Starting phenix.real_space_refine on Wed Mar 4 15:49:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uhc_20770/03_2026/6uhc_20770_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uhc_20770/03_2026/6uhc_20770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uhc_20770/03_2026/6uhc_20770_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uhc_20770/03_2026/6uhc_20770_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uhc_20770/03_2026/6uhc_20770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uhc_20770/03_2026/6uhc_20770.map" } resolution = 3.9 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= 0.006 sd= 0.088 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 72 5.16 5 C 9320 2.51 5 N 2540 2.21 5 O 2740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14680 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3099 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 26, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 5, 'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2587 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 16, 'TRANS': 357} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 438 Unresolved non-hydrogen angles: 558 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'ARG:plan': 9, 'ASP:plan': 9, 'ASN:plan1': 8, 'PHE:plan': 5, 'TYR:plan': 4, 'GLU:plan': 15, 'HIS:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 242 Chain: "C" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2681 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 339} Chain breaks: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 4, 'PHE:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2240 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 273} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1344 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 160} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1346 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 161} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 996 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 5, 'ASN:plan1': 1, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 20} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 161 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 23} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.23, per 1000 atoms: 0.22 Number of scatterers: 14680 At special positions: 0 Unit cell: (94.468, 130.416, 147.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 6 15.00 Mg 2 11.99 O 2740 8.00 N 2540 7.00 C 9320 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 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 593.4 milliseconds 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 21 sheets defined 42.4% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 85 through 99 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.504A pdb=" N ARG A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 124' Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.545A pdb=" N GLU A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE A 129 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N MET A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 removed outlier: 4.020A pdb=" N LEU A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.690A pdb=" N SER A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.686A pdb=" N ILE A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 283 No H-bonds generated for 'chain 'A' and resid 282 through 283' Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 295 through 307 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 311 through 317 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 330 through 353 removed outlier: 3.676A pdb=" N ARG A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASP A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 387 removed outlier: 3.508A pdb=" N THR A 387 " --> pdb=" O MET A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 394 removed outlier: 3.819A pdb=" N GLN A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.607A pdb=" N HIS A 410 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 81 through 94 Processing helix chain 'B' and resid 101 through 104 Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.535A pdb=" N ARG B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 