Starting phenix.real_space_refine on Wed Sep 17 16:18:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9grc_51520/09_2025/9grc_51520.cif Found real_map, /net/cci-nas-00/data/ceres_data/9grc_51520/09_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_51520/09_2025/9grc_51520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9grc_51520/09_2025/9grc_51520.map" model { file = "/net/cci-nas-00/data/ceres_data/9grc_51520/09_2025/9grc_51520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9grc_51520/09_2025/9grc_51520.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.48, per 1000 atoms: 0.26 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: 0.93 Conformation dependent library (CDL) restraints added in 406.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.42 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: 1.46 Time building geometry restraints manager: 1.17 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.690 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.910 ------------------------------------------------------------------------------- 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 9874 Z= 0.120 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 : 7.53 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG E 269 TYR 0.010 0.001 TYR E 250 PHE 0.011 0.001 PHE C 51 TRP 0.008 0.001 TRP C 246 HIS 0.002 0.000 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 9872) covalent geometry : angle 0.66333 (13347) hydrogen bonds : bond 0.21067 ( 396) hydrogen bonds : angle 6.72182 ( 1131) Misc. bond : bond 0.00014 ( 2) *********************** 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 : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ILE cc_start: 0.1739 (mt) cc_final: 0.1475 (mt) REVERT: E 267 MET cc_start: -0.0120 (ttp) cc_final: -0.0428 (tmm) REVERT: E 271 ILE cc_start: 0.3283 (mm) cc_final: 0.2891 (mm) 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: 0.5796 (t80) REVERT: D 212 MET cc_start: 0.0674 (tpp) cc_final: 0.0318 (mmp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1164 time to fit residues: 24.3681 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 : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 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 79 GLN C 143 ASN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 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 = 0.4448 r_free = 0.4448 target = 0.155886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.128794 restraints weight = 28744.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.132942 restraints weight = 14856.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.135602 restraints weight = 9445.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.137193 restraints weight = 6914.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.138207 restraints weight = 5661.376| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0912 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9874 Z= 0.126 Angle : 0.610 8.571 13347 Z= 0.301 Chirality : 0.042 0.153 1558 Planarity : 0.004 0.057 1710 Dihedral : 4.675 50.838 1398 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.67 % Allowed : 9.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.24), residues: 1251 helix: 0.57 (0.24), residues: 504 sheet: -1.16 (0.41), residues: 175 loop : -1.68 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 85 TYR 0.014 0.001 TYR E 322 PHE 0.011 0.001 PHE E 141 TRP 0.009 0.001 TRP E 165 HIS 0.011 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9872) covalent geometry : angle 0.61044 (13347) hydrogen bonds : bond 0.03932 ( 396) hydrogen bonds : angle 4.70363 ( 1131) Misc. bond : bond 0.00055 ( 2) *********************** 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 109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: -0.0551 (mmm) cc_final: -0.1259 (mmt) REVERT: C 59 ILE cc_start: 0.2528 (mt) cc_final: 0.2037 (mt) REVERT: C 315 MET cc_start: -0.2513 (mtp) cc_final: -0.4671 (tmm) REVERT: E 169 MET cc_start: 0.4956 (ppp) cc_final: 0.4489 (ttm) REVERT: E 271 ILE cc_start: 0.3458 (mm) cc_final: 0.3028 (mm) REVERT: F 73 MET cc_start: -0.4333 (mpp) cc_final: -0.4736 (mtm) REVERT: F 85 ARG cc_start: -0.1746 (tpt170) cc_final: -0.1968 (tpt170) REVERT: D 15 TYR cc_start: 0.6462 (t80) cc_final: 0.5657 (t80) REVERT: D 212 MET cc_start: 0.1615 (tpp) cc_final: 0.0748 (mmp) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.0997 time to fit residues: 15.3322 Evaluate side-chains 96 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 366 TYR Chi-restraints excluded: chain D residue 59 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 100 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 GLN C 303 GLN ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN D 107 ASN D 141 HIS V 4 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.154789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.128840 restraints weight = 29822.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.132801 restraints weight = 15907.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.135250 restraints weight = 10207.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.136837 restraints weight = 7537.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.137758 restraints weight = 6152.294| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1337 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9874 Z= 0.152 Angle : 0.667 8.175 13347 Z= 0.330 Chirality : 0.045 0.163 1558 Planarity : 0.005 0.053 1710 Dihedral : 5.519 54.005 1398 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.73 % Allowed : 14.22 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.24), residues: 1251 helix: 0.26 (0.23), residues: 521 sheet: -0.89 (0.39), residues: 186 loop : -1.58 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 401 TYR 0.012 0.001 TYR C 199 PHE 0.021 0.002 PHE E 319 TRP 0.016 0.001 TRP E 78 HIS 0.012 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9872) covalent geometry : angle 0.66667 (13347) hydrogen bonds : bond 0.03957 ( 396) hydrogen bonds : angle 4.84455 ( 1131) Misc. bond : bond 0.00181 ( 2) *********************** 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 130 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 315 MET cc_start: -0.2597 (mtp) cc_final: -0.4575 (ttp) REVERT: E 271 ILE cc_start: 0.3686 (mm) cc_final: 0.3270 (mm) REVERT: E 375 LEU cc_start: 0.3000 (OUTLIER) cc_final: 0.2705 (tp) REVERT: E 396 TRP cc_start: 0.0244 (t-100) cc_final: -0.0097 (t60) REVERT: F 38 MET cc_start: 0.2169 (pmm) cc_final: 0.1385 (mpp) REVERT: F 85 ARG cc_start: -0.1761 (tpt170) cc_final: -0.1970 (tpt170) REVERT: F 218 MET cc_start: 0.1179 (ppp) cc_final: 0.0748 (ppp) REVERT: D 15 TYR cc_start: 0.6518 (t80) cc_final: 0.6092 (t80) REVERT: D 212 MET cc_start: 0.1767 (tpp) cc_final: 0.0690 (mmp) outliers start: 18 outliers final: 9 residues processed: 123 average time/residue: 0.0977 time to fit residues: 17.4063 Evaluate side-chains 108 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 304 VAL Chi-restraints excluded: chain E residue 341 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 83 optimal weight: 0.0070 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 39 optimal weight: 0.0060 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 63 optimal weight: 0.0070 chunk 101 optimal weight: 7.9990 overall best weight: 0.2632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 GLN C 364 GLN ** 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 = 0.4462 r_free = 0.4462 target = 0.155630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.129302 restraints weight = 30391.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.133456 restraints weight = 15934.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.136036 restraints weight = 10149.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.137587 restraints weight = 7467.