Starting phenix.real_space_refine on Sat Aug 23 15:19:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpm_34933/08_2025/8hpm_34933.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpm_34933/08_2025/8hpm_34933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hpm_34933/08_2025/8hpm_34933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpm_34933/08_2025/8hpm_34933.map" model { file = "/net/cci-nas-00/data/ceres_data/8hpm_34933/08_2025/8hpm_34933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpm_34933/08_2025/8hpm_34933.cif" } resolution = 3.82 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 29 5.16 5 C 8181 2.51 5 N 2157 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12803 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2115 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 267} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2007 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 16, 'TRANS': 254} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2657 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ARG:plan': 11, 'PHE:plan': 2, 'GLU:plan': 9, 'ASP:plan': 3, 'GLN:plan1': 7, 'TYR:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 176 Chain: "D" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2658 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 12, 'ASN:plan1': 4, 'ASP:plan': 3, 'GLN:plan1': 7, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 165 Chain: "E" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3281 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 31, 'TRANS': 405} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 47 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.38, per 1000 atoms: 0.26 Number of scatterers: 12803 At special positions: 0 Unit cell: (83.64, 93.48, 165.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 6 15.00 O 2430 8.00 N 2157 7.00 C 8181 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=0, symmetry=0 Links applied ALPHA1-1 " GLC G 1 " - " GLC G 2 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 674.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 15 sheets defined 52.6% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 39 through 51 removed outlier: 3.620A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 76 Processing helix chain 'A' and resid 76 through 111 removed outlier: 3.715A pdb=" N TRP A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 82 " --> pdb=" O TYR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.691A pdb=" N ILE A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 129 through 141 removed outlier: 3.784A pdb=" N TRP A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 161 through 190 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 193 through 203 removed outlier: 4.050A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.838A pdb=" N LYS A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 236 Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 238 through 246 removed outlier: 4.456A pdb=" N LEU A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 removed outlier: 4.460A pdb=" N LEU A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 291 removed outlier: 3.530A pdb=" N PHE A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 37 Proline residue: B 27 - end of helix removed outlier: 4.344A pdb=" N ILE B 31 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 64 through 98 removed outlier: 4.129A pdb=" N SER B 68 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 114 removed outlier: 4.087A pdb=" N LEU B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.528A pdb=" N LEU B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 138 through 164 Proline residue: B 144 - end of helix Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.587A pdb=" N LYS B 170 " --> pdb=" O TRP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 206 removed outlier: 5.273A pdb=" N ARG B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Proline residue: B 189 - end of helix Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 241 through 263 Proline residue: B 255 - end of helix removed outlier: 3.789A pdb=" N ILE B 258 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'C' and resid 96 through 108 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.525A pdb=" N GLU C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 154 Processing helix chain 'C' and resid 170 through 189 Processing helix chain 'C' and resid 198 through 204 removed outlier: 3.649A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 266 through 275 removed outlier: 5.312A pdb=" N LEU C 272 " --> pdb=" O HIS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 96 through 108 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 140 through 154 removed outlier: 5.124A pdb=" N ARG D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET D 149 " --> pdb=" O GLN D 145 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 173 through 189 Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 222 through 229 Processing helix chain 'D' and resid 232 through 239 Processing helix chain 'D' and resid 266 through 274 removed outlier: 4.015A pdb=" N LEU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D 272 " --> pdb=" O HIS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 374 through 377 Processing helix chain 'E' and resid 40 through 55 Processing helix chain 'E' and resid 71 through 83 removed outlier: 3.920A pdb=" N LEU E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG E 80 " --> pdb=" O GLN E 76 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 105 removed outlier: 3.816A pdb=" N PHE E 101 " --> pdb=" O TRP E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 removed outlier: 4.150A pdb=" N ASP E 113 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 125 removed outlier: 4.388A pdb=" N ALA E 120 " --> pdb=" O GLY E 116 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASN E 125 " --> pdb=" O ASP