Starting phenix.real_space_refine on Fri Jul 3 07:48:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hpm_34933/07_2026/8hpm_34933.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpm_34933/07_2026/8hpm_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_34933/07_2026/8hpm_34933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpm_34933/07_2026/8hpm_34933.map" model { file = "/net/cci-nas-00/data/ceres_data/8hpm_34933/07_2026/8hpm_34933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpm_34933/07_2026/8hpm_34933.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hpm_34933/07_2026/8hpm_34933.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hpm_34933/07_2026/8hpm_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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: 3.36, 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: 1.06 Conformation dependent library (CDL) restraints added in 648.3 milliseconds 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: 0.37 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: 1.82 Time building geometry restraints manager: 1.44 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 1.410 1.549 -0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 13052 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 17274 3.91 - 7.83: 593 7.83 - 11.74: 15 11.74 - 15.65: 0 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: 7203 17.61 - 35.23: 431 35.23 - 52.84: 79 52.84 - 70.46: 19 70.46 - 88.07: 3 Dihedral angle restraints: 7735 sinusoidal: 2687 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 7732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.954: 2170 0.954 - 1.908: 0 1.908 - 2.862: 0 2.862 - 3.816: 0 3.816 - 4.770: 1 Chirality restraints: 2171 Sorted by residual: chirality pdb=" C1 GLC G 2 " pdb=" C2 GLC G 2 " pdb=" O1 GLC G 2 " pdb=" O5 GLC G 2 " both_signs ideal model delta sigma weight residual False 2.33 -2.44 4.77 2.00e-01 2.50e+01 5.69e+02 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 -2.47 -1.85 -0.62 2.00e-01 2.50e+01 9.57e+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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.170 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 0.139 13058 Z= 0.768 Angle : 1.818 19.566 17889 Z= 1.235 Chirality : 0.140 4.770 2171 Planarity : 0.012 0.120 2300 Dihedral : 12.592 88.073 4475 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 are 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/Z covalent geometry : bond 0.01234 / 0.77 (13057) covalent geometry : angle 1.81827 / 1.23 (17886) hydrogen bonds : bond 0.17081 / 11.40 ( 653) hydrogen bonds : angle 7.80896 / 5.57 ( 1857) glycosidic custom : bond 0.02907 / 1.53 ( 1) glycosidic custom : angle 1.92355 / 1.13 ( 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 : 0.478 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: 0.8652 (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: 0.8178 (t) cc_final: 0.7428 (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: 0.7257 (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: 0.1215 time to fit residues: 63.1904 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 : 0.493 ------------------------------------------------------------------------------- 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... A 55 ASN A 261 ASN B 127 ASN 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 E 39 ASN E 188 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.137568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.102617 restraints weight = 33411.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.103339 restraints weight = 18160.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.104080 restraints weight = 11647.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.104429 restraints weight = 9784.