 2.00e-02 2.50e+03 2.77e+00 bond pdb=" C19 Z41 V 101 " pdb=" C20 Z41 V 101 " ideal model delta sigma weight residual 1.506 1.532 -0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 9867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 13240 2.87 - 5.75: 87 5.75 - 8.62: 15 8.62 - 11.50: 4 11.50 - 14.37: 1 Bond angle restraints: 13347 Sorted by residual: angle pdb=" C VAL E 249 " pdb=" N TYR E 250 " pdb=" CA TYR E 250 " ideal model delta sigma weight residual 122.19 136.56 -14.37 2.30e+00 1.89e-01 3.90e+01 angle pdb=" CA TYR E 250 " pdb=" CB TYR E 250 " pdb=" CG TYR E 250 " ideal model delta sigma weight residual 113.90 121.75 -7.85 1.80e+00 3.09e-01 1.90e+01 angle pdb=" C19 Z41 V 101 " pdb=" C20 Z41 V 101 " pdb=" C21 Z41 V 101 " ideal model delta sigma weight residual 114.62 103.34 11.28 3.00e+00 1.11e-01 1.41e+01 angle pdb=" N THR E 76 " pdb=" CA THR E 76 " pdb=" C THR E 76 " ideal model delta sigma weight residual 114.04 109.65 4.39 1.24e+00 6.50e-01 1.26e+01 angle pdb=" C14 Z41 V 101 " pdb=" C15 Z41 V 101 " pdb=" C16 Z41 V 101 " ideal model delta sigma weight residual 114.11 103.70 10.41 3.00e+00 1.11e-01 1.20e+01 ... (remaining 13342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 5376 16.36 - 32.71: 491 32.71 - 49.07: 104 49.07 - 65.43: 23 65.43 - 81.79: 12 Dihedral angle restraints: 6006 sinusoidal: 2415 harmonic: 3591 Sorted by residual: dihedral pdb=" CA GLY C 348 " pdb=" C GLY C 348 " pdb=" N VAL C 349 " pdb=" CA VAL C 349 " ideal model delta harmonic sigma weight residual -180.00 -157.24 -22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ILE C 347 " pdb=" C ILE C 347 " pdb=" N GLY C 348 " pdb=" CA GLY C 348 " ideal model delta harmonic sigma weight residual -180.00 -161.83 -18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CB MET E 48 " pdb=" CG MET E 48 " pdb=" SD MET E 48 " pdb=" CE MET E 48 " ideal model delta sinusoidal sigma weight residual 60.00 118.18 -58.18 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 6003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 819 0.026 - 0.052: 496 0.052 - 0.078: 136 0.078 - 0.104: 76 0.104 - 0.130: 31 Chirality restraints: 1558 Sorted by residual: chirality pdb=" CA ILE D 92 " pdb=" N ILE D 92 " pdb=" C ILE D 92 " pdb=" CB ILE D 92 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CB THR E 101 " pdb=" CA THR E 101 " pdb=" OG1 THR E 101 " pdb=" CG2 THR E 101 " both_signs ideal model delta sigma weight residual False 2.55 2.68 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE E 224 " pdb=" N ILE E 224 " pdb=" C ILE E 224 " pdb=" CB ILE E 224 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1555 not shown) Planarity restraints: 1710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 Z41 V 101 " -0.046 2.00e-02 2.50e+03 2.68e-02 7.16e+00 pdb=" C20 Z41 V 101 " 0.013 2.00e-02 2.50e+03 pdb=" O3 Z41 V 101 " 0.016 2.00e-02 2.50e+03 pdb=" O4 Z41 V 101 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 129 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO E 130 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 130 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 130 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 306 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO C 307 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " -0.019 5.00e-02 4.00e+02 ... (remaining 1707 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 528 2.74 - 3.28: 9593 3.28 - 3.82: 15696 3.82 - 4.36: 18240 4.36 - 4.90: 31404 Nonbonded interactions: 75461 Sorted by model distance: nonbonded pdb=" O GLY E 242 " pdb=" OG1 THR E 245 " model vdw 2.197 3.040 nonbonded pdb=" OG SER C 70 " pdb=" O SER C 74 " model vdw 2.269 3.040 nonbonded pdb=" O ALA E 128 " pdb=" OG SER E 131 " model vdw 2.282 3.040 nonbonded pdb=" OG SER C 74 " pdb=" O ILE C 219 " model vdw 2.290 3.040 nonbonded pdb=" O ASN F 86 " pdb=" ND2 ASN F 162 " model vdw 2.316 3.120 ... (remaining 75456 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 