Starting phenix.real_space_refine on Fri Feb 14 02:50:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9grc_51520/02_2025/9grc_51520.cif Found real_map, /net/cci-nas-00/data/ceres_data/9grc_51520/02_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_51520/02_2025/9grc_51520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9grc_51520/02_2025/9grc_51520.map" model { file = "/net/cci-nas-00/data/ceres_data/9grc_51520/02_2025/9grc_51520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9grc_51520/02_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-5592/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: 6.01, per 1000 atoms: 0.62 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: 2.59 Conformation dependent library (CDL) restraints added in 1.3 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: 1.03 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: 2.71 Time building geometry restraints manager: 2.92 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.580 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- 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 : 0.989 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: 0.2576 time to fit residues: 53.4458 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 : 1.023 ------------------------------------------------------------------------------- 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 = 0.155819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.128838 restraints weight = 28699.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.132962 restraints weight = 14967.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.135590 restraints weight = 9543.381| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1016 moved from start: 0.2896 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 7.849 13347 Z= 0.303 Chirality : 0.043 0.148 1558 Planarity : 0.004 0.056 1710 Dihedral : 4.973 53.835 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 : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: -0.0575 (mmm) cc_final: -0.1240 (mmt) REVERT: C 59 ILE cc_start: 0.2201 (mt) cc_final: 0.1585 (mt) REVERT: C 267 MET cc_start: 0.5371 (tpp) cc_final: 0.4823 (tpp) REVERT: C 315 MET cc_start: -0.2911 (mtp) cc_final: -0.5078 (tmm) REVERT: E 169 MET cc_start: 0.4948 (ppp) cc_final: 0.4416 (ttm) REVERT: E 183 LYS cc_start: 0.2231 (OUTLIER) cc_final: 0.1979 (mmmt) REVERT: E 217 MET cc_start: -0.0622 (ptt) cc_final: -0.1461 (tpt) REVERT: F 21 GLN cc_start: 0.6806 (mm-40) cc_final: 0.5971 (pm20) REVERT: F 73 MET cc_start: -0.4229 (mpp) cc_final: -0.4629 (mtm) REVERT: F 218 MET cc_start: 0.0607 (ppp) cc_final: 0.0327 (ppp) REVERT: D 15 TYR cc_start: 0.6487 (t80) cc_final: 0.5927 (t80) REVERT: D 212 MET cc_start: 0.1729 (tpp) cc_final: 0.0821 (mmp) REVERT: D 218 MET cc_start: -0.3792 (mtt) cc_final: -0.4415 (ppp) outliers start: 10 outliers final: 5 residues processed: 110 average time/residue: 0.2282 time to fit residues: 35.5650 Evaluate side-chains 99 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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: 0.7980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 63 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4460 r_free = 0.4460 target = 0.155704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.128599 restraints weight = 29476.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.132749 restraints weight = 15266.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.135361 restraints weight = 9658.407| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1086 moved from start: 0.3498 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= 0.148 Angle : 0.551 8.172 13347 Z= 0.272 Chirality : 0.041 0.155 1558 Planarity : 0.004 0.043 1710 Dihedral : 4.650 56.327 1398 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.06 % Allowed : 12.97 % Favored : 85.98 % 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: -0.89 (0.39), residues: 186 loop : -1.54 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 78 HIS 0.003 0.001 HIS F 97 PHE 0.011 0.001 PHE C 172 TYR 0.016 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 