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.138609 restraints weight = 6095.463| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1214 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9874 Z= 0.102 Angle : 0.551 8.072 13347 Z= 0.271 Chirality : 0.041 0.143 1558 Planarity : 0.004 0.062 1710 Dihedral : 4.644 47.046 1398 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.54 % Allowed : 16.14 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.24), residues: 1251 helix: 0.71 (0.24), residues: 501 sheet: -0.91 (0.38), residues: 191 loop : -1.50 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 85 TYR 0.013 0.001 TYR E 260 PHE 0.008 0.001 PHE E 367 TRP 0.008 0.001 TRP E 78 HIS 0.010 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 9872) covalent geometry : angle 0.55092 (13347) hydrogen bonds : bond 0.03156 ( 396) hydrogen bonds : angle 4.41860 ( 1131) Misc. bond : bond 0.00018 ( 2) *********************** 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 118 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 4 PRO cc_start: 0.6521 (Cg_endo) cc_final: 0.6116 (Cg_exo) REVERT: C 175 MET cc_start: 0.2887 (ptp) cc_final: 0.2606 (ptt) REVERT: C 315 MET cc_start: -0.2340 (mtp) cc_final: -0.4399 (ttp) REVERT: E 169 MET cc_start: 0.6353 (ppp) cc_final: 0.4443 (ttp) REVERT: E 217 MET cc_start: -0.0342 (ptt) cc_final: -0.1102 (tpt) REVERT: E 316 ARG cc_start: 0.7312 (tpt170) cc_final: 0.6922 (tpt170) REVERT: E 321 TRP cc_start: 0.5503 (m-90) cc_final: 0.5059 (m-10) REVERT: F 14 ARG cc_start: 0.2686 (pmt-80) cc_final: 0.1628 (pmt-80) REVERT: F 38 MET cc_start: 0.1760 (pmm) cc_final: 0.1512 (mpp) REVERT: F 73 MET cc_start: -0.3989 (mpp) cc_final: -0.4363 (mtm) REVERT: F 218 MET cc_start: 0.0693 (ppp) cc_final: 0.0459 (ppp) REVERT: D 15 TYR cc_start: 0.6612 (t80) cc_final: 0.6083 (t80) REVERT: D 212 MET cc_start: 0.1399 (tpp) cc_final: 0.0398 (mmp) REVERT: D 218 MET cc_start: -0.3879 (mtt) cc_final: -0.4484 (ppp) outliers start: 16 outliers final: 9 residues processed: 112 average time/residue: 0.0908 time to fit residues: 14.8680 Evaluate side-chains 108 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 121 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 37 optimal weight: 0.4980 chunk 106 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 0.0060 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 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 = 0.4462 r_free = 0.4462 target = 0.155312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.129425 restraints weight = 30468.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.133433 restraints weight = 16324.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.135925 restraints weight = 10484.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.137492 restraints weight = 7732.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.138487 restraints weight = 6305.291| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1371 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9874 Z= 0.110 Angle : 0.570 8.630 13347 Z= 0.281 Chirality : 0.042 0.141 1558 Planarity : 0.004 0.049 1710 Dihedral : 4.943 57.988 1398 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.69 % Allowed : 16.81 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.24), residues: 1251 helix: 0.68 (0.24), residues: 517 sheet: -0.75 (0.41), residues: 170 loop : -1.54 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 14 TYR 0.009 0.001 TYR C 199 PHE 0.013 0.001 PHE C 172 TRP 0.010 0.001 TRP E 78 HIS 0.009 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9872) covalent geometry : angle 0.57020 (13347) hydrogen bonds : bond 0.03219 ( 396) hydrogen bonds : angle 4.51121 ( 1131) Misc. bond : bond 0.00084 ( 2) *********************** 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 122 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: C 4 PRO cc_start: 0.6300 (Cg_endo) cc_final: 0.5972 (Cg_exo) REVERT: C 175 MET cc_start: 0.3143 (ptp) cc_final: 0.2735 (ptt) REVERT: C 311 MET cc_start: -0.3798 (ptm) cc_final: -0.4108 (ptm) REVERT: C 315 MET cc_start: -0.2347 (mtp) cc_final: -0.4256 (ttp) REVERT: E 169 MET cc_start: 0.6413 (ppp) cc_final: 0.4052 (ttm) REVERT: E 217 MET cc_start: -0.0457 (ptt) cc_final: -0.1120 (tpt) REVERT: E 321 TRP cc_start: 0.5562 (m-90) cc_final: 0.5106 (m-10) REVERT: E 375 LEU cc_start: 0.2906 (OUTLIER) cc_final: 0.2297 (tp) REVERT: F 37 MET cc_start: -0.1759 (OUTLIER) cc_final: -0.2755 (tmm) REVERT: F 38 MET cc_start: 0.2349 (pmm) cc_final: 0.1773 (mpp) REVERT: F 73 MET cc_start: -0.3823 (mpp) cc_final: -0.4167 (mtm) REVERT: F 219 ARG cc_start: 0.3072 (mtt180) cc_final: 0.2754 (mmm160) REVERT: D 15 TYR cc_start: 0.6489 (t80) cc_final: 0.5977 (t80) REVERT: D 212 MET cc_start: 0.1719 (tpp) cc_final: 0.0707 (mmp) outliers start: 28 outliers final: 11 residues processed: 115 average time/residue: 0.0901 time to fit residues: 15.3279 Evaluate side-chains 101 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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 37 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 49 optimal weight: 0.0670 chunk 54 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 60 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN F 94 GLN ** D 94 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.155487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.129812 restraints weight = 30761.