E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 134 removed outlier: 3.742A pdb=" N LEU E 131 " --> pdb=" O LEU E 127 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA E 134 " --> pdb=" O PRO E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 180 Processing helix chain 'E' and resid 192 through 206 removed outlier: 3.554A pdb=" N VAL E 196 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 243 Processing helix chain 'E' and resid 254 through 264 removed outlier: 3.546A pdb=" N ALA E 258 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 286 removed outlier: 4.298A pdb=" N SER E 279 " --> pdb=" O TYR E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Proline residue: E 298 - end of helix Processing helix chain 'E' and resid 313 through 325 Processing helix chain 'E' and resid 360 through 371 Processing helix chain 'E' and resid 374 through 382 removed outlier: 3.979A pdb=" N TYR E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR E 379 " --> pdb=" O ASN E 375 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 380 " --> pdb=" O GLN E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 394 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 404 through 412 removed outlier: 3.628A pdb=" N ILE E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 435 Processing helix chain 'E' and resid 442 through 459 removed outlier: 3.509A pdb=" N ASP E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 31 removed outlier: 5.320A pdb=" N PHE C 27 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 159 through 161 removed outlier: 6.644A pdb=" N PHE C 160 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N VAL C 195 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N PHE C 36 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL C 210 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE C 38 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N MET C 212 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL C 40 " --> pdb=" O MET C 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 245 through 250 Processing sheet with id=AA5, first strand: chain 'C' and resid 292 through 293 removed outlier: 4.041A pdb=" N GLU C 366 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 315 through 316 Processing sheet with id=AA7, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.599A pdb=" N ILE D 67 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 192 through 196 removed outlier: 6.599A pdb=" N PHE D 36 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL D 210 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE D 38 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N MET D 212 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL D 40 " --> pdb=" O MET D 212 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU D 213 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 83 through 84 removed outlier: 6.928A pdb=" N ALA D 83 " --> pdb=" O LEU D 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 245 through 249 removed outlier: 3.785A pdb=" N SER D 378 " --> pdb=" O GLY D 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 256 through 258 Processing sheet with id=AB3, first strand: chain 'D' and resid 291 through 293 removed outlier: 4.062A pdb=" N GLU D 366 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 315 through 316 Processing sheet with id=AB5, first strand: chain 'E' and resid 60 through 66 removed outlier: 10.554A pdb=" N ASP E 94 " --> pdb=" O PRO E 37 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY E 347 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR E 147 " --> pdb=" O GLY E 347 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU E 349 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 269 through 270 653 hydrogen bonds defined for protein. 1857 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2432 1.32 - 1.45: 2961 1.45 - 1.57: 7600 1.57 - 1.70: 10 1.70 - 1.82: 54 Bond restraints: 13057 Sorted by residual: bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.87e+01 bond pdb=" C5 ATP D 501 " pdb=" C6 ATP D 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C5 GLC G 1 " pdb=" O5 GLC G 1 " ideal model delta sigma weight residual 1.415 1.549 -0.134 2.00e-02 2.50e+03 4.50e+01 ... (remaining 13052 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 17270 3.91 - 7.83: 597 7.83 - 11.74: 13 11.74 - 15.65: 2 15.65 - 19.57: 4 Bond angle restraints: 17886 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.30 19.57 1.00e+00 1.00e+00 3.83e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.33 16.50 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 120.39 16.44 1.00e+00 1.00e+00 2.70e+02 angle pdb=" C5 ATP C 501 " pdb=" C4 ATP C 501 " pdb=" N3 ATP C 501 " ideal model delta sigma weight residual 126.80 118.62 8.18 1.00e+00 1.00e+00 6.68e+01 ... (remaining 17881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 7249 17.61 - 35.23: 458 35.23 - 52.84: 90 52.84 - 70.46: 23 70.46 - 88.07: 4 Dihedral angle restraints: 7824 sinusoidal: 2776 harmonic: 5048 Sorted by residual: dihedral pdb=" CA ASP C 321 " pdb=" C ASP C 321 " pdb=" N LYS C 322 " pdb=" CA LYS C 322 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA LEU A 151 " pdb=" C LEU A 151 " pdb=" N LEU A 152 " pdb=" CA LEU A 152 " ideal model delta harmonic sigma weight residual 180.00 150.98 29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA SER D 156 " pdb=" C SER D 156 " pdb=" N PRO D 157 " pdb=" CA PRO D 157 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 7821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 1836 0.130 - 0.260: 310 0.260 - 0.390: 20 0.390 - 0.520: 4 0.520 - 0.650: 1 Chirality restraints: 2171 Sorted by residual: chirality pdb=" C1 GLC G 1 " pdb=" C2 GLC G 1 " pdb=" O5 GLC G 1 " pdb=" O1 GLC G 2 " both_signs ideal model delta sigma weight residual False 2.40 2.29 0.11 2.00e-02 2.50e+03 3.03e+01 chirality pdb=" C5 GLC G 2 " pdb=" C4 GLC G 2 " pdb=" C6 GLC G 2 " pdb=" O5 GLC G 2 " both_signs