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.104495 restraints weight = 9194.603| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13058 Z= 0.204 Angle : 0.802 9.631 17889 Z= 0.419 Chirality : 0.050 0.236 2171 Planarity : 0.005 0.078 2300 Dihedral : 6.886 82.426 1876 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.81 % Allowed : 13.23 % Favored : 82.95 % 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 are not related in a simple way. whole: -1.49 (0.19), residues: 1744 helix: -0.35 (0.17), residues: 836 sheet: -1.32 (0.38), residues: 170 loop : -1.56 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 174 TYR 0.021 0.002 TYR D 194 PHE 0.032 0.002 PHE A 83 TRP 0.015 0.002 TRP B 207 HIS 0.011 0.002 HIS C 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (13057) covalent geometry : angle 0.79468 / 0.42 (17886) hydrogen bonds : bond 0.05168 / 3.47 ( 653) hydrogen bonds : angle 5.45536 / 3.94 ( 1857) glycosidic custom : bond 0.00953 / 0.50 ( 1) glycosidic custom : angle 8.30994 / 3.98 ( 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 286 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 0.479 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: A 21 ARG cc_start: 0.7893 (ttt180) cc_final: 0.7148 (tmm160) REVERT: A 147 TYR cc_start: 0.7841 (p90) cc_final: 0.7586 (p90) REVERT: A 181 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8174 (mtp) REVERT: B 68 SER cc_start: 0.8353 (t) cc_final: 0.7142 (t) REVERT: C 149 MET cc_start: 0.8774 (mtp) cc_final: 0.8573 (mtp) REVERT: C 316 GLU cc_start: 0.8771 (pt0) cc_final: 0.8400 (tt0) REVERT: C 380 PHE cc_start: 0.7677 (m-80) cc_final: 0.6913 (m-80) REVERT: D 100 ASN cc_start: 0.8329 (m-40) cc_final: 0.7824 (t0) REVERT: D 265 LEU cc_start: 0.5743 (mt) cc_final: 0.5491 (mt) REVERT: D 269 MET cc_start: 0.5096 (mmp) cc_final: 0.4260 (mtt) REVERT: D 380 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8695 (m-80) REVERT: E 281 LEU cc_start: 0.9224 (mt) cc_final: 0.9006 (mm) outliers start: 47 outliers final: 27 residues processed: 266 average time/residue: 0.1026 time to fit residues: 39.9121 Evaluate side-chains 237 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE 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 A residue 290 ILE 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 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 149 MET Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 318 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: 0.9980 chunk 147 optimal weight: 0.9980 chunk 129 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN C 87 GLN C 168 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.138061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.101704 restraints weight = 33506.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.103355 restraints weight = 16871.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.104737 restraints weight = 10729.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.105149 restraints weight = 8547.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.105428 restraints weight = 7990.721| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13058 Z= 0.153 Angle : 0.707 8.454 17889 Z= 0.361 Chirality : 0.047 0.232 2171 Planarity : 0.005 0.046 2300 Dihedral : 6.159 69.366 1874 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.49 % Allowed : 17.21 % 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 are not related in a simple way. whole: -1.12 (0.20), residues: 1744 helix: 0.17 (0.17), residues: 827 sheet: -1.42 (0.37), residues: 182 loop : -1.55 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 119 TYR 0.022 0.002 TYR A 139 PHE 0.023 0.002 PHE E 328 TRP 0.013 0.001 TRP B 207 HIS 0.007 0.001 HIS C 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (13057) covalent geometry : angle 0.70180 / 0.36 (17886) hydrogen bonds : bond 0.04522 / 3.01 ( 653) hydrogen bonds : angle 5.13407 / 3.74 ( 1857) glycosidic custom : bond 0.00193 / 0.10 ( 1) glycosidic custom : angle 6.41080 / 3.24 ( 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 274 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.576 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: A 21 ARG cc_start: 0.7849 (ttt180) cc_final: 0.7276 (ppt170) REVERT: A 41 TYR cc_start: 0.8677 (t80) cc_final: 0.8465 (t80) REVERT: A 181 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8164 (ttm) REVERT: B 242 THR cc_start: 0.7850 (t) cc_final: 0.7355 (t) REVERT: C 164 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8158 (tm-30) REVERT: C 316 GLU cc_start: 0.8843 (pt0) cc_final: 0.8544 (tt0) REVERT: C 380 PHE cc_start: 0.7715 (m-80) cc_final: 0.6921 (m-80) REVERT: D 100 ASN cc_start: 0.8434 (m-40) cc_final: 0.7783 (t0) REVERT: D 174 ARG cc_start: 0.9221 (mmm-85) cc_final: 0.8899 (mmm160) REVERT: D 265 LEU cc_start: 0.5666 (mt) cc_final: 0.5442 (mt) REVERT: D 269 MET cc_start: 0.5218 (mmp) cc_final: 0.4856 (mtt) REVERT: D 322 LYS cc_start: 0.7794 (mmtp) cc_final: 0.7509 (mmtm) REVERT: D 367 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8962 (mm-40) REVERT: D 380 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8707 (m-80) REVERT: D 390 ARG cc_start: 0.8200 (tpt170) cc_final: 0.7859 (mpt90) REVERT: E 281 LEU cc_start: 0.9252 (mt) cc_final: 0.9032 (mm) outliers start: 43 outliers final: 21 residues processed: 257 average time/residue: 0.1141 time to fit residues: 42.4185 Evaluate side-chains 230 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 89 TYR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 355 ARG 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 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: 5.9990 chunk 78 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 134 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 167 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 0.0870 chunk 154 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.8698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 87 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.139606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.101095 restraints weight = 32808.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.104212 restraints weight = 16360.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.106257 restraints weight = 10409.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.107433 restraints weight = 7765.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.108323 restraints weight = 6495.928| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13058 Z= 0.134 Angle : 0.670 10.036 17889 Z= 0.339 Chirality : 0.046 0.214 2171 Planarity : 0.005 0.044 2300 Dihedral : 5.690 59.054 1874 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.81 % Allowed : 19.89 % Favored : 76.30 % 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 are not related in a simple way. whole: -0.94 (0.20), residues: 1744 helix: 0.43 (0.18), residues: 828 sheet: -1.40 (0.37), residues: 178 loop : -1.60 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 178 TYR 0.022 0.002 TYR D 194 PHE 0.034 0.002 PHE A 83 TRP 0.012 0.001 TRP B 207 HIS 0.005 0.001 HIS C 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (13057) covalent geometry : angle 0.66611 / 0.34 (17886) hydrogen bonds : bond 0.04066 / 2.71 ( 653) hydrogen bonds : angle 4.93817 / 3.61 ( 1857) glycosidic custom : bond 0.00049 / 0.03 ( 1) glycosidic custom : angle 5.87763 / 2.96 ( 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 282 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 235 time to evaluate : 0.482 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: 0.7870 (ttt180) cc_final: 0.7351 (ppt170) REVERT: B 173 LYS cc_start: 0.8504 (mtmt) cc_final: 0.7997 (mmtm) REVERT: C 53 MET cc_start: 0.8586 (mtp) cc_final: 0.8267 (ptp) REVERT: C 95 MET cc_start: 0.8669 (ptp) cc_final: 0.8392 (ptt) REVERT: C 164 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8044 (tm-30) REVERT: C 380 PHE cc_start: 0.7827 (m-80) cc_final: 0.6904 (m-80) REVERT: D 100 ASN cc_start: 0.8283 (m-40) cc_final: 0.7798 (t0) REVERT: D 194 TYR cc_start: 0.6773 (t80) cc_final: 0.6518 (t80) REVERT: D 265 LEU cc_start: 0.5724 (mt) cc_final: 0.5466 (mt) REVERT: D 269 MET cc_start: 0.5141 (mmp) cc_final: 0.4775 (mtt) REVERT: D 380 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8867 (m-80) REVERT: D 390 ARG cc_start: 0.8284 (tpt170) cc_final: 0.7809 (mmt-90) REVERT: E 263 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7508 (pt0) outliers start: 47 outliers final: 22 residues processed: 261 average time/residue: 0.1040 time to fit residues: 40.4348 Evaluate side-chains 225 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 68 SER 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 149 MET Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 372 ILE 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 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: 4.9990 chunk 168 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 70 optimal weight: 0.0670 chunk 106 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 87 GLN C 99 GLN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 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 = 0.4055 r_free = 0.4055 target = 0.135923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.100428 restraints weight = 33930.