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.133827 restraints weight = 16418.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.136373 restraints weight = 10537.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.137951 restraints weight = 7743.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.138893 restraints weight = 6320.458| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1408 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9874 Z= 0.111 Angle : 0.580 10.384 13347 Z= 0.284 Chirality : 0.042 0.180 1558 Planarity : 0.004 0.045 1710 Dihedral : 4.815 56.093 1398 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.59 % Allowed : 17.39 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.24), residues: 1251 helix: 0.69 (0.24), residues: 508 sheet: -0.64 (0.42), residues: 165 loop : -1.50 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 142 TYR 0.011 0.001 TYR E 322 PHE 0.028 0.001 PHE F 95 TRP 0.008 0.001 TRP E 78 HIS 0.009 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9872) covalent geometry : angle 0.58001 (13347) hydrogen bonds : bond 0.03265 ( 396) hydrogen bonds : angle 4.44459 ( 1131) Misc. bond : bond 0.00060 ( 2) *********************** 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 118 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.359 Fit side-chains REVERT: C 165 MET cc_start: 0.0246 (OUTLIER) cc_final: -0.0117 (tpp) REVERT: C 175 MET cc_start: 0.2782 (ptp) cc_final: 0.2399 (ptt) REVERT: C 315 MET cc_start: -0.2259 (mtp) cc_final: -0.4087 (ttp) REVERT: E 217 MET cc_start: -0.0229 (ptt) cc_final: -0.0841 (tpt) REVERT: E 293 MET cc_start: 0.0864 (ppp) cc_final: -0.0315 (tmm) REVERT: E 321 TRP cc_start: 0.5532 (m-90) cc_final: 0.5055 (m-10) REVERT: E 375 LEU cc_start: 0.2948 (OUTLIER) cc_final: 0.2570 (tp) REVERT: F 37 MET cc_start: -0.1544 (OUTLIER) cc_final: -0.2438 (tmm) REVERT: F 38 MET cc_start: 0.2272 (pmm) cc_final: 0.1717 (mpp) REVERT: F 73 MET cc_start: -0.3750 (mpp) cc_final: -0.4091 (mtm) REVERT: F 219 ARG cc_start: 0.3136 (mtt180) cc_final: 0.2853 (mmm160) REVERT: D 15 TYR cc_start: 0.6441 (t80) cc_final: 0.5948 (t80) REVERT: D 142 ARG cc_start: 0.5759 (tpp80) cc_final: 0.4903 (tpt90) REVERT: D 212 MET cc_start: 0.1714 (tpp) cc_final: 0.0716 (mmp) outliers start: 27 outliers final: 14 residues processed: 112 average time/residue: 0.0883 time to fit residues: 14.4218 Evaluate side-chains 104 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 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 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 F residue 37 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 119 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 81 optimal weight: 0.0370 chunk 117 optimal weight: 0.1980 chunk 92 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 14 optimal weight: 0.0670 chunk 46 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 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 = 0.4463 r_free = 0.4463 target = 0.155752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.130181 restraints weight = 30553.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.134178 restraints weight = 16339.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.136746 restraints weight = 10516.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.138242 restraints weight = 7720.