ideal model delta sigma weight residual False -2.50 -1.85 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CA LYS C 109 " pdb=" N LYS C 109 " pdb=" C LYS C 109 " pdb=" CB LYS C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.38e+00 ... (remaining 2168 not shown) Planarity restraints: 2300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 106 " -0.118 2.00e-02 2.50e+03 6.65e-02 1.11e+02 pdb=" CG TRP E 106 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP E 106 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP E 106 " 0.052 2.00e-02 2.50e+03 pdb=" NE1 TRP E 106 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP E 106 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 106 " 0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 106 " -0.076 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 106 " 0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP E 106 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 333 " -0.120 2.00e-02 2.50e+03 6.73e-02 9.06e+01 pdb=" CG TYR E 333 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR E 333 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR E 333 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR E 333 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR E 333 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR E 333 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 333 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 80 " 0.100 2.00e-02 2.50e+03 5.74e-02 8.24e+01 pdb=" CG TRP A 80 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A 80 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 80 " -0.064 2.00e-02 2.50e+03 pdb=" NE1 TRP A 80 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TRP A 80 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP A 80 " -0.086 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 80 " 0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 80 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 80 " 0.074 2.00e-02 2.50e+03 ... (remaining 2297 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 779 2.76 - 3.29: 14479 3.29 - 3.83: 20019 3.83 - 4.36: 25123 4.36 - 4.90: 40654 Nonbonded interactions: 101054 Sorted by model distance: nonbonded pdb=" O ALA D 23 " pdb=" C VAL D 24 " model vdw 2.225 3.270 nonbonded pdb=" O ALA C 90 " pdb=" NH1 ARG C 151 " model vdw 2.249 3.120 nonbonded pdb=" O ALA D 23 " pdb=" O VAL D 24 " model vdw 2.261 3.040 nonbonded pdb=" CG PRO E 37 " pdb=" NE2 GLN E 73 " model vdw 2.282 3.520 nonbonded pdb=" N LYS D 11 " pdb=" O VAL D 24 " model vdw 2.302 3.120 ... (remaining 101049 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 'C' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 72 or (resid 73 and (name N or name \ CA or name C or name O or name CB )) or resid 74 or (resid 75 through 76 and (n \ ame N or name CA or name C or name O or name CB )) or resid 77 through 79 or (re \ sid 80 through 81 and (name N or name CA or name C or name O or name CB )) or re \ sid 82 through 95 or (resid 96 and (name N or name CA or name C or name O or nam \ e CB )) or resid 97 through 126 or (resid 127 and (name N or name CA or name C o \ r name O or name CB )) or resid 128 through 143 or (resid 144 and (name N or nam \ e CA or name C or name O or name CB )) or resid 145 through 165 or (resid 166 an \ d (name N or name CA or name C or name O or name CB )) or resid 167 through 168 \ or (resid 169 through 172 and (name N or name CA or name C or name O or name CB \ )) or resid 173 through 176 or (resid 177 through 179 and (name N or name CA or \ name C or name O or name CB )) or resid 180 through 204 or (resid 205 and (name \ N or name CA or name C or name O or name CB )) or resid 206 through 211 or (resi \ d 212 and (name N or name CA or name C or name O or name CB )) or resid 213 thro \ ugh 231 or (resid 232 through 233 and (name N or name CA or name C or name O or \ name CB )) or resid 234 through 244 or (resid 245 and (name N or name CA or name \ C or name O or name CB )) or resid 246 through 286 or (resid 287 and (name N or \ name CA or name C or name O or name CB )) or resid 288 through 316 or (resid 31 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 318 through \ 339 or (resid 340 and (name N or name CA or name C or name O or name CB )) or re \ sid 341 through 367 or (resid 368 through 369 and (name N or name CA or name C o \ r name O or name CB )) or resid 370 through 501)) selection = (chain 'D' and (resid 2 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 14 or (resid 21 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 131 or (res \ id 132 and (name N or name CA or name C or name O or name CB )) or resid 133 thr \ ough 171 or (resid 172 and (name N or name CA or name C or name O or name CB )) \ or resid 173 through 177 or (resid 178 through 179 and (name N or name CA or nam \ e C or name O or name CB )) or resid 180 through 190 or (resid 191 through 192 a \ nd (name N or name CA or name C or name O or name CB )) or resid 193 or (resid 1 \ 94 through 195 and (name N or name CA or name C or name O or name CB )) or resid \ 196 through 226 or (resid 227 and (name N or name CA or name C or name O or nam \ e CB )) or resid 228 or (resid 229 and (name N or name CA or name C or name O or \ name CB )) or resid 230 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 289 or (resid 290 and (name N o \ r name CA or name C or name O or name CB )) or resid 291 through 292 or (resid 2 \ 93 and (name N or name CA or name C or name O or name CB )) or resid 294 through \ 325 or (resid 326 and (name N or name CA or name C or name O or name CB )) or r \ esid 327 through 365 or (resid 366 and (name N or name CA or name C or name O or \ name CB )) or resid 367 through 501)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.380 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.012 0.134 13058 Z= 0.769 Angle : 1.823 19.566 17889 Z= 1.236 Chirality : 0.095 0.650 2171 Planarity : 0.012 0.120 2300 