148 removed outlier: 3.790A pdb=" N ALA B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.573A pdb=" N LEU B 178 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 175 through 179' Processing helix chain 'B' and resid 185 through 200 Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.757A pdb=" N LYS B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 277 through 288 Processing helix chain 'B' and resid 290 through 299 removed outlier: 3.642A pdb=" N SER B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 312 through 329 Processing helix chain 'B' and resid 353 through 365 Processing helix chain 'B' and resid 375 through 380 removed outlier: 3.568A pdb=" N GLU B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 234 No H-bonds generated for 'chain 'C' and resid 232 through 234' Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 48 through 51 Processing helix chain 'D' and resid 63 through 69 Processing helix chain 'D' and resid 71 through 81 removed outlier: 3.582A pdb=" N LEU D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 115 Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.590A pdb=" N CYS D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 171 through 187 removed outlier: 3.531A pdb=" N VAL D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 176 " --> pdb=" O ASP D 172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 185 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU D 187 " --> pdb=" O GLN D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 Processing helix chain 'D' and resid 236 through 245 Processing helix chain 'D' and resid 246 through 281 removed outlier: 3.517A pdb=" N THR D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 274 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU D 277 " --> pdb=" O PHE D 273 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 53 removed outlier: 4.632A pdb=" N LYS E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ALA E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 83 removed outlier: 3.836A pdb=" N ARG E 66 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 101 Processing helix chain 'E' and resid 123 through 149 removed outlier: 3.502A pdb=" N GLU E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE E 149 " --> pdb=" O CYS E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'F' and resid 4 through 20 removed outlier: 3.839A pdb=" N TYR F 8 " --> pdb=" O THR F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 43 through 47 Processing helix chain 'F' and resid 80 through 97 removed outlier: 3.553A pdb=" N PHE F 93 " --> pdb=" O LYS F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 127 through 166 removed outlier: 3.817A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 49 removed outlier: 3.630A pdb=" N CYS G 45 " --> pdb=" O GLU G 41 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 59 Processing helix chain 'G' and resid 68 through 86 removed outlier: 3.661A pdb=" N LYS G 72 " --> pdb=" O SER G 68 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 89 No H-bonds generated for 'chain 'G' and resid 87 through 89' Processing helix chain 'G' and resid 90 through 96 removed outlier: 3.699A pdb=" N ALA G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 114 removed outlier: 3.505A pdb=" N MET G 107 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS G 108 " --> pdb=" O ASP G 104 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 147 removed outlier: 3.957A pdb=" N MET G 124 " --> pdb=" O ASN G 120 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL G 138 " --> pdb=" O ALA G 134 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLY G 139 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE G 141 " --> pdb=" O GLY G 137 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL G 144 " --> pdb=" O SER G 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 467 Processing helix chain 'H' and resid 471 through 476 removed outlier: 3.680A pdb=" N LYS H 476 " --> pdb=" O GLN H 472 " (cutoff:3.500A) Processing helix chain 'I' and resid 460 through 475 removed outlier: 3.556A pdb=" N GLU I 469 " --> pdb=" O GLY I 465 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN I 472 " --> pdb=" O MET I 468 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS I 473 " --> pdb=" O GLU I 