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.139263 restraints weight = 6312.993| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1364 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9874 Z= 0.102 Angle : 0.569 10.852 13347 Z= 0.281 Chirality : 0.041 0.143 1558 Planarity : 0.004 0.045 1710 Dihedral : 4.666 53.637 1398 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.25), residues: 1251 helix: 0.80 (0.24), residues: 509 sheet: -0.68 (0.40), residues: 174 loop : -1.45 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 85 TYR 0.009 0.001 TYR E 322 PHE 0.021 0.001 PHE E 141 TRP 0.009 0.001 TRP E 75 HIS 0.012 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9872) covalent geometry : angle 0.56911 (13347) hydrogen bonds : bond 0.03073 ( 396) hydrogen bonds : angle 4.25576 ( 1131) Misc. bond : bond 0.00031 ( 2) *********************** 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 109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.444 Fit side-chains REVERT: C 165 MET cc_start: 0.0372 (OUTLIER) cc_final: 0.0165 (tpp) REVERT: C 175 MET cc_start: 0.2751 (ptp) cc_final: 0.2372 (ptt) REVERT: C 315 MET cc_start: -0.2809 (mtp) cc_final: -0.4114 (ttp) REVERT: E 169 MET cc_start: 0.6366 (ppp) cc_final: 0.4059 (ttp) REVERT: E 217 MET cc_start: -0.0088 (ptt) cc_final: -0.0516 (tpt) REVERT: E 321 TRP cc_start: 0.5369 (m-90) cc_final: 0.4863 (m-10) REVERT: E 375 LEU cc_start: 0.2999 (OUTLIER) cc_final: 0.2615 (tp) REVERT: F 37 MET cc_start: -0.1619 (OUTLIER) cc_final: -0.2559 (tmm) REVERT: F 73 MET cc_start: -0.3816 (mpp) cc_final: -0.4159 (mtm) REVERT: F 129 MET cc_start: 0.0701 (mtt) cc_final: 0.0319 (mtm) REVERT: D 15 TYR cc_start: 0.6475 (t80) cc_final: 0.5963 (t80) REVERT: D 212 MET cc_start: 0.1386 (tpp) cc_final: 0.0449 (mmp) outliers start: 20 outliers final: 14 residues processed: 104 average time/residue: 0.0969 time to fit residues: 14.6532 Evaluate side-chains 101 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 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 369 ASP Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain F residue 37 MET 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 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 108 optimal weight: 0.0870 chunk 57 optimal weight: 5.9990 chunk 21 optimal weight: 0.0980 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.155560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.130218 restraints weight = 30788.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.134270 restraints weight = 16386.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.136840 restraints weight = 10472.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.138406 restraints weight = 7646.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.139347 restraints weight = 6227.238| |-----------------------------------------------------------------------------| r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1406 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9874 Z= 0.102 Angle : 0.573 10.951 13347 Z= 0.281 Chirality : 0.041 0.145 1558 Planarity : 0.004 0.044 1710 Dihedral : 4.616 56.391 1398 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.11 % Allowed : 18.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.24), residues: 1251 helix: 0.82 (0.24), residues: 514 sheet: -0.53 (0.42), residues: 160 loop : -1.54 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 85 TYR 0.011 0.001 TYR F 15 PHE 0.009 0.001 PHE E 319 TRP 0.010 0.001 TRP E 75 HIS 0.011 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 9872) covalent geometry : angle 0.57273 (13347) hydrogen bonds : bond 0.03073 ( 396) hydrogen bonds : angle 4.25253 ( 1131) Misc. bond : bond 0.00060 ( 2) *********************** 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 108 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.291 Fit side-chains REVERT: C 175 MET cc_start: 0.2769 (ptp) cc_final: 0.2388 (ptt) REVERT: C 311 MET cc_start: -0.3900 (ptm) cc_final: -0.4104 (ptm) REVERT: C 315 MET cc_start: -0.2872 (mtp) cc_final: -0.4099 (ttp) REVERT: E 98 ILE cc_start: -0.1386 (OUTLIER) cc_final: -0.2408 (tp) REVERT: E 169 MET cc_start: 0.6155 (ppp) cc_final: 0.3800 (ttt) REVERT: E 217 MET cc_start: 0.0189 (ptt) cc_final: -0.0136 (tpt) REVERT: E 293 MET cc_start: 0.0831 (ppp) cc_final: -0.0781 (tmm) REVERT: E 321 TRP cc_start: 0.5293 (m-90) cc_final: 0.4855 (m-10) REVERT: E 375 LEU cc_start: 0.2888 (OUTLIER) cc_final: 0.2523 (tp) REVERT: F 37 MET cc_start: -0.2008 (OUTLIER) cc_final: -0.2553 (tmm) REVERT: F 73 MET cc_start: -0.3384 (mpp) cc_final: -0.3720 (mtm) REVERT: F 129 MET cc_start: 0.0620 (mtt) cc_final: -0.0767 (ptm) REVERT: F 218 MET cc_start: 0.1252 (ppp) cc_final: 0.1018 (ppp) REVERT: D 15 TYR cc_start: 0.6470 (t80) cc_final: 0.5966 (t80) REVERT: D 212 MET cc_start: 0.1237 (tpp) cc_final: 0.0324 (mmp) outliers start: 22 outliers final: 11 residues processed: 103 average time/residue: 0.0933 time to fit residues: 14.1081 Evaluate side-chains 99 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 224 LEU 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 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 37 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 10 optimal weight: 0.0980 chunk 21 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.155890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.131031 restraints weight = 30956.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.134960 restraints weight = 16645.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.137453 restraints weight = 10737.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.138966 restraints weight = 7887.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.139939 restraints weight = 6426.603| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1443 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9874 Z= 0.102 Angle : 0.589 11.505 13347 Z= 0.289 Chirality : 0.041 0.147 1558 Planarity : 0.004 0.048 1710 Dihedral : 4.665 57.945 1398 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.92 % Allowed : 18.35 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.24), residues: 1251 helix: 0.85 (0.24), residues: 513 sheet: -0.52 (0.42), residues: 160 loop : -1.59 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 401 TYR 0.006 0.001 TYR C 199 PHE 0.021 0.001 PHE E 329 TRP 0.012 0.001 TRP E 75 HIS 0.013 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 9872) covalent geometry : angle 0.58915 (13347) hydrogen bonds : bond 0.03101 ( 396) hydrogen bonds : angle 4.28001 ( 1131) Misc. bond : bond 0.00058 ( 2) *********************** 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 106 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.379 Fit side-chains REVERT: C 175 MET cc_start: 0.3042 (ptp) cc_final: 0.2708 (ptt) REVERT: C 315 MET cc_start: -0.2890 (mtp) cc_final: -0.4092 (ttp) REVERT: E 48 MET cc_start: -0.1362 (tpp) cc_final: -0.2814 (tpp) REVERT: E 98 ILE cc_start: -0.1372 (OUTLIER) cc_final: -0.2384 (tp) REVERT: E 169 MET cc_start: 0.5990 (ppp) cc_final: 0.3627 (ttt) REVERT: E 183 LYS cc_start: 0.3857 (tttt) cc_final: 0.3515 (tttt) REVERT: E 217 MET cc_start: 0.0158 (ptt) cc_final: -0.0103 (tpt) REVERT: F 37 MET cc_start: -0.0964 (OUTLIER) cc_final: -0.1890 (tmm) REVERT: F 73 MET cc_start: -0.3260 (mpp) cc_final: -0.3565 (mtm) REVERT: F 129 MET cc_start: 0.0544 (mtt) cc_final: -0.0797 (ptm) REVERT: F 218 MET cc_start: 0.1283 (ppp) cc_final: 0.0974 (ppp) REVERT: D 15 TYR cc_start: 0.6529 (t80) cc_final: 0.6058 (t80) REVERT: D 212 MET cc_start: 0.1298 (tpp) cc_final: 0.0397 (mmp) outliers start: 20 outliers final: 13 residues processed: 103 average time/residue: 0.0792 time to fit residues: 12.5117 Evaluate side-chains 97 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 178 ILE Chi-restraints excluded: chain C residue 224 LEU 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 346 THR Chi-restraints excluded: chain E residue 366 TYR Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 401 ARG Chi-restraints excluded: chain F residue 37 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 0.0570 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 GLN E 86 GLN E 146 GLN F 107 ASN D 86 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 4 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.156624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.132413 restraints weight = 31209.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.136366 restraints weight = 16780.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.138845 restraints weight = 10719.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.140385 restraints weight = 7826.