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.101580 restraints weight = 18307.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.102032 restraints weight = 11811.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.102351 restraints weight = 9941.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.102449 restraints weight = 9253.389| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13058 Z= 0.210 Angle : 0.714 8.843 17889 Z= 0.363 Chirality : 0.047 0.217 2171 Planarity : 0.005 0.041 2300 Dihedral : 5.693 54.659 1874 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.14 % Allowed : 20.86 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.20), residues: 1744 helix: 0.51 (0.18), residues: 823 sheet: -1.40 (0.38), residues: 176 loop : -1.76 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 230 TYR 0.021 0.002 TYR B 145 PHE 0.022 0.002 PHE B 100 TRP 0.016 0.002 TRP B 207 HIS 0.005 0.001 HIS C 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (13057) covalent geometry : angle 0.71138 / 0.36 (17886) hydrogen bonds : bond 0.04400 / 2.96 ( 653) hydrogen bonds : angle 4.97561 / 3.66 ( 1857) glycosidic custom : bond 0.00541 / 0.28 ( 1) glycosidic custom : angle 5.13304 / 2.61 ( 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 250 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.7979 (tt) REVERT: A 279 PHE cc_start: 0.8967 (t80) cc_final: 0.8516 (t80) REVERT: B 64 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.6173 (t70) REVERT: B 146 ILE cc_start: 0.9101 (mt) cc_final: 0.8853 (mt) REVERT: C 95 MET cc_start: 0.8612 (ptp) cc_final: 0.8394 (ptt) REVERT: C 164 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8048 (tm-30) REVERT: C 380 PHE cc_start: 0.7710 (m-80) cc_final: 0.6857 (m-80) REVERT: D 100 ASN cc_start: 0.8369 (m-40) cc_final: 0.8078 (t0) REVERT: D 265 LEU cc_start: 0.5761 (mt) cc_final: 0.5439 (mt) REVERT: D 269 MET cc_start: 0.5065 (mmp) cc_final: 0.4441 (mtt) REVERT: D 367 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8863 (tp40) REVERT: D 390 ARG cc_start: 0.8202 (tpt170) cc_final: 0.7308 (tpp-160) REVERT: E 263 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7559 (pt0) REVERT: E 310 PHE cc_start: 0.8942 (t80) cc_final: 0.8657 (t80) outliers start: 51 outliers final: 34 residues processed: 232 average time/residue: 0.1049 time to fit residues: 36.2912 Evaluate side-chains 220 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU 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 183 LEU 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 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 195 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 99 GLN 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 35 GLU 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 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 240 VAL Chi-restraints excluded: chain E residue 277 LEU 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: 5.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 20 optimal weight: 0.0570 chunk 160 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 98 optimal weight: 10.0000 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN C 87 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN E 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.137933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.102030 restraints weight = 33264.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.103902 restraints weight = 18138.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.104408 restraints weight = 11228.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.104719 restraints weight = 11059.