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 5.267A pdb=" N CYS A 12 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A 110 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA A 142 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 112 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 193 removed outlier: 3.645A pdb=" N THR A 175 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR A 166 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N SER A 322 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE A 168 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 254 through 259 removed outlier: 3.567A pdb=" N TYR A 256 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 33 removed outlier: 3.612A pdb=" N THR B 110 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASN B 13 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE B 107 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA B 139 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU B 109 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 74 through 75 Processing sheet with id=AA9, first strand: chain 'B' and resid 180 through 182 removed outlier: 6.741A pdb=" N ILE B 301 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 245 Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 5 removed outlier: 4.026A pdb=" N GLY C 353 " --> pdb=" O GLY C 349 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP C 357 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE C 345 " --> pdb=" O TRP C 357 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN C 344 " --> pdb=" O LEU C 335 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.460A pdb=" N VAL C 32 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU C 47 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE C 34 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 55 through 61 removed outlier: 3.982A pdb=" N ALA C 76 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 102 through 104 removed outlier: 3.540A pdb=" N PHE C 111 " --> pdb=" O CYS C 123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.164A pdb=" N GLY C 160 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU C 148 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA C 158 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TRP C 150 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU C 156 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C 169 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 159 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG C 167 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C 168 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 205 through 210 removed outlier: 3.726A pdb=" N GLY C 207 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 247 through 254 removed outlier: 6.667A pdb=" N ALA C 261 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU C 250 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 259 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE C 252 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER C 257 " --> pdb=" O PHE C 252 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LEU C 269 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET C 278 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 32 through 37 removed outlier: 3.732A pdb=" N VAL D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER D 94 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 142 through 147 removed outlier: 3.808A pdb=" N TYR D 146 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU D 150 " --> pdb=" O TYR D 146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AC3, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.734A pdb=" N SER F 69 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE F 114 " --> pdb=" O ILE F 74 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 2443 1.26 - 1.40: 3663 1.40 - 1.54: 8264 1.54 - 1.68: 505 1.68 - 1.82: 112 Bond restraints: 14987 Sorted by residual: bond pdb=" C PRO A 116 " pdb=" N LEU A 117 " ideal model delta sigma weight residual 1.331 1.462 -0.130 1.14e-02 7.69e+03 1.30e+02 bond pdb=" N PRO B 347 " pdb=" CD PRO B 347 " ideal model delta sigma weight residual 1.473 1.615 -0.142 1.40e-02 5.10e+03 1.03e+02 bond pdb=" C ALA A 196 " pdb=" N GLY A 197 " ideal model delta sigma weight residual 1.331 