118 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 MET cc_start: 0.0349 (mmm) cc_final: -0.0121 (mmt) REVERT: C 267 MET cc_start: 0.5662 (tpp) cc_final: 0.4966 (tpp) REVERT: C 315 MET cc_start: -0.2382 (mtp) cc_final: -0.4496 (ttp) REVERT: E 217 MET cc_start: -0.0409 (ptt) cc_final: -0.1435 (tpt) REVERT: F 21 GLN cc_start: 0.6811 (mm-40) cc_final: 0.6005 (pm20) REVERT: F 38 MET cc_start: 0.1810 (pmm) cc_final: 0.1123 (mpp) REVERT: F 73 MET cc_start: -0.4326 (mpp) cc_final: -0.4707 (mtm) REVERT: D 15 TYR cc_start: 0.6473 (t80) cc_final: 0.5910 (t80) REVERT: D 212 MET cc_start: 0.1502 (tpp) cc_final: 0.0425 (mmp) REVERT: D 218 MET cc_start: -0.3766 (mtt) cc_final: -0.4300 (ppp) outliers start: 11 outliers final: 5 residues processed: 115 average time/residue: 0.2131 time to fit residues: 35.4030 Evaluate side-chains 98 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 39 optimal weight: 0.0980 chunk 116 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 ASN ** 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 = 0.4465 r_free = 0.4465 target = 0.155900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.129206 restraints weight = 29370.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.133322 restraints weight = 15452.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.135947 restraints weight = 9845.417| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1170 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9872 Z= 0.144 Angle : 0.542 8.714 13347 Z= 0.266 Chirality : 0.041 0.138 1558 Planarity : 0.004 0.038 1710 Dihedral : 4.582 46.171 1398 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.44 % Allowed : 14.99 % Favored : 83.57 % 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: -0.73 (0.25), residues: 1251 helix: 0.79 (0.24), residues: 501 sheet: -0.92 (0.39), residues: 182 loop : -1.50 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 78 HIS 0.003 0.001 HIS D 97 PHE 0.009 0.001 PHE E 367 TYR 0.011 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 117 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: -0.0214 (mmt) cc_final: -0.0560 (mmt) REVERT: C 114 MET cc_start: 0.0531 (mmm) cc_final: 0.0131 (mmt) REVERT: C 175 MET cc_start: 0.2606 (ptp) cc_final: 0.2351 (ptt) REVERT: C 267 MET cc_start: 0.5957 (tpp) cc_final: 0.5602 (tpp) REVERT: C 315 MET cc_start: -0.2424 (mtp) cc_final: -0.4479 (ttp) REVERT: E 169 MET cc_start: 0.6269 (ppp) cc_final: 0.4385 (ttp) REVERT: E 217 MET cc_start: -0.0327 (ptt) cc_final: -0.1138 (tpt) REVERT: E 321 TRP cc_start: 0.5510 (m-90) cc_final: 0.5081 (m-10) REVERT: E 375 LEU cc_start: 0.3161 (OUTLIER) cc_final: 0.2643 (tp) REVERT: F 21 GLN cc_start: 0.6806 (mm-40) cc_final: 0.6105 (pm20) REVERT: F 73 MET cc_start: -0.4176 (mpp) cc_final: -0.4492 (mtm) REVERT: F 218 MET cc_start: 0.0557 (ppp) cc_final: 0.0224 (ppp) REVERT: D 15 TYR cc_start: 0.6493 (t80) cc_final: 0.5945 (t80) REVERT: D 212 MET cc_start: 0.1421 (tpp) cc_final: 0.0418 (mmp) REVERT: D 218 MET cc_start: -0.3860 (mtt) cc_final: -0.4354 (ppp) outliers start: 15 outliers final: 9 residues processed: 115 average time/residue: 0.2298 time to fit residues: 37.2818 Evaluate side-chains 103 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 375 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 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 107 ASN D 141 HIS ** 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 = 0.4457 r_free = 0.4457 target = 0.155365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.129337 restraints weight = 29784.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.133271 restraints weight = 16063.