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.104947 restraints weight = 9166.372| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13058 Z= 0.128 Angle : 0.677 14.195 17889 Z= 0.336 Chirality : 0.045 0.258 2171 Planarity : 0.005 0.045 2300 Dihedral : 5.435 59.040 1874 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.65 % Allowed : 21.67 % 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 are not related in a simple way. whole: -0.77 (0.20), residues: 1744 helix: 0.68 (0.18), residues: 829 sheet: -1.54 (0.36), residues: 185 loop : -1.60 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 178 TYR 0.025 0.002 TYR A 147 PHE 0.040 0.001 PHE A 83 TRP 0.014 0.001 TRP B 207 HIS 0.004 0.001 HIS C 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (13057) covalent geometry : angle 0.67318 / 0.34 (17886) hydrogen bonds : bond 0.03826 / 2.59 ( 653) hydrogen bonds : angle 4.77999 / 3.51 ( 1857) glycosidic custom : bond 0.00044 / 0.02 ( 1) glycosidic custom : angle 5.78946 / 2.86 ( 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 261 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.7902 (tt) REVERT: A 261 ASN cc_start: 0.8510 (m-40) cc_final: 0.8307 (m-40) REVERT: B 64 ASP cc_start: 0.6632 (OUTLIER) cc_final: 0.6396 (t70) REVERT: B 66 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7375 (t80) REVERT: B 68 SER cc_start: 0.8204 (OUTLIER) cc_final: 0.7661 (t) REVERT: B 173 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8077 (mmtm) REVERT: C 53 MET cc_start: 0.8597 (mtp) cc_final: 0.8292 (ptp) REVERT: C 95 MET cc_start: 0.8796 (ptp) cc_final: 0.8462 (ptp) REVERT: C 164 GLN cc_start: 0.8583 (tm-30) cc_final: 0.7876 (tm-30) REVERT: C 212 MET cc_start: 0.8118 (mmp) cc_final: 0.7457 (mmp) REVERT: C 269 MET cc_start: 0.7753 (mtt) cc_final: 0.7488 (tpt) REVERT: D 99 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8797 (tm-30) REVERT: D 100 ASN cc_start: 0.8521 (m-40) cc_final: 0.8068 (t0) REVERT: D 269 MET cc_start: 0.5109 (mmp) cc_final: 0.4780 (mmm) REVERT: D 367 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8899 (tp40) REVERT: D 390 ARG cc_start: 0.8281 (tpt170) cc_final: 0.7402 (tpp-160) REVERT: E 263 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7488 (pt0) outliers start: 45 outliers final: 29 residues processed: 241 average time/residue: 0.1037 time to fit residues: 37.4372 Evaluate side-chains 237 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 183 LEU 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 25 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 99 GLN 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 175 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 149 THR Chi-restraints excluded: chain E residue 150 GLN Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 237 ILE 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: 0.5980 chunk 32 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 105 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.0670 chunk 66 optimal weight: 0.4980 chunk 44 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.139141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.100946 restraints weight = 33625.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.104097 restraints weight = 17055.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.106073 restraints weight = 10862.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.107393 restraints weight = 8113.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.108107 restraints weight = 6709.803| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13058 Z= 0.123 Angle : 0.664 11.116 17889 Z= 0.329 Chirality : 0.044 0.218 2171 Planarity : 0.005 0.046 2300 Dihedral : 5.261 58.631 1874 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.17 % Allowed : 22.56 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.20), residues: 1744 helix: 0.78 (0.18), residues: 831 sheet: -1.48 (0.36), residues: 185 loop : -1.60 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 178 TYR 0.025 0.001 TYR D 194 PHE 0.028 0.001 PHE C 234 TRP 0.013 0.001 TRP A 141 HIS 0.003 0.001 HIS C 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (13057) covalent geometry : angle 0.66015 / 0.33 (17886) hydrogen bonds : bond 0.03663 / 2.48 ( 653) hydrogen bonds : angle 4.62130 / 3.39 ( 1857) glycosidic custom : bond 0.00246 / 0.13 ( 1) glycosidic custom : angle 5.30758 / 2.67 ( 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 256 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8553 (ttt) cc_final: 0.8303 (ttt) REVERT: B 66 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7444 (t80) REVERT: B 68 SER cc_start: 0.8125 (m) cc_final: 0.7160 (t) REVERT: B 169 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8564 (mp0) REVERT: B 173 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8030 (mmtm) REVERT: C 53 