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' } 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 group one per residue 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.030 Find NCS groups from input model: 0.150 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0539 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 0.038 9872 Z= 0.139 Angle : 0.663 14.371 13347 Z= 0.348 Chirality : 0.040 0.130 1558 Planarity : 0.003 0.051 1710 Dihedral : 13.800 81.785 3694 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.24), residues: 1251 helix: 0.28 (0.24), residues: 517 sheet: -0.93 (0.41), residues: 175 loop : -1.76 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 246 HIS 0.002 0.000 HIS F 96 PHE 0.011 0.001 PHE C 51 TYR 0.010 0.001 TYR E 250 ARG 0.001 0.000 ARG E 269 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ILE cc_start: 0.1739 (mt) cc_final: 0.1479 (mt) REVERT: C 267 MET cc_start: 0.4047 (tpp) cc_final: 0.3829 (tpp) REVERT: E 267 MET cc_start: -0.0120 (ttp) cc_final: -0.0423 (tmm) REVERT: E 271 ILE cc_start: 0.3283 (mm) cc_final: 0.2885 (mm) REVERT: F 14 ARG cc_start: 0.4570 (mmt90) cc_final: 0.4291 (mpt-90) REVERT: F 21 GLN cc_start: 0.6698 (mm-40) cc_final: 0.6190 (pm20) REVERT: F 38 MET cc_start: 0.0728 (pmm) cc_final: 0.0222 (pmm) REVERT: D 15 TYR cc_start: 0.6093 (t80) cc_final: 0.5794 (t80) REVERT: D 212 MET cc_start: 0.0674 (tpp) cc_final: 0.0319 (mmp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2542 time to fit residues: 52.7966 Evaluate side-chains 99 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 7.9990 chunk 93 optimal weight: 0.0670 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 0.0010 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.2130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN E 172 ASN V 4 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.155820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.128840 restraints weight = 28699.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.132966 restraints weight = 14978.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.135595 restraints weight = 9537.226| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1016 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9872 Z= 0.180 Angle : 0.611 7.850 13347 Z= 0.303 Chirality : 0.043 0.148 1558 Planarity : 0.004 0.056 1710 Dihedral : 4.974 53.851 1398 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.96 % Allowed : 9.03 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.24), residues: 1251 helix: 0.42 (0.24), residues: 513 sheet: -1.13 (0.41), residues: 173 loop : -1.62 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 165 HIS 0.004 0.001 HIS D 97 PHE 0.011 0.001 PHE E 141 TYR 0.015 0.001 TYR E 322 ARG 0.007 0.001 ARG F 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: -0.0573 (mmm) cc_final: -0.1238 (mmt) REVERT: C 59 ILE cc_start: 0.2201 (mt) cc_final: 0.1586 (mt) REVERT: C 267 MET cc_start: 0.5368 (tpp) cc_final: 0.4821 (tpp) REVERT: C 315 MET cc_start: -0.2911 (mtp) cc_final: -0.5078 (tmm) REVERT: E 169 MET cc_start: 0.4945 (ppp) cc_final: 0.4412 (ttm) REVERT: E 183 LYS cc_start: 0.2233 (OUTLIER) cc_final: 0.1981 (mmmt) REVERT: E 217 MET cc_start: -0.0621 (ptt) cc_final: -0.1460 (tpt) REVERT: F 21 GLN cc_start: 0.6806 (mm-40) cc_final: 0.5971 (pm20) REVERT: F 73 MET cc_start: -0.4231 (mpp) cc_final: -0.4630 (mtm) REVERT: F 218 MET cc_start: 0.0607 (ppp) cc_final: 0.0329 (ppp) REVERT: D 15 TYR cc_start: 0.6489 (t80) cc_final: 0.5932 (t80) REVERT: D 212 MET cc_start: 0.1736 (tpp) cc_final: 0.0827 (mmp) REVERT: D 218 MET cc_start: -0.3788 (mtt) cc_final: -0.4413 (ppp) outliers start: 10 outliers final: 5 residues processed: 110 average time/residue: 0.2194 time to fit residues: 34.4617 Evaluate side-chains 100 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 366 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 364 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 4 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.155696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.128598 restraints weight = 29489.