Dihedral : 12.983 88.073 4564 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.42 % Favored : 93.46 % Rotamer: Outliers : 0.65 % Allowed : 4.95 % Favored : 94.40 % Cbeta Deviations : 0.31 % 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: -2.52 (0.18), residues: 1744 helix: -1.59 (0.15), residues: 810 sheet: -1.15 (0.43), residues: 143 loop : -1.74 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 79 TYR 0.120 0.015 TYR E 333 PHE 0.062 0.012 PHE D 238 TRP 0.118 0.023 TRP E 106 HIS 0.013 0.003 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.01235 (13057) covalent geometry : angle 1.82323 (17886) hydrogen bonds : bond 0.17081 ( 653) hydrogen bonds : angle 7.80896 ( 1857) glycosidic custom : bond 0.02907 ( 1) glycosidic custom : angle 1.92355 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 361 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7553 (ttt180) cc_final: 0.7203 (tmm160) REVERT: A 186 LEU cc_start: 0.9459 (tp) cc_final: 0.9247 (tt) REVERT: A 203 ASP cc_start: 0.8131 (m-30) cc_final: 0.7923 (t0) REVERT: A 279 PHE cc_start: 0.8653 (t80) cc_final: 0.8357 (t80) REVERT: B 13 TRP cc_start: 0.8172 (m100) cc_final: 0.7916 (m100) REVERT: B 68 SER cc_start: 0.8177 (t) cc_final: 0.7427 (t) REVERT: C 91 LEU cc_start: 0.8082 (mt) cc_final: 0.7824 (mp) REVERT: C 149 MET cc_start: 0.8851 (mtp) cc_final: 0.8273 (mtp) REVERT: C 316 GLU cc_start: 0.8770 (pt0) cc_final: 0.8388 (tt0) REVERT: C 380 PHE cc_start: 0.7776 (m-80) cc_final: 0.7028 (m-80) REVERT: D 99 GLN cc_start: 0.8718 (mt0) cc_final: 0.8267 (mt0) REVERT: D 100 ASN cc_start: 0.8012 (m-40) cc_final: 0.7763 (m110) REVERT: D 101 ILE cc_start: 0.8197 (mt) cc_final: 0.7907 (mm) REVERT: D 269 MET cc_start: 0.4923 (mmp) cc_final: 0.4373 (mtt) REVERT: D 386 LEU cc_start: 0.8926 (mt) cc_final: 0.8704 (mm) REVERT: E 76 GLN cc_start: 0.7464 (mm-40) cc_final: 0.7256 (mm-40) REVERT: E 281 LEU cc_start: 0.9194 (mt) cc_final: 0.8807 (mm) outliers start: 8 outliers final: 1 residues processed: 368 average time/residue: 0.1248 time to fit residues: 64.3277 Evaluate side-chains 224 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 275 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 261 ASN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 ASN C 87 GLN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.137005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.098438 restraints weight = 33398.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.101570 restraints weight = 16407.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.103571 restraints weight = 10382.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.104904 restraints weight = 7744.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.105713 restraints weight = 6393.935| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13058 Z= 0.197 Angle : 0.789 8.247 17889 Z= 0.418 Chirality : 0.049 0.232 2171 Planarity : 0.005 0.084 2300 Dihedral : 8.514 86.529 1965 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.73 % Allowed : 13.07 % Favored : 83.20 % 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: -1.46 (0.19), residues: 1744 helix: -0.32 (0.17), residues: 830 sheet: -1.25 (0.39), residues: 164 loop : -1.56 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 174 TYR 0.020 0.002 TYR D 194 PHE 0.031 0.002 PHE A 83 TRP 0.017 0.002 TRP B 207 HIS 0.010 0.002 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00431 (13057) covalent geometry : angle 0.78811 (17886) hydrogen bonds : bond 0.05427 ( 653) hydrogen bonds : angle 5.51339 ( 1857) glycosidic custom : bond 0.00254 ( 1) glycosidic custom : angle 2.14269 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7894 (ttt180) cc_final: 0.7190 (tmm160) REVERT: A 147 TYR cc_start: 0.7819 (p90) cc_final: 0.7573 (p90) REVERT: A 181 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8174 (mtp) REVERT: B 13 TRP cc_start: 0.8101 (m100) cc_final: 0.7886 (m100) REVERT: B 68 SER cc_start: 0.8281 (t) cc_final: 0.7027 (t) REVERT: B 173 LYS cc_start: 0.8727 (mtmt) cc_final: 0.8188 (mmtm) REVERT: B 220 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7792 (tp-100) REVERT: C 66 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7521 (mmm160) REVERT: C 109 LYS cc_start: 0.7284 (tptp) cc_final: 0.6283 (ptpp) REVERT: C 316 GLU cc_start: 0.8940 (pt0) cc_final: 0.8568 (tt0) REVERT: C 380 PHE cc_start: 0.7762 (m-80) cc_final: 0.6965 (m-80) REVERT: D 95 MET cc_start: 0.8486 (mmt) cc_final: 0.7742 (mmt) REVERT: D 100 ASN cc_start: 0.8343 (m-40) cc_final: 0.7990 (t0) REVERT: D 265 LEU cc_start: 0.5740 (mt) cc_final: 0.5464 (mt) REVERT: D 269 MET cc_start: 0.5107 (mmp) cc_final: 0.4305 (mtt) REVERT: D 380 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8760 (m-80) REVERT: E 76 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7549 (mm-40) REVERT: E 169 MET cc_start: 0.8491 (ttt) cc_final: 0.8283 (ttt) REVERT: E 281 LEU cc_start: 0.9276 (mt) cc_final: 0.9057 (mm) outliers start: 46 outliers final: 25 residues processed: 267 average time/residue: 0.1094 time to fit residues: 42.0906 Evaluate side-chains 238 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 344 ASP Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 130 optimal weight: 20.0000 chunk 173 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 98 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 117 optimal weight: 20.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN C 87 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN E 411 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.138626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.102624 restraints weight = 33445.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.104440 restraints weight = 16995.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.105284 restraints weight = 11146.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.105515 restraints weight = 9064.