MET cc_start: 0.8462 (mtp) cc_final: 0.8116 (ptp) REVERT: C 95 MET cc_start: 0.8670 (ptp) cc_final: 0.8363 (ptt) REVERT: C 103 PHE cc_start: 0.9363 (t80) cc_final: 0.9077 (t80) REVERT: C 109 LYS cc_start: 0.6513 (tptp) cc_final: 0.5462 (mtmt) REVERT: C 164 GLN cc_start: 0.8620 (tm-30) cc_final: 0.7966 (tm-30) REVERT: C 212 MET cc_start: 0.7842 (mmp) cc_final: 0.7553 (mmp) REVERT: C 269 MET cc_start: 0.7788 (mtt) cc_final: 0.7523 (tpt) REVERT: C 380 PHE cc_start: 0.8239 (m-80) cc_final: 0.7356 (m-80) REVERT: D 99 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8207 (tp-100) REVERT: D 100 ASN cc_start: 0.8284 (m-40) cc_final: 0.8053 (t0) REVERT: D 269 MET cc_start: 0.5018 (mmp) cc_final: 0.4683 (mmm) REVERT: D 367 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8884 (tp40) REVERT: D 390 ARG cc_start: 0.8275 (tpt170) cc_final: 0.7432 (tpp-160) REVERT: E 263 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7430 (pt0) outliers start: 39 outliers final: 23 residues processed: 242 average time/residue: 0.1049 time to fit residues: 38.2828 Evaluate side-chains 223 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE 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 66 PHE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 99 GLN 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 318 LEU Chi-restraints excluded: chain D residue 351 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 ASN C 99 GLN C 351 GLN D 351 GLN E 188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.142044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.110211 restraints weight = 34735.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.109501 restraints weight = 18578.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.110096 restraints weight = 15708.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.110305 restraints weight = 11965.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.110499 restraints weight = 10504.110| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4698 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= 0.140 Angle : 0.681 10.420 17889 Z= 0.339 Chirality : 0.045 0.210 2171 Planarity : 0.006 0.176 2300 Dihedral : 5.260 59.202 1874 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.49 % Allowed : 22.65 % Favored : 73.86 % 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 are not related in a simple way. whole: -0.57 (0.20), residues: 1744 helix: 0.89 (0.18), residues: 829 sheet: -1.47 (0.36), residues: 185 loop : -1.56 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 22 TYR 0.018 0.001 TYR D 89 PHE 0.030 0.002 PHE A 83 TRP 0.013 0.001 TRP A 141 HIS 0.006 0.001 HIS C 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (13057) covalent geometry : angle 0.67795 / 0.34 (17886) hydrogen bonds : bond 0.03740 / 2.54 ( 653) hydrogen bonds : angle 4.65519 / 3.42 ( 1857) glycosidic custom : bond 0.00002 / 0.00 ( 1) glycosidic custom : angle 4.82831 / 2.46 ( 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 254 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 MET cc_start: 0.8312 (ttt) cc_final: 0.8085 (ttt) REVERT: B 66 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7641 (t80) REVERT: B 68 SER cc_start: 0.8023 (OUTLIER) cc_final: 0.7448 (t) REVERT: B 146 ILE cc_start: 0.9098 (mt) cc_final: 0.8856 (mt) REVERT: B 173 LYS cc_start: 0.8459 (mtmt) cc_final: 0.8047 (mmtm) REVERT: C 103 PHE cc_start: 0.9261 (t80) cc_final: 0.9030 (t80) REVERT: C 109 LYS cc_start: 0.6283 (tptp) cc_final: 0.5331 (mtpt) REVERT: C 164 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8116 (tm-30) REVERT: C 212 MET cc_start: 0.7537 (mmp) cc_final: 0.7276 (mmp) REVERT: C 269 MET cc_start: 0.7743 (mtt) cc_final: 0.7480 (tpt) REVERT: C 380 PHE cc_start: 0.8086 (m-80) cc_final: 0.7247 (m-80) REVERT: D 99 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8184 (tp-100) REVERT: D 100 ASN cc_start: 0.8370 (m-40) cc_final: 0.7989 (t0) REVERT: D 172 LYS cc_start: 0.6972 (tptt) cc_final: 0.5715 (tmtt) REVERT: D 188 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8595 (mm) REVERT: D 269 MET cc_start: 0.5075 (mmp) cc_final: 0.4737 (mmm) REVERT: D 390 ARG cc_start: 0.8051 (tpt170) cc_final: 0.7256 (tpp-160) outliers start: 43 outliers final: 27 residues processed: 235 average time/residue: 0.1053 time to fit residues: 37.2835 Evaluate side-chains 234 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 128 ILE 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 36 LEU Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 317 SER 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 318 LEU 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 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: 5.9990 chunk 41 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 84 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 125 optimal weight: 30.