1.470 -0.139 1.46e-02 4.69e+03 9.11e+01 bond pdb=" N PRO C 180 " pdb=" CD PRO C 180 " ideal model delta sigma weight residual 1.473 1.602 -0.129 1.40e-02 5.10e+03 8.52e+01 bond pdb=" C PRO A 6 " pdb=" O PRO A 6 " ideal model delta sigma weight residual 1.232 1.116 0.117 1.27e-02 6.20e+03 8.43e+01 ... (remaining 14982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 19793 3.59 - 7.17: 437 7.17 - 10.76: 85 10.76 - 14.35: 20 14.35 - 17.94: 9 Bond angle restraints: 20344 Sorted by residual: angle pdb=" PB ATP B 502 " pdb=" O3B ATP B 502 " pdb=" PG ATP B 502 " ideal model delta sigma weight residual 139.87 121.93 17.94 1.00e+00 1.00e+00 3.22e+02 angle pdb=" PB ATP A 502 " pdb=" O3B ATP A 502 " pdb=" PG ATP A 502 " ideal model delta sigma weight residual 139.87 123.50 16.37 1.00e+00 1.00e+00 2.68e+02 angle pdb=" PA ATP B 502 " pdb=" O3A ATP B 502 " pdb=" PB ATP B 502 " ideal model delta sigma weight residual 136.83 121.29 15.54 1.00e+00 1.00e+00 2.42e+02 angle pdb=" PA ATP A 502 " pdb=" O3A ATP A 502 " pdb=" PB ATP A 502 " ideal model delta sigma weight residual 136.83 124.22 12.61 1.00e+00 1.00e+00 1.59e+02 angle pdb=" N PHE D 121 " pdb=" CA PHE D 121 " pdb=" C PHE D 121 " ideal model delta sigma weight residual 113.19 127.71 -14.52 1.19e+00 7.06e-01 1.49e+02 ... (remaining 20339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 8194 17.34 - 34.68: 607 34.68 - 52.02: 140 52.02 - 69.36: 37 69.36 - 86.70: 17 Dihedral angle restraints: 8995 sinusoidal: 3369 harmonic: 5626 Sorted by residual: dihedral pdb=" N TYR A 375 " pdb=" C TYR A 375 " pdb=" CA TYR A 375 " pdb=" CB TYR A 375 " ideal model delta harmonic sigma weight residual 122.80 138.51 -15.71 0 2.50e+00 1.60e-01 3.95e+01 dihedral pdb=" N LYS F 107 " pdb=" C LYS F 107 " pdb=" CA LYS F 107 " pdb=" CB LYS F 107 " ideal model delta harmonic sigma weight residual 122.80 108.54 14.26 0 2.50e+00 1.60e-01 3.25e+01 dihedral pdb=" N ASP I 497 " pdb=" C ASP I 497 " pdb=" CA ASP I 497 " pdb=" CB ASP I 497 " ideal model delta harmonic sigma weight residual 122.80 136.21 -13.41 0 2.50e+00 1.60e-01 2.88e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 2064 0.130 - 0.260: 189 0.260 - 0.390: 25 0.390 - 0.520: 5 0.520 - 0.650: 3 Chirality restraints: 2286 Sorted by residual: chirality pdb=" CA TYR A 375 " pdb=" N TYR A 375 " pdb=" C TYR A 375 " pdb=" CB TYR A 375 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CA TYR A 184 " pdb=" N TYR A 184 " pdb=" C TYR A 184 " pdb=" CB TYR A 184 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.63 2.00e-01 2.50e+01 9.77e+00 chirality pdb=" CA ASP I 497 " pdb=" N ASP I 497 " pdb=" C ASP I 497 " pdb=" CB ASP I 497 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.34e+00 ... (remaining 2283 not shown) Planarity restraints: 2628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 112 " -0.033 2.00e-02 2.50e+03 6.50e-02 4.22e+01 pdb=" C ALA C 112 " 0.112 2.00e-02 2.50e+03 pdb=" O ALA C 112 " -0.043 2.00e-02 2.50e+03 pdb=" N VAL C 113 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 155 " 0.034 2.00e-02 2.50e+03 6.41e-02 4.11e+01 pdb=" C SER A 155 " -0.111 2.00e-02 2.50e+03 pdb=" O SER A 155 " 0.041 2.00e-02 2.50e+03 pdb=" N ARG A 156 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 30 " -0.032 2.00e-02 2.50e+03 6.13e-02 3.75e+01 pdb=" C GLY G 30 " 0.106 2.00e-02 2.50e+03 pdb=" O GLY G 30 " -0.039 2.00e-02 2.50e+03 pdb=" N GLY G 31 " -0.035 2.00e-02 2.50e+03 ... (remaining 2625 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 66 2.55 - 3.14: 11292 3.14 - 3.72: 21431 3.72 - 4.31: 31411 4.31 - 4.90: 50648 Nonbonded interactions: 114848 Sorted by model distance: nonbonded pdb=" O SER H 475 " pdb=" N ALA H 477 " model vdw 1.961 3.120 nonbonded pdb=" O GLU B 171 " pdb=" OE1 GLU B 171 " model vdw 1.971 3.040 nonbonded pdb=" OE2 GLU D 126 " pdb=" NE ARG D 237 " model vdw 2.119 3.120 nonbonded pdb=" O ASP C 322 " pdb=" OG SER C 323 " model vdw 2.131 3.040 nonbonded pdb=" O GLU B 171 " pdb=" CD GLU B 171 " model vdw 2.165 3.270 ... (remaining 114843 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 'H' and (resid 462 through 471 or (resid 472 through 474 and (name N or n \ ame CA or name C or name O or name CB )) or resid 475 or (resid 476 through 477 \ and (name N or name CA or name C or name O or name CB )) or resid 498 through 