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.141276 restraints weight = 6359.270| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1668 moved from start: 0.7127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9874 Z= 0.125 Angle : 0.650 11.837 13347 Z= 0.318 Chirality : 0.043 0.210 1558 Planarity : 0.004 0.046 1710 Dihedral : 5.012 46.064 1398 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.83 % Allowed : 19.12 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.24), residues: 1251 helix: 0.58 (0.23), residues: 516 sheet: -0.55 (0.42), residues: 149 loop : -1.69 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 401 TYR 0.012 0.001 TYR E 273 PHE 0.017 0.001 PHE C 184 TRP 0.008 0.001 TRP E 377 HIS 0.009 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9872) covalent geometry : angle 0.64990 (13347) hydrogen bonds : bond 0.03597 ( 396) hydrogen bonds : angle 4.59205 ( 1131) Misc. bond : bond 0.00099 ( 2) ********************** 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 112 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: C 315 MET cc_start: -0.2822 (mtp) cc_final: -0.4657 (ttp) REVERT: E 80 GLU cc_start: 0.7646 (mp0) cc_final: 0.7092 (pm20) REVERT: E 169 MET cc_start: 0.6455 (ppp) cc_final: 0.3595 (ttt) REVERT: E 183 LYS cc_start: 0.4072 (tttt) cc_final: 0.3769 (tttt) REVERT: E 217 MET cc_start: 0.0236 (ptt) cc_final: -0.0141 (tpt) REVERT: E 260 TYR cc_start: 0.0896 (p90) cc_final: 0.0682 (p90) REVERT: F 37 MET cc_start: -0.0578 (OUTLIER) cc_final: -0.1463 (tmm) REVERT: F 73 MET cc_start: -0.2453 (mpp) cc_final: -0.2690 (mtm) REVERT: F 129 MET cc_start: 0.0380 (mtt) cc_final: -0.0746 (ptm) REVERT: F 218 MET cc_start: 0.1818 (ppp) cc_final: 0.1532 (ppp) REVERT: D 15 TYR cc_start: 0.6671 (t80) cc_final: 0.6240 (t80) REVERT: D 212 MET cc_start: 0.1737 (tpp) cc_final: 0.1383 (mmp) outliers start: 19 outliers final: 15 residues processed: 109 average time/residue: 0.0934 time to fit residues: 14.8673 Evaluate side-chains 103 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 MET 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 178 ILE Chi-restraints excluded: chain C residue 346 ILE 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 346 THR Chi-restraints excluded: chain E residue 366 TYR Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain F residue 37 MET 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 93 optimal weight: 0.0000 chunk 95 optimal weight: 0.8980 chunk 45 optimal weight: 0.0010 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 107 optimal weight: 0.0170 chunk 94 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.2628 ------------------------------------------------------------------------------- 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** D 86 ASN D 96 HIS D 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.155773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.132114 restraints weight = 30874.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.136000 restraints weight = 16605.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.138470 restraints weight = 10593.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.139982 restraints weight = 7674.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.140941 restraints weight = 6198.650| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1550 moved from start: 0.7114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9874 Z= 0.108 Angle : 0.634 12.809 13347 Z= 0.308 Chirality : 0.042 0.232 1558 Planarity : 0.004 0.049 1710 Dihedral : 4.903 48.456 1398 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.34 % Allowed : 19.69 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.24), residues: 1251 helix: 0.71 (0.23), residues: 516 sheet: -0.75 (0.40), residues: 160 loop : -1.58 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 401 TYR 0.010 0.001 TYR E 322 PHE 0.017 0.001 PHE E 329 TRP 0.012 0.001 TRP C 246 HIS 0.013 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9872) covalent geometry : angle 0.63385 (13347) hydrogen bonds : bond 0.03226 ( 396) hydrogen bonds : angle 4.34176 ( 1131) Misc. bond : bond 0.00003 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2189.05 seconds wall clock time: 38 minutes 18.91 seconds (2298.91 seconds total)