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.105794 restraints weight = 8653.503| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13058 Z= 0.153 Angle : 0.693 8.708 17889 Z= 0.358 Chirality : 0.047 0.226 2171 Planarity : 0.005 0.048 2300 Dihedral : 7.579 83.798 1963 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.06 % Allowed : 16.64 % Favored : 79.30 % 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: -1.03 (0.20), residues: 1744 helix: 0.25 (0.18), residues: 826 sheet: -1.38 (0.38), residues: 178 loop : -1.53 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 287 TYR 0.024 0.002 TYR E 34 PHE 0.024 0.002 PHE C 234 TRP 0.013 0.001 TRP B 207 HIS 0.005 0.002 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00339 (13057) covalent geometry : angle 0.69279 (17886) hydrogen bonds : bond 0.04385 ( 653) hydrogen bonds : angle 5.00593 ( 1857) glycosidic custom : bond 0.00674 ( 1) glycosidic custom : angle 1.68292 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 237 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7849 (ttt180) cc_final: 0.7316 (ppt170) REVERT: A 181 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7780 (tpp) REVERT: B 68 SER cc_start: 0.8363 (t) cc_final: 0.7102 (t) REVERT: B 103 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8853 (tppt) REVERT: B 127 ASN cc_start: 0.9039 (t0) cc_final: 0.8518 (t0) REVERT: B 173 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8219 (mmtm) REVERT: B 256 ILE cc_start: 0.8753 (pt) cc_final: 0.8397 (mt) REVERT: C 66 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7481 (mmm160) REVERT: C 164 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8114 (tm-30) REVERT: C 177 MET cc_start: 0.9389 (mmp) cc_final: 0.9112 (mmm) REVERT: C 287 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8338 (ptp90) REVERT: C 316 GLU cc_start: 0.8773 (pt0) cc_final: 0.8392 (mt-10) REVERT: C 380 PHE cc_start: 0.7701 (m-80) cc_final: 0.6927 (m-80) REVERT: D 100 ASN cc_start: 0.8220 (m-40) cc_final: 0.7406 (t0) REVERT: D 174 ARG cc_start: 0.9210 (mmm-85) cc_final: 0.8810 (mmp-170) REVERT: D 265 LEU cc_start: 0.5678 (mt) cc_final: 0.5457 (mt) REVERT: D 269 MET cc_start: 0.5238 (mmp) cc_final: 0.4884 (mtt) REVERT: D 367 GLN cc_start: 0.9168 (mm-40) cc_final: 0.8954 (mm-40) REVERT: D 380 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8673 (m-80) REVERT: D 390 ARG cc_start: 0.8192 (tpt170) cc_final: 0.7862 (mpt90) REVERT: E 263 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7542 (pt0) outliers start: 50 outliers final: 23 residues processed: 270 average time/residue: 0.1084 time to fit residues: 42.1301 Evaluate side-chains 237 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 0.0170 chunk 49 optimal weight: 0.0070 chunk 134 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 87 GLN C 168 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.139336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.103758 restraints weight = 33405.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.105641 restraints weight = 17043.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.106594 restraints weight = 10903.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.106607 restraints weight = 8843.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.107076 restraints weight = 8560.294| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13058 Z= 0.132 Angle : 0.662 8.504 17889 Z= 0.336 Chirality : 0.045 0.230 2171 Planarity : 0.005 0.044 2300 Dihedral : 7.011 81.846 1963 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.73 % Allowed : 19.72 % Favored : 76.54 % 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: -0.89 (0.20), residues: 1744 helix: 0.50 (0.18), residues: 829 sheet: -1.54 (0.36), residues: 190 loop : -1.56 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 178 TYR 0.022 0.002 TYR D 194 PHE 0.031 0.002 PHE A 83 TRP 0.012 0.001 TRP B 13 HIS 0.005 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00285 (13057) covalent geometry : angle 0.66229 (17886) hydrogen bonds : bond 0.04036 ( 653) hydrogen bonds : angle 4.87045 ( 1857) glycosidic custom : bond 0.00243 ( 1) glycosidic custom : angle 1.41101 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.326 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: A 21 ARG cc_start: 0.7800 (ttt180) cc_final: 0.7313 (ppt170) REVERT: A 45 TYR cc_start: 0.8577 (t80) cc_final: 0.8067 (t80) REVERT: B 64 ASP cc_start: 0.6750 (OUTLIER) cc_final: 0.6477 (t70) REVERT: B 127 ASN cc_start: 0.8946 (t0) cc_final: 0.8445 (t0) REVERT: B 173 LYS cc_start: 0.8611 (mtmt) cc_final: 0.8248 (mmtm) REVERT: C 95 MET cc_start: 0.8691 (ptp) cc_final: 0.8488 (ptt) REVERT: C 103 PHE cc_start: 0.9388 (t80) cc_final: 0.9140 (t80) REVERT: C 164 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8100 (tm-30) REVERT: C 212 MET cc_start: 0.8067 (mmp) cc_final: 0.7612 (mmp) REVERT: C 287 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8346 (ptp90) REVERT: C 316 GLU cc_start: 0.8712 (pt0) cc_final: 0.8444 (tt0) REVERT: C 380 PHE cc_start: 0.7721 (m-80) cc_final: 0.6798 (m-80) REVERT: D 100 ASN cc_start: 0.8250 (m-40) cc_final: 0.7442 (t0) REVERT: D 265 LEU cc_start: 0.5698 (mt) cc_final: 0.5432 (mt) REVERT: D 269 MET cc_start: 0.5076 (mmp) cc_final: 0.4690 (mtt) REVERT: D 380 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8778 (m-80) REVERT: D 390 ARG cc_start: 0.8212 (tpt170) cc_final: 0.7787 (mmt-90) REVERT: E 263 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7510 (pt0) outliers start: 46 outliers final: 19 residues processed: 260 average time/residue: 0.1027 time to fit residues: 39.0250 Evaluate side-chains 224 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 140 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 106 optimal weight: 0.0870 chunk 164 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 overall best weight: 1.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN E 188 GLN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.138102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101884 restraints weight = 33929.