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.132751 restraints weight = 15281.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.135354 restraints weight = 9676.044| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1089 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9872 Z= 0.147 Angle : 0.554 8.376 13347 Z= 0.273 Chirality : 0.041 0.142 1558 Planarity : 0.004 0.043 1710 Dihedral : 4.664 56.335 1398 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.25 % Allowed : 12.58 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.25), residues: 1251 helix: 0.72 (0.24), residues: 501 sheet: -0.88 (0.39), residues: 186 loop : -1.54 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 78 HIS 0.003 0.001 HIS F 97 PHE 0.013 0.001 PHE F 95 TYR 0.017 0.001 TYR E 260 ARG 0.006 0.000 ARG E 401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 MET cc_start: 0.0347 (mmm) cc_final: -0.0106 (mmt) REVERT: C 267 MET cc_start: 0.5662 (tpp) cc_final: 0.4953 (tpp) REVERT: C 315 MET cc_start: -0.2405 (mtp) cc_final: -0.4853 (ttp) REVERT: E 169 MET cc_start: 0.4934 (ppp) cc_final: 0.4379 (ttm) REVERT: E 217 MET cc_start: -0.0398 (ptt) cc_final: -0.1432 (tpt) REVERT: E 375 LEU cc_start: 0.3194 (OUTLIER) cc_final: 0.1928 (mt) REVERT: F 21 GLN cc_start: 0.6812 (mm-40) cc_final: 0.6007 (pm20) REVERT: F 38 MET cc_start: 0.1817 (pmm) cc_final: 0.1116 (mpp) REVERT: F 73 MET cc_start: -0.4319 (mpp) cc_final: -0.4698 (mtm) REVERT: D 15 TYR cc_start: 0.6475 (t80) cc_final: 0.5913 (t80) REVERT: D 212 MET cc_start: 0.1517 (tpp) cc_final: 0.0437 (mmp) REVERT: D 218 MET cc_start: -0.3763 (mtt) cc_final: -0.4299 (ppp) outliers start: 13 outliers final: 5 residues processed: 117 average time/residue: 0.2035 time to fit residues: 34.8129 Evaluate side-chains 101 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 375 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 39 optimal weight: 0.0270 chunk 116 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.155678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.128862 restraints weight = 29105.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.132941 restraints weight = 15257.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.135564 restraints weight = 9707.924| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1114 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9872 Z= 0.135 Angle : 0.532 8.610 13347 Z= 0.261 Chirality : 0.040 0.138 1558 Planarity : 0.004 0.038 1710 Dihedral : 4.440 43.428 1398 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.15 % Allowed : 14.70 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1251 helix: 0.84 (0.24), residues: 501 sheet: -0.90 (0.39), residues: 182 loop : -1.50 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 246 HIS 0.003 0.001 HIS D 97 PHE 0.009 0.001 PHE E 367 TYR 0.019 0.001 TYR F 15 ARG 0.004 0.000 ARG F 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: -0.0170 (mmt) cc_final: -0.0575 (mmt) REVERT: C 114 MET cc_start: 0.0496 (mmm) cc_final: 0.0144 (mmt) REVERT: C 175 MET cc_start: 0.2650 (ptp) cc_final: 0.2382 (ptt) REVERT: C 267 MET cc_start: 0.5841 (tpp) cc_final: 0.5577 (tpp) REVERT: C 315 MET cc_start: -0.2600 (mtp) cc_final: -0.5163 (ttp) REVERT: E 217 MET cc_start: -0.0411 (ptt) cc_final: -0.1180 (tpt) REVERT: E 321 TRP cc_start: 0.5538 (m-90) cc_final: 0.5028 (m-10) REVERT: F 21 GLN cc_start: 0.6781 (mm-40) cc_final: 0.6305 (mm-40) REVERT: F 73 MET cc_start: -0.4353 (mpp) cc_final: -0.4656 (mtm) REVERT: F 218 MET cc_start: 0.0417 (ppp) cc_final: 0.0141 (ppp) REVERT: D 15 TYR cc_start: 0.6477 (t80) cc_final: 0.5923 (t80) REVERT: D 153 ARG cc_start: 0.7342 (mmm160) cc_final: 0.6371 (mmm160) REVERT: D 212 MET cc_start: 0.1363 (tpp) cc_final: 0.0371 (mmp) REVERT: D 218 MET cc_start: -0.3933 (mtt) cc_final: -0.4402 (ppp) outliers start: 12 outliers final: 9 residues processed: 111 average time/residue: 0.2311 time to fit residues: 36.5311 Evaluate side-chains 103 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 366 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 ASN D 107 ASN D 141 HIS ** D 152 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 = 0.4462 r_free = 0.4462 target = 0.155793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.129552 restraints weight = 29680.