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 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 = 0.4202 r_free = 0.4202 target = 0.142837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.110959 restraints weight = 34967.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.110810 restraints weight = 18790.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.111838 restraints weight = 14014.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.111990 restraints weight = 10866.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.112260 restraints weight = 10175.920| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13058 Z= 0.133 Angle : 0.683 10.178 17889 Z= 0.337 Chirality : 0.045 0.227 2171 Planarity : 0.005 0.048 2300 Dihedral : 5.169 60.525 1874 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.17 % Allowed : 23.30 % Favored : 73.54 % 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 are not related in a simple way. whole: -0.54 (0.20), residues: 1744 helix: 0.87 (0.18), residues: 838 sheet: -1.36 (0.37), residues: 176 loop : -1.53 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 178 TYR 0.023 0.001 TYR D 194 PHE 0.022 0.001 PHE C 234 TRP 0.023 0.001 TRP A 141 HIS 0.008 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (13057) covalent geometry : angle 0.67997 / 0.34 (17886) hydrogen bonds : bond 0.03611 / 2.44 ( 653) hydrogen bonds : angle 4.66791 / 3.42 ( 1857) glycosidic custom : bond 0.00094 / 0.05 ( 1) glycosidic custom : angle 4.81728 / 2.44 ( 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 247 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8604 (t80) cc_final: 0.8217 (t80) REVERT: B 68 SER cc_start: 0.8120 (OUTLIER) cc_final: 0.7606 (t) REVERT: B 146 ILE cc_start: 0.9085 (mt) cc_final: 0.8839 (mt) REVERT: B 169 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8569 (mp0) REVERT: B 173 LYS cc_start: 0.8416 (mtmt) cc_final: 0.8033 (mmtm) REVERT: C 53 MET cc_start: 0.8251 (mtp) cc_final: 0.7937 (ptp) REVERT: C 103 PHE cc_start: 0.9164 (t80) cc_final: 0.8855 (t80) REVERT: C 109 LYS cc_start: 0.6110 (tptp) cc_final: 0.5280 (mtpt) REVERT: C 164 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8220 (tm-30) REVERT: C 212 MET cc_start: 0.7415 (mmp) cc_final: 0.7186 (mmp) REVERT: C 380 PHE cc_start: 0.7962 (m-80) cc_final: 0.7167 (m-80) REVERT: D 100 ASN cc_start: 0.8334 (m-40) cc_final: 0.8076 (t0) REVERT: D 172 LYS cc_start: 0.7050 (tptt) cc_final: 0.6067 (tmtt) REVERT: D 188 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8536 (mm) REVERT: D 269 MET cc_start: 0.4912 (mmp) cc_final: 0.4557 (mmm) REVERT: D 367 GLN cc_start: 0.8714 (tp40) cc_final: 0.8452 (tp40) REVERT: D 390 ARG cc_start: 0.7862 (tpt170) cc_final: 0.7151 (tpp-160) outliers start: 39 outliers final: 30 residues processed: 234 average time/residue: 0.1075 time to fit residues: 37.4078 Evaluate side-chains 230 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 128 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 267 ASN 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 68 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 317 SER 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 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: 0.9990 chunk 134 optimal weight: 0.5980 chunk 95 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 0.1980 chunk 85 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 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 = 0.4210 r_free = 0.4210 target = 0.142873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.110841 restraints weight = 34796.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.111288 restraints weight = 18463.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.111837 restraints weight = 13094.