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.135849 restraints weight = 10343.621| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1326 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9872 Z= 0.156 Angle : 0.554 7.688 13347 Z= 0.275 Chirality : 0.041 0.183 1558 Planarity : 0.004 0.071 1710 Dihedral : 4.891 57.592 1398 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.50 % Allowed : 16.23 % Favored : 81.27 % 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: -0.78 (0.25), residues: 1251 helix: 0.63 (0.24), residues: 525 sheet: -0.76 (0.40), residues: 173 loop : -1.56 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 396 HIS 0.003 0.001 HIS E 358 PHE 0.022 0.001 PHE F 199 TYR 0.011 0.001 TYR E 397 ARG 0.006 0.000 ARG E 401 *********************** 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 127 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 4 PRO cc_start: 0.6302 (Cg_endo) cc_final: 0.5959 (Cg_exo) REVERT: C 114 MET cc_start: 0.0741 (mmm) cc_final: 0.0279 (mmt) REVERT: C 175 MET cc_start: 0.2842 (ptp) cc_final: 0.2447 (ptt) REVERT: C 248 ASP cc_start: 0.4698 (p0) cc_final: 0.4387 (p0) REVERT: C 267 MET cc_start: 0.6368 (tpp) cc_final: 0.5949 (tpp) REVERT: C 315 MET cc_start: -0.2525 (mtp) cc_final: -0.4170 (ttp) REVERT: E 217 MET cc_start: -0.0296 (ptt) cc_final: -0.0981 (tpt) REVERT: E 293 MET cc_start: -0.0149 (tmm) cc_final: -0.0936 (ppp) REVERT: E 375 LEU cc_start: 0.2821 (OUTLIER) cc_final: 0.2175 (tp) REVERT: F 37 MET cc_start: -0.0195 (mmt) cc_final: -0.0651 (tpt) REVERT: F 73 MET cc_start: -0.3540 (mpp) cc_final: -0.3743 (mtm) REVERT: D 15 TYR cc_start: 0.6475 (t80) cc_final: 0.5975 (t80) REVERT: D 212 MET cc_start: 0.1778 (tpp) cc_final: 0.0741 (mmp) REVERT: D 218 MET cc_start: -0.3741 (mtt) cc_final: -0.4104 (ppp) outliers start: 26 outliers final: 15 residues processed: 119 average time/residue: 0.2086 time to fit residues: 36.2321 Evaluate side-chains 111 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 186 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 375 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 154 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 91 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 123 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 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 = 0.4460 r_free = 0.4460 target = 0.155558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.129837 restraints weight = 30177.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.133844 restraints weight = 16149.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.136364 restraints weight = 10385.911| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1344 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9872 Z= 0.147 Angle : 0.573 10.880 13347 Z= 0.279 Chirality : 0.041 0.173 1558 Planarity : 0.004 0.074 1710 Dihedral : 4.767 56.013 1398 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.11 % Allowed : 17.68 % Favored : 80.21 % 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: -0.77 (0.24), residues: 1251 helix: 0.68 (0.24), residues: 514 sheet: -0.72 (0.42), residues: 163 loop : -1.56 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 246 HIS 0.003 0.001 HIS E 358 PHE 0.012 0.001 PHE E 319 TYR 0.006 0.001 TYR E 322 ARG 0.010 0.000 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 122 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 4 PRO cc_start: 0.6379 (Cg_endo) cc_final: 0.6087 (Cg_exo) REVERT: C 114 MET cc_start: 0.0497 (mmm) cc_final: 0.0158 (mmt) REVERT: C 175 MET cc_start: 0.2947 (ptp) cc_final: 0.2555 (ptt) REVERT: C 248 ASP cc_start: 0.4389 (p0) cc_final: 0.4150 (p0) REVERT: C 267 MET cc_start: 0.6401 (tpp) cc_final: 0.5921 (tpp) REVERT: C 315 MET cc_start: -0.2382 (mtp) cc_final: -0.4425 (ttp) REVERT: E 169 MET cc_start: 0.6605 (ppp) cc_final: 0.4055 (ttt) REVERT: E 217 MET cc_start: -0.0222 (ptt) cc_final: -0.0777 (tpt) REVERT: E 321 TRP cc_start: 0.5503 (m-90) cc_final: 0.5103 (m-10) REVERT: E 375 LEU cc_start: 0.2773 (OUTLIER) cc_final: 0.2349 (tp) REVERT: E 396 TRP cc_start: -0.1227 (t60) cc_final: -0.1807 (t60) REVERT: F 37 MET cc_start: -0.0096 (mmt) cc_final: -0.0621 (tpt) REVERT: F 129 MET cc_start: 0.0672 (mtt) cc_final: -0.0924 (ptm) REVERT: F 219 ARG cc_start: 0.3162 (mtt180) cc_final: 0.2839 (mmm160) REVERT: D 15 TYR cc_start: 0.6387 (t80) cc_final: 0.5884 (t80) REVERT: D 212 MET cc_start: 0.1787 (tpp) cc_final: 0.0778 (mmp) outliers start: 22 outliers final: 12 residues processed: 119 average time/residue: 0.2194 time to fit residues: 37.3798 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 : 1.182 ------------------------------------------------------------------------------- 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 186 VAL Chi-restraints excluded: chain C residue 224 LEU 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 375 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 45 optimal weight: 0.3980 chunk 16 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.155880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.130334 restraints weight = 30361.