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.133672 restraints weight = 15894.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.136188 restraints weight = 10145.812| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1354 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9872 Z= 0.161 Angle : 0.559 8.062 13347 Z= 0.276 Chirality : 0.041 0.140 1558 Planarity : 0.004 0.038 1710 Dihedral : 4.835 53.063 1398 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.11 % Allowed : 16.52 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.25), residues: 1251 helix: 0.59 (0.23), residues: 532 sheet: -0.74 (0.41), residues: 168 loop : -1.60 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 78 HIS 0.004 0.001 HIS E 358 PHE 0.017 0.001 PHE F 199 TYR 0.015 0.001 TYR F 15 ARG 0.009 0.000 ARG F 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: C 4 PRO cc_start: 0.6257 (Cg_endo) cc_final: 0.5921 (Cg_exo) REVERT: C 14 MET cc_start: 0.0185 (mmt) cc_final: -0.0056 (mmt) REVERT: C 114 MET cc_start: 0.0794 (mmm) cc_final: 0.0296 (mmt) REVERT: C 175 MET cc_start: 0.2816 (ptp) cc_final: 0.2437 (ptt) REVERT: C 248 ASP cc_start: 0.4816 (p0) cc_final: 0.4475 (p0) REVERT: C 267 MET cc_start: 0.6342 (tpp) cc_final: 0.5865 (tpp) REVERT: C 315 MET cc_start: -0.2380 (mtp) cc_final: -0.4045 (ttp) REVERT: E 169 MET cc_start: 0.6195 (ppp) cc_final: 0.4318 (ttp) REVERT: E 217 MET cc_start: -0.0449 (ptt) cc_final: -0.1131 (tpt) REVERT: E 267 MET cc_start: -0.0225 (tmm) cc_final: -0.0535 (tmm) REVERT: E 321 TRP cc_start: 0.5646 (m-90) cc_final: 0.5231 (m-10) REVERT: E 375 LEU cc_start: 0.2913 (OUTLIER) cc_final: 0.2287 (tp) REVERT: F 37 MET cc_start: 0.0175 (mmt) cc_final: -0.0644 (tpt) REVERT: D 15 TYR cc_start: 0.6467 (t80) cc_final: 0.5965 (t80) REVERT: D 153 ARG cc_start: 0.7581 (mmm160) cc_final: 0.6837 (mmm160) REVERT: D 212 MET cc_start: 0.1760 (tpp) cc_final: 0.0729 (mmp) outliers start: 22 outliers final: 12 residues processed: 124 average time/residue: 0.2152 time to fit residues: 38.0040 Evaluate side-chains 108 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 366 TYR Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain D residue 127 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 4 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.157080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.133124 restraints weight = 31426.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.136988 restraints weight = 17138.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.139316 restraints weight = 10980.063| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1842 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 9872 Z= 0.309 Angle : 0.811 11.774 13347 Z= 0.402 Chirality : 0.048 0.228 1558 Planarity : 0.008 0.261 1710 Dihedral : 6.325 59.033 1398 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.59 % Allowed : 17.77 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.23), residues: 1251 helix: -0.34 (0.22), residues: 512 sheet: -1.03 (0.40), residues: 159 loop : -1.86 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 246 HIS 0.005 0.001 HIS E 358 PHE 0.029 0.003 PHE E 319 TYR 0.020 0.002 TYR C 199 ARG 0.026 0.001 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 MET cc_start: 0.3429 (ptp) cc_final: 0.3122 (ptt) REVERT: C 248 ASP cc_start: 0.5290 (p0) cc_final: 0.4820 (p0) REVERT: C 267 MET cc_start: 0.6539 (tpp) cc_final: 0.5547 (tpp) REVERT: C 315 MET cc_start: -0.2682 (mtp) cc_final: -0.4434 (ttp) REVERT: C 344 MET cc_start: 0.0524 (pmm) cc_final: 0.0109 (pmm) REVERT: E 80 GLU cc_start: 