50 \ 0 or (resid 501 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'I' and (resid 462 through 477 or resid 498 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.510 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 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 : 0.009 0.142 14987 Z= 0.647 Angle : 1.464 17.936 20344 Z= 1.003 Chirality : 0.083 0.650 2286 Planarity : 0.007 0.080 2628 Dihedral : 14.088 86.703 5355 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.81 % Favored : 91.61 % Rotamer: Outliers : 0.21 % Allowed : 8.39 % Favored : 91.40 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -3.16 (0.17), residues: 1908 helix: -2.25 (0.16), residues: 655 sheet: -1.26 (0.26), residues: 366 loop : -2.27 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 47 TYR 0.026 0.003 TYR D 250 PHE 0.023 0.003 PHE F 134 TRP 0.027 0.003 TRP C 357 HIS 0.009 0.002 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00909 (14987) covalent geometry : angle 1.46436 (20344) hydrogen bonds : bond 0.24294 ( 675) hydrogen bonds : angle 8.76725 ( 1863) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 550 time to evaluate : 0.523 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 170 SER cc_start: 0.9047 (t) cc_final: 0.8683 (m) REVERT: A 260 ASN cc_start: 0.8070 (t0) cc_final: 0.7727 (t0) REVERT: B 123 ILE cc_start: 0.7587 (mt) cc_final: 0.7290 (tp) REVERT: B 368 LYS cc_start: 0.4392 (mmtp) cc_final: 0.3929 (tttm) REVERT: C 101 CYS cc_start: 0.8454 (p) cc_final: 0.8122 (p) REVERT: C 219 TRP cc_start: 0.8212 (p90) cc_final: 0.7679 (p90) REVERT: C 279 LEU cc_start: 0.8592 (mt) cc_final: 0.8010 (mt) REVERT: D 80 TYR cc_start: 0.8311 (m-80) cc_final: 0.8069 (m-80) REVERT: D 97 TYR cc_start: 0.8405 (m-80) cc_final: 0.7966 (m-10) REVERT: E 5 HIS cc_start: 0.6539 (m90) cc_final: 0.5470 (m170) REVERT: E 40 ASP cc_start: 0.8101 (p0) cc_final: 0.7281 (p0) REVERT: E 43 ASP cc_start: 0.7882 (m-30) cc_final: 0.7639 (m-30) REVERT: E 48 TYR cc_start: 0.8155 (m-10) cc_final: 0.7560 (m-10) REVERT: E 61 LYS cc_start: 0.8672 (mmtp) cc_final: 0.8337 (mmtt) REVERT: E 74 TYR cc_start: 0.6524 (t80) cc_final: 0.6113 (t80) REVERT: E 81 LYS cc_start: 0.8239 (tptt) cc_final: 0.7759 (tmmt) REVERT: G 43 ASP cc_start: 0.8199 (m-30) cc_final: 0.7947 (m-30) outliers start: 3 outliers final: 0 residues processed: 551 average time/residue: 0.1280 time to fit residues: 101.1685 Evaluate side-chains 237 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 192 HIS A 371 HIS ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 129 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN D 202 HIS E 18 ASN E 83 GLN ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.122428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.087574 restraints weight = 28630.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.091086 restraints weight = 15486.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093485 restraints weight = 10395.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094996 restraints weight = 7987.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.096154 restraints weight = 6743.073| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14987 Z= 0.204 Angle : 0.723 8.431 20344 Z= 0.386 Chirality : 0.048 0.180 2286 Planarity : 0.006 0.056 2628 Dihedral : 6.280 86.301 2142 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.46 % Favored : 96.33 % Rotamer: Outliers : 4.44 % Allowed : 18.31 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -1.43 (0.18), residues: 1908 helix: -0.45 (0.18), residues: 724 sheet: -0.65 (0.25), residues: 369 loop : -1.45 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 97 TYR 0.026 0.002 TYR C 172 PHE 0.022 0.002 PHE F 134 TRP 0.025 0.003 TRP C 86 HIS 0.009 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00475 (14987) covalent geometry : angle 0.72277 (20344) hydrogen bonds : bond 0.05340 ( 675) hydrogen bonds : angle 5.36312 ( 1863) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 254 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.7771 (t0) cc_final: 0.7448 (t0) REVERT: A 170 SER cc_start: 0.8914 (t) cc_final: 0.8268 (p) REVERT: A 202 TYR cc_start: 0.8362 (t80) cc_final: 0.8110 (m-10) REVERT: A 260 ASN cc_start: 0.7886 (t0) cc_final: 0.7305 (t0) REVERT: B 112 PRO cc_start: 0.7528 (Cg_exo) cc_final: 