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.103208 restraints weight = 17814.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.104534 restraints weight = 11605.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.104836 restraints weight = 9567.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.105087 restraints weight = 8969.181| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13058 Z= 0.139 Angle : 0.654 13.236 17889 Z= 0.331 Chirality : 0.045 0.209 2171 Planarity : 0.004 0.042 2300 Dihedral : 6.675 80.285 1963 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.14 % Allowed : 19.48 % Favored : 76.38 % 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: -0.75 (0.20), residues: 1744 helix: 0.69 (0.18), residues: 822 sheet: -1.54 (0.35), residues: 188 loop : -1.56 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 183 TYR 0.021 0.002 TYR E 34 PHE 0.021 0.002 PHE B 100 TRP 0.013 0.001 TRP B 207 HIS 0.004 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00310 (13057) covalent geometry : angle 0.65388 (17886) hydrogen bonds : bond 0.03923 ( 653) hydrogen bonds : angle 4.79855 ( 1857) glycosidic custom : bond 0.00475 ( 1) glycosidic custom : angle 1.62251 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.7974 (tt) REVERT: B 64 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6535 (t70) REVERT: B 173 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8266 (mmtm) REVERT: C 53 MET cc_start: 0.8652 (mtp) cc_final: 0.8346 (ptp) REVERT: C 66 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7561 (mmm160) REVERT: C 103 PHE cc_start: 0.9419 (t80) cc_final: 0.9172 (t80) REVERT: C 164 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8094 (tm-30) REVERT: C 212 MET cc_start: 0.8030 (mmp) cc_final: 0.7445 (mmp) REVERT: C 269 MET cc_start: 0.7723 (mtt) cc_final: 0.7480 (tpt) REVERT: C 316 GLU cc_start: 0.8772 (pt0) cc_final: 0.8532 (tt0) REVERT: D 100 ASN cc_start: 0.8307 (m-40) cc_final: 0.8027 (m110) REVERT: D 265 LEU cc_start: 0.5837 (mt) cc_final: 0.5500 (mt) REVERT: D 269 MET cc_start: 0.5029 (mmp) cc_final: 0.4729 (mtt) REVERT: D 367 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8891 (tp40) REVERT: D 390 ARG cc_start: 0.8258 (tpt170) cc_final: 0.7834 (mmt-90) REVERT: E 150 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8306 (mt0) REVERT: E 310 PHE cc_start: 0.8932 (t80) cc_final: 0.8717 (t80) outliers start: 51 outliers final: 26 residues processed: 247 average time/residue: 0.0928 time to fit residues: 33.5641 Evaluate side-chains 227 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 150 GLN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 102 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 160 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 113 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.140520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.106890 restraints weight = 34919.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106540 restraints weight = 23005.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.107022 restraints weight = 15360.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.107580 restraints weight = 12535.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.107816 restraints weight = 11172.245| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13058 Z= 0.176 Angle : 0.674 10.311 17889 Z= 0.342 Chirality : 0.045 0.202 2171 Planarity : 0.005 0.060 2300 Dihedral : 6.562 79.836 1963 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.30 % Allowed : 20.78 % Favored : 74.92 % 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: -0.80 (0.20), residues: 1744 helix: 0.66 (0.18), residues: 824 sheet: -1.61 (0.35), residues: 190 loop : -1.59 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 178 TYR 0.022 0.002 TYR D 194 PHE 0.036 0.002 PHE A 83 TRP 0.012 0.001 TRP B 207 HIS 0.004 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00406 (13057) covalent geometry : angle 0.67348 (17886) hydrogen bonds : bond 0.04073 ( 653) hydrogen bonds : angle 4.80348 ( 1857) glycosidic custom : bond 0.00838 ( 1) glycosidic custom : angle 1.92377 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 202 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.8213 (mmm) cc_final: 0.7957 (mtp) REVERT: A 218 MET cc_start: 0.8486 (ttt) cc_final: 0.8235 (ttt) REVERT: A 230 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7199 (mmm-85) REVERT: A 257 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.7970 (tt) REVERT: A 279 PHE cc_start: 0.8871 (t80) cc_final: 0.8466 (t80) REVERT: B 64 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6644 (t70) REVERT: B 68 SER cc_start: 0.8115 (t) cc_final: 0.7853 (t) REVERT: B 173 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8262 (mmtm) REVERT: C 164 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8202 (tm-30) REVERT: C 269 MET cc_start: 0.7708 (mtt) cc_final: 0.7413 (tpt) REVERT: D 100 ASN cc_start: 0.8250 (m-40) cc_final: 0.7997 (m-40) REVERT: D 172 LYS cc_start: 0.8300 (tmtt) cc_final: 0.8058 (tmmt) REVERT: D 269 MET cc_start: 0.5174 (mmp) cc_final: 0.4842 (mmm) REVERT: D 367 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8854 (tp40) REVERT: D 390 ARG cc_start: 0.8159 (tpt170) cc_final: 0.7310 (tpp-160) REVERT: E 310 PHE cc_start: 0.8888 (t80) cc_final: 0.8654 (t80) outliers start: 53 outliers final: 40 residues processed: 234 average time/residue: 0.0954 time to fit residues: 33.1369 Evaluate side-chains 234 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.140706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.106692 restraints weight = 34969.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.106691 restraints weight = 23659.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.107079 restraints weight = 15362.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.107865 restraints weight = 12557.