0.7342 (mp0) cc_final: 0.7067 (pm20) REVERT: E 217 MET cc_start: 0.0282 (ptt) cc_final: -0.0474 (tpt) REVERT: E 267 MET cc_start: 0.0083 (tmm) cc_final: -0.0128 (tmm) REVERT: E 316 ARG cc_start: 0.7467 (tpt170) cc_final: 0.6705 (tpp-160) REVERT: F 38 MET cc_start: 0.3040 (pmm) cc_final: 0.2707 (mpp) REVERT: F 129 MET cc_start: 0.0138 (mtt) cc_final: -0.1316 (ptm) REVERT: D 15 TYR cc_start: 0.6484 (t80) cc_final: 0.6114 (t80) REVERT: D 153 ARG cc_start: 0.7752 (mmm160) cc_final: 0.7095 (mmm160) REVERT: D 212 MET cc_start: 0.2163 (tpp) cc_final: 0.1685 (mmp) outliers start: 27 outliers final: 16 residues processed: 121 average time/residue: 0.1960 time to fit residues: 34.7130 Evaluate side-chains 109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 366 TYR Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 154 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 112 optimal weight: 0.0020 chunk 4 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 4 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.156323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.131925 restraints weight = 31081.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.135874 restraints weight = 16727.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.138358 restraints weight = 10672.365| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1663 moved from start: 0.6975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9872 Z= 0.159 Angle : 0.622 11.737 13347 Z= 0.303 Chirality : 0.042 0.148 1558 Planarity : 0.004 0.047 1710 Dihedral : 5.328 46.576 1398 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.63 % Allowed : 20.08 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.24), residues: 1251 helix: 0.28 (0.23), residues: 502 sheet: -1.14 (0.41), residues: 148 loop : -1.61 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 246 HIS 0.004 0.001 HIS E 358 PHE 0.020 0.002 PHE E 329 TYR 0.021 0.001 TYR E 250 ARG 0.008 0.000 ARG F 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 175 MET cc_start: 0.3115 (ptp) cc_final: 0.2859 (ptt) REVERT: C 248 ASP cc_start: 0.5333 (p0) cc_final: 0.4882 (p0) REVERT: C 267 MET cc_start: 0.6580 (tpp) cc_final: 0.5840 (tpp) REVERT: C 315 MET cc_start: -0.2642 (mtp) cc_final: -0.4102 (ttp) REVERT: C 344 MET cc_start: 0.0369 (pmm) cc_final: 0.0117 (pmm) REVERT: E 169 MET cc_start: 0.6911 (ppp) cc_final: 0.3766 (ttp) REVERT: E 217 MET cc_start: 0.0086 (ptt) cc_final: -0.0171 (tpt) REVERT: E 293 MET cc_start: 0.0343 (tmm) cc_final: -0.0923 (ptt) REVERT: F 38 MET cc_start: 0.2824 (pmm) cc_final: 0.2521 (mpp) REVERT: F 129 MET cc_start: 0.0178 (mtt) cc_final: -0.1026 (ptm) REVERT: D 15 TYR cc_start: 0.6569 (t80) cc_final: 0.6227 (t80) REVERT: D 153 ARG cc_start: 0.7655 (mmm160) cc_final: 0.7008 (mmm160) REVERT: D 212 MET cc_start: 0.1798 (tpp) cc_final: 0.0863 (mmp) outliers start: 17 outliers final: 12 residues processed: 110 average time/residue: 0.2096 time to fit residues: 33.0322 Evaluate side-chains 104 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 366 TYR Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 7 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 0.0270 chunk 39 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.156311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.132210 restraints weight = 31281.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.136129 restraints weight = 16672.