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.134348 restraints weight = 16163.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.136896 restraints weight = 10331.646| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1355 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9872 Z= 0.142 Angle : 0.569 10.927 13347 Z= 0.276 Chirality : 0.041 0.137 1558 Planarity : 0.004 0.040 1710 Dihedral : 4.597 58.558 1398 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.83 % Allowed : 18.64 % Favored : 79.54 % 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: -0.66 (0.25), residues: 1251 helix: 0.77 (0.24), residues: 520 sheet: -0.82 (0.40), residues: 174 loop : -1.46 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 75 HIS 0.003 0.000 HIS E 358 PHE 0.013 0.001 PHE C 172 TYR 0.015 0.001 TYR E 260 ARG 0.005 0.000 ARG E 401 *********************** 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 110 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: -0.0914 (mmt) cc_final: -0.1343 (mmt) REVERT: C 165 MET cc_start: 0.0865 (OUTLIER) cc_final: 0.0409 (tpp) REVERT: C 175 MET cc_start: 0.2644 (ptp) cc_final: 0.2284 (ptt) REVERT: C 267 MET cc_start: 0.6373 (tpp) cc_final: 0.5847 (tpp) REVERT: C 315 MET cc_start: -0.2604 (mtp) cc_final: -0.4696 (ttp) REVERT: C 344 MET cc_start: 0.0585 (pmm) cc_final: 0.0164 (pmm) REVERT: E 169 MET cc_start: 0.6436 (ppp) cc_final: 0.4000 (ttt) REVERT: E 217 MET cc_start: 0.0097 (ptt) cc_final: -0.0381 (tpt) REVERT: E 293 MET cc_start: -0.0047 (tmm) cc_final: -0.1766 (ptt) REVERT: E 321 TRP cc_start: 0.5464 (m-90) cc_final: 0.5041 (m-10) REVERT: E 375 LEU cc_start: 0.2833 (OUTLIER) cc_final: 0.2410 (tp) REVERT: F 37 MET cc_start: 0.0031 (mmt) cc_final: -0.0448 (tpt) REVERT: F 129 MET cc_start: 0.0626 (mtt) cc_final: -0.0822 (ptm) REVERT: D 15 TYR cc_start: 0.6388 (t80) cc_final: 0.5887 (t80) REVERT: D 212 MET cc_start: 0.1545 (tpp) cc_final: 0.0529 (mmp) outliers start: 19 outliers final: 11 residues processed: 106 average time/residue: 0.2207 time to fit residues: 33.7125 Evaluate side-chains 100 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 224 LEU 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 V residue 4 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 0.0070 chunk 89 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 0.0970 chunk 39 optimal weight: 0.0070 chunk 72 optimal weight: 2.9990 overall best weight: 0.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN ** 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 = 0.4467 r_free = 0.4467 target = 0.156020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.130668 restraints weight = 30625.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.134700 restraints weight = 16330.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.137248 restraints weight = 10411.645| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1338 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9872 Z= 0.137 Angle : 0.579 11.406 13347 Z= 0.277 Chirality : 0.041 0.141 1558 Planarity : 0.004 0.041 1710 Dihedral : 4.505 59.539 1398 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.92 % Allowed : 18.44 % 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: -0.60 (0.25), residues: 1251 helix: 0.84 (0.24), residues: 520 sheet: -0.76 (0.40), residues: 174 loop : -1.46 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 75 HIS 0.003 0.000 HIS E 358 PHE 0.024 0.001 PHE E 329 TYR 0.008 0.001 TYR F 15 ARG 0.004 0.000 ARG D 153 *********************** 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 109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: -0.0927 (mmt) cc_final: -0.1136 (mmt) REVERT: C 175 MET cc_start: 0.2530 (ptp) cc_final: 0.2190 (ptt) REVERT: C 267 MET cc_start: 0.6309 (tpp) cc_final: 0.5752 (tpp) REVERT: C 315 MET cc_start: -0.3165 (mtp) cc_final: -0.5066 (ttp) REVERT: C 344 MET cc_start: 0.0631 (pmm) cc_final: 0.0240 (pmm) REVERT: E 169 MET cc_start: 0.6130 (ppp) cc_final: 0.3743 (ttt) REVERT: E 217 MET cc_start: 0.0031 (ptt) cc_final: -0.0292 (tpt) REVERT: E 293 MET cc_start: 0.0004 (tmm) cc_final: -0.1544 (ptt) REVERT: E 306 ARG cc_start: 0.6616 (tpt-90) cc_final: 0.6026 (tpt170) REVERT: E 321 TRP cc_start: 0.5380 (m-90) cc_final: 0.5029 (m-10) REVERT: E 375 LEU cc_start: 0.3023 (OUTLIER) cc_final: 0.2704 (tp) REVERT: E 401 ARG cc_start: 0.3531 (tmm160) cc_final: 0.3068 (tmm160) REVERT: F 37 MET cc_start: 0.0004 (mmt) cc_final: -0.0420 (tpt) REVERT: F 129 MET cc_start: 0.0550 (mtt) cc_final: -0.0947 (ptt) REVERT: D 15 TYR cc_start: 0.6362 (t80) cc_final: 0.5862 (t80) REVERT: D 153 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.5670 (tpt170) REVERT: D 212 MET cc_start: 0.1593 (tpp) cc_final: 0.0600 (mmp) outliers start: 20 outliers final: 12 residues processed: 105 average time/residue: 0.2187 time to fit residues: 32.3779 Evaluate side-chains 102 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 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 369 ASP Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 153 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 8 optimal weight: 0.0070 chunk 89 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 6 optimal weight: 0.0970 chunk 1 optimal weight: 6.9990 overall best weight: 2.4202 ------------------------------------------------------------------------------- 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** C 143 ASN C 247 GLN C 339 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.156973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.133499 restraints weight = 31988.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.137364 restraints weight = 17315.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.139786 restraints weight = 11054.331| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1925 moved from start: 0.7740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9872 Z= 0.283 Angle : 0.821 12.230 13347 Z= 0.400 Chirality : 0.048 0.188 1558 Planarity : 0.005 0.057 1710 Dihedral : 6.470 58.544 1398 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.44 % Allowed : 19.69 % Favored : 78.87 % 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: -1.66 (0.23), residues: 1251 helix: -0.25 (0.22), residues: 517 sheet: -0.79 (0.42), residues: 139 loop : -1.96 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 385 HIS 0.005 0.001 HIS E 201 PHE 0.033 0.002 PHE C 184 TYR 0.024 0.002 TYR E 322 ARG 0.007 0.001 ARG C 308 *********************** 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 112 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: C 267 MET cc_start: 0.6740 (tpp) cc_final: 0.5944 (tpp) REVERT: C 315 MET cc_start: -0.2371 (mtp) cc_final: -0.3918 (ttp) REVERT: C 344 MET cc_start: 0.0270 (pmm) cc_final: 0.0011 (pmm) REVERT: E 217 MET cc_start: 0.0594 (ptt) cc_final: 0.0035 (tpt) REVERT: E 260 TYR cc_start: 0.1536 (p90) cc_final: 0.0608 (p90) REVERT: E 271 ILE cc_start: 0.3784 (mm) cc_final: 0.3405 (mm) REVERT: E 293 MET cc_start: 0.0422 (tmm) cc_final: -0.0723 (ptt) REVERT: E 316 ARG cc_start: 0.7486 (tpt170) cc_final: 0.6868 (tpt170) REVERT: E 401 ARG cc_start: 0.4003 (tmm160) cc_final: 0.3737 (tmm160) REVERT: F 37 MET cc_start: 0.0839 (mmt) cc_final: 0.0486 (tpp) REVERT: F 129 MET cc_start: 0.0526 (mtt) cc_final: -0.0751 (ptm) REVERT: D 15 TYR cc_start: 0.6671 (t80) cc_final: 0.6298 (t80) REVERT: D 136 ASP cc_start: 0.1704 (OUTLIER) cc_final: 0.1421 (m-30) REVERT: D 212 MET cc_start: 0.2273 (tpp) cc_final: 0.1895 (mmp) outliers start: 15 outliers final: 12 residues processed: 110 average time/residue: 0.2201 time to fit residues: 35.0042 Evaluate side-chains 100 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 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 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 