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.107985 restraints weight = 10927.031| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13058 Z= 0.154 Angle : 0.671 9.807 17889 Z= 0.340 Chirality : 0.045 0.212 2171 Planarity : 0.005 0.118 2300 Dihedral : 6.395 79.409 1963 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.14 % Allowed : 21.19 % Favored : 74.68 % 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: -0.72 (0.20), residues: 1744 helix: 0.73 (0.18), residues: 831 sheet: -1.46 (0.37), residues: 173 loop : -1.62 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 22 TYR 0.022 0.002 TYR A 138 PHE 0.021 0.001 PHE C 234 TRP 0.012 0.001 TRP B 207 HIS 0.004 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00350 (13057) covalent geometry : angle 0.67098 (17886) hydrogen bonds : bond 0.03966 ( 653) hydrogen bonds : angle 4.75958 ( 1857) glycosidic custom : bond 0.00390 ( 1) glycosidic custom : angle 1.74627 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.8342 (mmm) cc_final: 0.7827 (mtp) REVERT: A 218 MET cc_start: 0.8418 (ttt) cc_final: 0.8164 (ttt) REVERT: A 230 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7590 (mmm-85) REVERT: A 279 PHE cc_start: 0.8836 (t80) cc_final: 0.8423 (t80) REVERT: B 64 ASP cc_start: 0.6805 (OUTLIER) cc_final: 0.6574 (t70) REVERT: B 173 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8220 (mmtm) REVERT: C 53 MET cc_start: 0.8413 (mtp) cc_final: 0.8099 (ptp) REVERT: C 164 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8165 (tm-30) REVERT: C 212 MET cc_start: 0.7442 (tpp) cc_final: 0.7187 (tpp) REVERT: C 216 GLU cc_start: 0.7807 (pt0) cc_final: 0.6404 (mp0) REVERT: D 188 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8586 (mm) REVERT: D 269 MET cc_start: 0.5075 (mmp) cc_final: 0.4722 (mmm) REVERT: D 390 ARG cc_start: 0.8105 (tpt170) cc_final: 0.7283 (tpp-160) outliers start: 51 outliers final: 36 residues processed: 245 average time/residue: 0.0930 time to fit residues: 33.4953 Evaluate side-chains 234 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 chunk 138 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.142195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.108101 restraints weight = 34650.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.109178 restraints weight = 22330.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.110200 restraints weight = 13002.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.110604 restraints weight = 11503.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.110894 restraints weight = 9973.520| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13058 Z= 0.131 Angle : 0.671 10.672 17889 Z= 0.339 Chirality : 0.045 0.223 2171 Planarity : 0.005 0.046 2300 Dihedral : 6.236 79.149 1963 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.33 % Allowed : 22.24 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.57 (0.20), residues: 1744 helix: 0.88 (0.18), residues: 827 sheet: -1.34 (0.37), residues: 178 loop : -1.59 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 22 TYR 0.024 0.002 TYR D 194 PHE 0.033 0.002 PHE A 83 TRP 0.012 0.001 TRP B 207 HIS 0.004 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00291 (13057) covalent geometry : angle 0.67050 (17886) hydrogen bonds : bond 0.03795 ( 653) hydrogen bonds : angle 4.67576 ( 1857) glycosidic custom : bond 0.00021 ( 1) glycosidic custom : angle 1.15358 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.8333 (mmm) cc_final: 0.7863 (mtp) REVERT: A 218 MET cc_start: 0.8416 (ttt) cc_final: 0.8179 (ttt) REVERT: A 230 ARG cc_start: 0.8015 (mmm-85) cc_final: 0.7550 (mmm-85) REVERT: B 173 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8198 (mmtm) REVERT: C 53 MET cc_start: 0.8383 (mtp) cc_final: 0.8041 (ptp) REVERT: C 95 MET cc_start: 0.7773 (tmm) cc_final: 0.7525 (tmm) REVERT: C 109 LYS cc_start: 0.6298 (tptp) cc_final: 0.5411 (mtmt) REVERT: C 164 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8185 (tm-30) REVERT: C 216 GLU cc_start: 0.7856 (pt0) cc_final: 0.6296 (mp0) REVERT: D 100 ASN cc_start: 0.8183 (m-40) cc_final: 0.7454 (t0) REVERT: D 188 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8614 (mm) REVERT: D 269 MET cc_start: 0.5025 (mmp) cc_final: 0.4677 (mmm) REVERT: D 390 ARG cc_start: 0.8092 (tpt170) cc_final: 0.7293 (tpp-160) outliers start: 41 outliers final: 30 residues processed: 235 average time/residue: 0.0949 time to fit residues: 32.9784 Evaluate side-chains 230 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 134 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 41 optimal weight: 0.0670 chunk 72 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 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 = 0.4178 r_free = 0.4178 target = 0.141450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.109861 restraints weight = 34795.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.110420 restraints weight = 18006.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.111258 restraints weight = 12963.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.111482 restraints weight = 10547.