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.138537 restraints weight = 10594.231| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1636 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9872 Z= 0.151 Angle : 0.619 11.333 13347 Z= 0.303 Chirality : 0.042 0.146 1558 Planarity : 0.004 0.043 1710 Dihedral : 5.021 41.914 1398 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.83 % Allowed : 20.17 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.24), residues: 1251 helix: 0.48 (0.24), residues: 511 sheet: -0.88 (0.40), residues: 160 loop : -1.62 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 246 HIS 0.003 0.001 HIS E 358 PHE 0.020 0.001 PHE E 329 TYR 0.020 0.001 TYR E 250 ARG 0.007 0.000 ARG F 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: C 165 MET cc_start: 0.1504 (tmm) cc_final: 0.1245 (tmm) REVERT: C 175 MET cc_start: 0.3147 (ptp) cc_final: 0.2934 (ptt) REVERT: C 248 ASP cc_start: 0.5231 (p0) cc_final: 0.4881 (p0) REVERT: C 267 MET cc_start: 0.6578 (tpp) cc_final: 0.5796 (tpp) REVERT: C 312 MET cc_start: 0.0620 (mmt) cc_final: 0.0230 (mmt) REVERT: C 315 MET cc_start: -0.2692 (mtp) cc_final: -0.4087 (ttp) REVERT: C 344 MET cc_start: 0.0293 (pmm) cc_final: 0.0064 (pmm) REVERT: E 80 GLU cc_start: 0.7678 (mp0) cc_final: 0.7112 (pm20) REVERT: E 271 ILE cc_start: 0.3499 (mm) cc_final: 0.3120 (mm) REVERT: E 293 MET cc_start: -0.0008 (tmm) cc_final: -0.0535 (ptm) REVERT: F 37 MET cc_start: -0.4122 (tpt) cc_final: -0.4614 (tpt) REVERT: F 38 MET cc_start: 0.3301 (pmm) cc_final: 0.2655 (mpp) REVERT: F 129 MET cc_start: 0.0067 (mtt) cc_final: -0.1061 (ptm) REVERT: D 15 TYR cc_start: 0.6666 (t80) cc_final: 0.6244 (t80) REVERT: D 153 ARG cc_start: 0.7621 (mmm160) cc_final: 0.6971 (mmm160) REVERT: D 212 MET cc_start: 0.1667 (tpp) cc_final: 0.0988 (mmp) outliers start: 19 outliers final: 15 residues processed: 108 average time/residue: 0.2048 time to fit residues: 32.0229 Evaluate side-chains 105 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 366 TYR Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain V residue 7 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.0970 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN E 124 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN ** D 152 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 = 0.4498 r_free = 0.4498 target = 0.156982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.133280 restraints weight = 31918.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.137176 restraints weight = 17144.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.139594 restraints weight = 10910.318| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1838 moved from start: 0.7885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9872 Z= 0.190 Angle : 0.675 11.004 13347 Z= 0.329 Chirality : 0.043 0.151 1558 Planarity : 0.004 0.042 1710 Dihedral : 5.460 48.164 1398 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.63 % Allowed : 20.75 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1251 helix: 0.47 (0.23), residues: 497 sheet: -1.00 (0.40), residues: 155 loop : -1.70 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 246 HIS 0.005 0.001 HIS E 358 PHE 0.023 0.002 PHE E 319 TYR 0.018 0.001 TYR E 250 ARG 0.007 0.001 ARG F 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 248 ASP cc_start: 0.5375 (p0) cc_final: 0.4904 (p0) REVERT: C 267 MET cc_start: 0.6750 (tpp) cc_final: 0.6086 (tpp) REVERT: C 315 MET cc_start: -0.2774 (mtp) cc_final: -0.4170 (ttp) REVERT: C 344 MET cc_start: 0.0260 (pmm) cc_final: 0.0059 (pmm) REVERT: E 80 GLU cc_start: 0.7559 (mp0) cc_final: 0.7035 (pm20) REVERT: E 169 MET cc_start: 0.6707 (ppp) cc_final: 0.3529 (ttt) REVERT: E 271 ILE cc_start: 0.3682 (mm) cc_final: 0.3306 (mm) REVERT: E 293 MET cc_start: 0.0671 (tmm) cc_final: -0.0533 (ptt) REVERT: E 401 ARG cc_start: 0.2781 (tmm160) cc_final: 0.2541 (tmm160) REVERT: F 37 MET cc_start: -0.3403 (tpt) cc_final: -0.3833 (tpt) REVERT: F 38 MET cc_start: 0.3486 (pmm) cc_final: 0.3132 (mpp) REVERT: F 129 MET cc_start: 0.0290 (mtt) cc_final: -0.0867 (ptm) REVERT: D 15 TYR cc_start: 0.6795 (t80) cc_final: 0.6467 (t80) REVERT: D 153 ARG cc_start: 0.7625 (mmm160) cc_final: 0.7063 (mmm160) REVERT: D 212 MET cc_start: 0.1885 (mpp) cc_final: 0.1131 (mmp) outliers start: 17 outliers final: 13 residues processed: 111 average time/residue: 0.2139 time to fit residues: 34.0184 Evaluate side-chains 107 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 366 TYR Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain V residue 7 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 0.0030 chunk 108 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 56 optimal weight: 0.0470 chunk 50 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 122 optimal weight: 0.0370 chunk 9 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 overall best weight: 0.