D residue 105 LEU Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain V residue 4 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 0.2980 chunk 108 optimal weight: 0.0060 chunk 22 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 56 optimal weight: 0.0980 chunk 50 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 34 optimal weight: 0.0020 overall best weight: 0.2204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 GLN E 146 GLN ** 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 = 0.4493 r_free = 0.4493 target = 0.156874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.132988 restraints weight = 31530.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.136971 restraints weight = 16879.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.139442 restraints weight = 10764.986| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1634 moved from start: 0.7499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9872 Z= 0.159 Angle : 0.652 12.334 13347 Z= 0.314 Chirality : 0.042 0.167 1558 Planarity : 0.004 0.044 1710 Dihedral : 5.496 47.784 1398 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.54 % Allowed : 19.98 % Favored : 78.48 % 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: -1.21 (0.24), residues: 1251 helix: 0.21 (0.23), residues: 526 sheet: -0.62 (0.43), residues: 139 loop : -1.81 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 246 HIS 0.003 0.001 HIS E 358 PHE 0.014 0.001 PHE E 329 TYR 0.012 0.001 TYR E 322 ARG 0.003 0.000 ARG F 85 ********************** 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 106 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: C 267 MET cc_start: 0.6708 (tpp) cc_final: 0.6039 (tpp) REVERT: C 315 MET cc_start: -0.2589 (mtp) cc_final: -0.3903 (ttp) REVERT: C 344 MET cc_start: 0.0067 (pmm) cc_final: -0.0164 (pmm) REVERT: E 169 MET cc_start: 0.6616 (ppp) cc_final: 0.3365 (ttt) REVERT: E 260 TYR cc_start: 0.0307 (p90) cc_final: -0.0026 (p90) REVERT: E 267 MET cc_start: -0.0541 (tmm) cc_final: -0.1035 (tmm) REVERT: E 271 ILE cc_start: 0.3427 (mm) cc_final: 0.3008 (mm) REVERT: E 293 MET cc_start: 0.0346 (tmm) cc_final: -0.0801 (ptt) REVERT: E 401 ARG cc_start: 0.3591 (tmm160) cc_final: 0.3318 (tmm160) REVERT: F 129 MET cc_start: 0.0498 (mtt) cc_final: -0.0977 (ptt) REVERT: D 15 TYR cc_start: 0.6585 (t80) cc_final: 0.6158 (t80) REVERT: D 136 ASP cc_start: 0.1097 (OUTLIER) cc_final: 0.0740 (m-30) REVERT: D 212 MET cc_start: 0.1746 (tpp) cc_final: 0.0964 (mmp) outliers start: 16 outliers final: 11 residues processed: 104 average time/residue: 0.1916 time to fit residues: 29.6237 Evaluate side-chains 94 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 369 ASP Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 153 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 7 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 93 optimal weight: 0.0870 chunk 46 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN E 124 GLN F 107 ASN D 86 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.157651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.134471 restraints weight = 31710.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.138308 restraints weight = 17106.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.140741 restraints weight = 10893.171| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1859 moved from start: 0.8148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9872 Z= 0.208 Angle : 0.729 14.250 13347 Z= 0.350 Chirality : 0.044 0.152 1558 Planarity : 0.005 0.041 1710 Dihedral : 5.426 48.729 1398 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.25 % Allowed : 21.33 % Favored : 77.43 % 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: -1.20 (0.24), residues: 1251 helix: 0.23 (0.23), residues: 511 sheet: -0.68 (0.40), residues: 152 loop : -1.77 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 246 HIS 0.005 0.001 HIS E 358 PHE 0.023 0.002 PHE E 319 TYR 0.015 0.001 TYR E 322 ARG 0.006 0.001 ARG E 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3351.87 seconds wall clock time: 60 minutes 32.57 seconds (3632.57 seconds total)