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.111645 restraints weight = 9927.552| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13058 Z= 0.134 Angle : 0.681 10.463 17889 Z= 0.340 Chirality : 0.045 0.255 2171 Planarity : 0.004 0.041 2300 Dihedral : 6.089 78.986 1963 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.25 % Allowed : 22.97 % Favored : 73.78 % 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: -0.55 (0.20), residues: 1744 helix: 0.89 (0.18), residues: 834 sheet: -1.34 (0.38), residues: 171 loop : -1.58 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 174 TYR 0.019 0.001 TYR E 34 PHE 0.021 0.001 PHE C 103 TRP 0.011 0.001 TRP B 207 HIS 0.003 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00303 (13057) covalent geometry : angle 0.68061 (17886) hydrogen bonds : bond 0.03698 ( 653) hydrogen bonds : angle 4.68131 ( 1857) glycosidic custom : bond 0.00179 ( 1) glycosidic custom : angle 1.30114 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8788 (t80) cc_final: 0.8325 (t80) REVERT: A 181 MET cc_start: 0.8372 (mmm) cc_final: 0.7927 (mtp) REVERT: A 218 MET cc_start: 0.8410 (ttt) cc_final: 0.8176 (ttt) REVERT: B 64 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6548 (t70) REVERT: B 169 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8514 (mp0) REVERT: B 173 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8184 (mmtm) REVERT: C 53 MET cc_start: 0.8195 (mtp) cc_final: 0.7870 (ptp) REVERT: C 92 TYR cc_start: 0.7542 (m-80) cc_final: 0.7338 (m-80) REVERT: C 95 MET cc_start: 0.7810 (tmm) cc_final: 0.7480 (tmm) REVERT: C 109 LYS cc_start: 0.6123 (tptp) cc_final: 0.5327 (mtpt) REVERT: C 164 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8142 (tm-30) REVERT: D 188 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8569 (mm) REVERT: D 269 MET cc_start: 0.4981 (mmp) cc_final: 0.4685 (mmm) REVERT: D 390 ARG cc_start: 0.7880 (tpt170) cc_final: 0.7174 (tpp-160) outliers start: 40 outliers final: 30 residues processed: 229 average time/residue: 0.0877 time to fit residues: 30.4295 Evaluate side-chains 228 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 31 optimal weight: 5.9990 chunk 134 optimal weight: 0.0020 chunk 95 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 0.0270 chunk 85 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 11 optimal weight: 0.1980 chunk 105 optimal weight: 0.7980 overall best weight: 0.3846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN E 188 GLN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.142873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.110329 restraints weight = 34953.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.109584 restraints weight = 18010.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.111170 restraints weight = 12426.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.111082 restraints weight = 11057.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.111102 restraints weight = 9971.791| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13058 Z= 0.125 Angle : 0.699 10.807 17889 Z= 0.348 Chirality : 0.045 0.241 2171 Planarity : 0.004 0.042 2300 Dihedral : 5.934 78.881 1963 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.19 % Allowed : 24.35 % Favored : 73.46 % 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: -0.49 (0.20), residues: 1744 helix: 0.96 (0.18), residues: 833 sheet: -1.28 (0.37), residues: 174 loop : -1.59 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 21 TYR 0.020 0.001 TYR E 34 PHE 0.021 0.001 PHE C 234 TRP 0.025 0.001 TRP A 79 HIS 0.003 0.001 HIS C 325 Details of bonding type rmsd covalent geometry : bond 0.00275 (13057) covalent geometry : angle 0.69901 (17886) hydrogen bonds : bond 0.03661 ( 653) hydrogen bonds : angle 4.60721 ( 1857) glycosidic custom : bond 0.00069 ( 1) glycosidic custom : angle 0.78435 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.8285 (mmm) cc_final: 0.7842 (mtp) REVERT: B 25 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8635 (tt) REVERT: B 169 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8525 (mp0) REVERT: B 173 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8163 (mmmt) REVERT: C 53 MET cc_start: 0.8389 (mtp) cc_final: 0.8028 (ptp) REVERT: C 95 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7653 (tmm) REVERT: C 109 LYS cc_start: 0.6344 (tptp) cc_final: 0.5463 (mtpt) REVERT: C 164 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8120 (tm-30) REVERT: D 188 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8624 (mm) REVERT: D 269 MET cc_start: 0.5082 (mmp) cc_final: 0.4781 (mmm) REVERT: D 316 GLU cc_start: 0.8485 (pt0) cc_final: 0.8246 (pp20) REVERT: E 88 LEU cc_start: 0.8220 (tt) cc_final: 0.7370 (tp) REVERT: E 424 TYR cc_start: 0.7207 (t80) cc_final: 0.6985 (t80) outliers start: 27 outliers final: 22 residues processed: 229 average time/residue: 0.0932 time to fit residues: 32.1680 Evaluate side-chains 224 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 162 optimal weight: 0.0870 chunk 59 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 0.0020 chunk 36 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 overall best weight: 1.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 HIS ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN E 188 GLN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.143543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.111302 restraints weight = 34920.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.111748 restraints weight = 18680.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.112433 restraints weight = 12355.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.112820 restraints weight = 11149.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.112906 restraints weight = 9854.997| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.167 13058 Z= 0.262 Angle : 0.920 59.200 17889 Z= 0.516 Chirality : 0.053 1.178 2171 Planarity : 0.005 0.041 2300 Dihedral : 5.940 78.878 1963 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.07 % Favored : 95.87 % Rotamer: Outliers : 2.03 % Allowed : 24.35 % Favored : 73.62 % Cbeta Deviations : 0.06 % 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: -0.49 (0.20), residues: 1744 helix: 0.96 (0.18), residues: 833 sheet: -1.30 (0.37), residues: 174 loop : -1.59 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 174 TYR 0.019 0.001 TYR E 34 PHE 0.020 0.001 PHE C 234 TRP 0.021 0.001 TRP A 79 HIS 0.003 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00483 (13057) covalent geometry : angle 0.91994 (17886) hydrogen bonds : bond 0.03673 ( 653) hydrogen bonds : angle 4.61022 ( 1857) glycosidic custom : bond 0.01651 ( 1) glycosidic custom : angle 2.34850 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1977.12 seconds wall clock time: 34 minutes 52.94 seconds (2092.94 seconds total)