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 124 GLN D 86 ASN ** D 152 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 = 0.4502 r_free = 0.4502 target = 0.157439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.133702 restraints weight = 31621.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.137632 restraints weight = 16864.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.140044 restraints weight = 10668.682| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1645 moved from start: 0.7756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9872 Z= 0.157 Angle : 0.647 14.918 13347 Z= 0.308 Chirality : 0.041 0.169 1558 Planarity : 0.004 0.040 1710 Dihedral : 5.279 58.071 1398 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.25 % Allowed : 21.13 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.24), residues: 1251 helix: 0.64 (0.24), residues: 508 sheet: -0.86 (0.40), residues: 155 loop : -1.55 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 246 HIS 0.004 0.001 HIS F 97 PHE 0.022 0.001 PHE E 329 TYR 0.017 0.001 TYR E 250 ARG 0.006 0.000 ARG F 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 248 ASP cc_start: 0.5154 (p0) cc_final: 0.4830 (p0) REVERT: C 267 MET cc_start: 0.6715 (tpp) cc_final: 0.6107 (tpp) REVERT: C 315 MET cc_start: -0.2896 (mtp) cc_final: -0.3897 (ttp) REVERT: E 80 GLU cc_start: 0.7807 (mp0) cc_final: 0.7248 (pm20) REVERT: E 169 MET cc_start: 0.6394 (ppp) cc_final: 0.3034 (ttt) REVERT: E 267 MET cc_start: -0.0432 (tmm) cc_final: -0.0863 (tmm) REVERT: E 271 ILE cc_start: 0.3563 (mm) cc_final: 0.3136 (mm) REVERT: E 293 MET cc_start: -0.0364 (tmm) cc_final: -0.0826 (ptt) REVERT: E 401 ARG cc_start: 0.3590 (tmm160) cc_final: 0.3234 (tmm160) REVERT: F 37 MET cc_start: -0.3879 (tpt) cc_final: -0.4311 (tpt) REVERT: F 38 MET cc_start: 0.3430 (pmm) cc_final: 0.3017 (mpp) REVERT: F 129 MET cc_start: 0.0428 (mtt) cc_final: -0.1018 (ptt) REVERT: D 15 TYR cc_start: 0.6944 (t80) cc_final: 0.6323 (t80) REVERT: D 153 ARG cc_start: 0.7611 (mmm160) cc_final: 0.7000 (mmm160) REVERT: D 212 MET cc_start: 0.1624 (mpp) cc_final: 0.0956 (mmp) outliers start: 13 outliers final: 10 residues processed: 104 average time/residue: 0.1960 time to fit residues: 30.2233 Evaluate side-chains 100 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 366 TYR Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain V residue 7 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 46 optimal weight: 0.0670 chunk 80 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 4 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.157866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.134889 restraints weight = 31603.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.138734 restraints weight = 17098.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.141187 restraints weight = 10871.988| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1856 moved from start: 0.8406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9872 Z= 0.186 Angle : 0.683 13.335 13347 Z= 0.327 Chirality : 0.043 0.150 1558 Planarity : 0.004 0.041 1710 Dihedral : 5.241 51.030 1398 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.54 % Allowed : 21.23 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.24), residues: 1251 helix: 0.52 (0.23), residues: 502 sheet: -0.87 (0.40), residues: 154 loop : -1.58 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 222 HIS 0.004 0.001 HIS E 358 PHE 0.026 0.002 PHE E 319 TYR 0.015 0.001 TYR E 250 ARG 0.006 0.000 ARG F 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3387.07 seconds wall clock time: 59 minutes 33.47 seconds (3573.47 seconds total)