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.112210 restraints weight = 10456.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.112228 restraints weight = 9713.322| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 13058 Z= 0.133 Angle : 0.701 9.937 17889 Z= 0.347 Chirality : 0.045 0.220 2171 Planarity : 0.005 0.042 2300 Dihedral : 5.151 61.240 1874 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.68 % Allowed : 24.11 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1744 helix: 0.89 (0.18), residues: 838 sheet: -1.52 (0.36), residues: 181 loop : -1.48 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 178 TYR 0.018 0.001 TYR D 89 PHE 0.026 0.002 PHE C 27 TRP 0.017 0.001 TRP A 141 HIS 0.005 0.001 HIS C 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (13057) covalent geometry : angle 0.69822 / 0.35 (17886) hydrogen bonds : bond 0.03721 / 2.55 ( 653) hydrogen bonds : angle 4.65654 / 3.41 ( 1857) glycosidic custom : bond 0.00193 / 0.10 ( 1) glycosidic custom : angle 4.61485 / 2.35 ( 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 238 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8759 (t80) cc_final: 0.8499 (t80) REVERT: B 68 SER cc_start: 0.8092 (OUTLIER) cc_final: 0.7597 (t) REVERT: B 146 ILE cc_start: 0.9113 (mt) cc_final: 0.8863 (mt) REVERT: B 169 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8579 (mp0) REVERT: B 173 LYS cc_start: 0.8395 (mtmt) cc_final: 0.8024 (mmtm) REVERT: C 53 MET cc_start: 0.8256 (mtp) cc_final: 0.7912 (ptp) REVERT: C 92 TYR cc_start: 0.7535 (m-80) cc_final: 0.7330 (m-80) REVERT: C 95 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7376 (tmm) REVERT: C 103 PHE cc_start: 0.9065 (t80) cc_final: 0.8835 (t80) REVERT: C 109 LYS cc_start: 0.6114 (tptp) cc_final: 0.5311 (mtpt) REVERT: C 164 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8244 (tm-30) REVERT: C 212 MET cc_start: 0.7449 (mmp) cc_final: 0.7229 (mmp) REVERT: C 380 PHE cc_start: 0.8051 (m-80) cc_final: 0.7169 (m-80) REVERT: D 188 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8629 (mm) REVERT: D 269 MET cc_start: 0.5050 (mmp) cc_final: 0.4714 (mmm) REVERT: D 367 GLN cc_start: 0.8798 (tp40) cc_final: 0.8429 (tp-100) REVERT: D 390 ARG cc_start: 0.7994 (tpt170) cc_final: 0.7236 (tpp-160) outliers start: 33 outliers final: 28 residues processed: 228 average time/residue: 0.1065 time to fit residues: 36.4088 Evaluate side-chains 227 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 128 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 267 ASN 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 68 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 317 SER 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 162 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 0.0050 chunk 36 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** 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 = 0.4186 r_free = 0.4186 target = 0.141456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.109228 restraints weight = 34792.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.110045 restraints weight = 18234.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.110541 restraints weight = 12772.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.110888 restraints weight = 10263.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.110902 restraints weight = 9556.056| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 13058 Z= 0.145 Angle : 0.708 10.358 17889 Z= 0.351 Chirality : 0.045 0.203 2171 Planarity : 0.005 0.041 2300 Dihedral : 5.151 62.294 1874 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.00 % Allowed : 23.94 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1744 helix: 0.92 (0.18), residues: 830 sheet: -1.47 (0.36), residues: 181 loop : -1.45 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 22 TYR 0.020 0.001 TYR D 194 PHE 0.024 0.001 PHE E 328 TRP 0.016 0.001 TRP A 141 HIS 0.004 0.001 HIS C 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (13057) covalent geometry : angle 0.70589 / 0.35 (17886) hydrogen bonds : bond 0.03782 / 2.59 ( 653) hydrogen bonds : angle 4.70678 / 3.45 ( 1857) glycosidic custom : bond 0.00122 / 0.06 ( 1) glycosidic custom : angle 4.45490 / 2.27 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2282.61 seconds wall clock time: 40 minutes 20.59 seconds (2420.59 seconds total)