0.7272 (Cg_endo) REVERT: B 272 ASN cc_start: 0.8019 (m-40) cc_final: 0.7321 (p0) REVERT: B 297 PHE cc_start: 0.8366 (m-10) cc_final: 0.8025 (m-80) REVERT: C 14 HIS cc_start: 0.8789 (p90) cc_final: 0.8501 (p-80) REVERT: C 79 TRP cc_start: 0.8179 (m100) cc_final: 0.7715 (m100) REVERT: C 211 SER cc_start: 0.9067 (OUTLIER) cc_final: 0.8421 (m) REVERT: C 223 ASP cc_start: 0.7568 (p0) cc_final: 0.7231 (p0) REVERT: C 278 MET cc_start: 0.6724 (ppp) cc_final: 0.6107 (mmm) REVERT: C 279 LEU cc_start: 0.8722 (mt) cc_final: 0.8355 (mt) REVERT: D 37 ASP cc_start: 0.8135 (t70) cc_final: 0.7480 (t0) REVERT: D 170 LYS cc_start: 0.8380 (tttt) cc_final: 0.8014 (ttpt) REVERT: D 184 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8353 (mm-30) REVERT: E 40 ASP cc_start: 0.7789 (p0) cc_final: 0.7274 (p0) REVERT: E 43 ASP cc_start: 0.8107 (m-30) cc_final: 0.7562 (m-30) REVERT: E 74 TYR cc_start: 0.6621 (t80) cc_final: 0.6274 (t80) REVERT: E 77 GLU cc_start: 0.8717 (tp30) cc_final: 0.8500 (tp30) REVERT: E 126 ASP cc_start: 0.7215 (m-30) cc_final: 0.6844 (m-30) REVERT: F 91 MET cc_start: 0.7729 (mmt) cc_final: 0.7488 (mmm) REVERT: G 26 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6690 (t0) REVERT: G 64 ILE cc_start: 0.8877 (mt) cc_final: 0.8669 (tt) REVERT: G 73 ASP cc_start: 0.8885 (m-30) cc_final: 0.8521 (p0) REVERT: G 124 MET cc_start: 0.7219 (mmp) cc_final: 0.6966 (tpp) REVERT: H 468 MET cc_start: 0.8672 (mtm) cc_final: 0.8290 (mtt) REVERT: I 468 MET cc_start: 0.7660 (mmm) cc_final: 0.7192 (mmt) outliers start: 64 outliers final: 39 residues processed: 303 average time/residue: 0.0969 time to fit residues: 46.5905 Evaluate side-chains 230 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 467 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 85 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 140 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 48 optimal weight: 50.0000 chunk 60 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN B 132 GLN B 267 GLN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 HIS C 28 ASN C 65 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 HIS ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.116430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.088333 restraints weight = 29024.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.088663 restraints weight = 20414.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.089345 restraints weight = 18773.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.090119 restraints weight = 15516.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.090292 restraints weight = 14466.486| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 14987 Z= 0.292 Angle : 0.744 9.252 20344 Z= 0.398 Chirality : 0.049 0.147 2286 Planarity : 0.006 0.063 2628 Dihedral : 6.023 72.358 2142 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.45 % Favored : 95.28 % Rotamer: Outliers : 5.96 % Allowed : 19.14 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -1.04 (0.18), residues: 1908 helix: 0.14 (0.19), residues: 734 sheet: -0.72 (0.25), residues: 375 loop : -1.38 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 66 TYR 0.027 0.002 TYR G 111 PHE 0.026 0.003 PHE A 60 TRP 0.025 0.003 TRP H 499 HIS 0.027 0.002 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00688 (14987) covalent geometry : angle 0.74421 (20344) hydrogen bonds : bond 0.06368 ( 675) hydrogen bonds : angle 5.22675 ( 1863) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 201 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8671 (tpp) cc_final: 0.8289 (tpp) REVERT: A 260 ASN cc_start: 0.8093 (t0) cc_final: 0.7673 (t0) REVERT: B 272 ASN cc_start: 0.7343 (m-40) cc_final: 0.7060 (p0) REVERT: B 307 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8381 (p) REVERT: C 14 HIS cc_start: 0.8197 (p-80) cc_final: 0.7893 (p-80) REVERT: C 79 TRP cc_start: 0.8677 (m100) cc_final: 0.8396 (m100) REVERT: C 211 SER cc_start: 0.9082 (OUTLIER) cc_final: 0.8625 (m) REVERT: C 223 ASP cc_start: 0.7609 (p0) cc_final: 0.7365 (p0) REVERT: D 121 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7783 (t80) REVERT: D 170 LYS cc_start: 0.8107 (ttpt) cc_final: 0.7737 (ttpt) REVERT: D 182 MET cc_start: 0.8028 (mmm) cc_final: 0.7661 (mmm) REVERT: D 264 THR cc_start: 0.9163 (p) cc_final: 0.8851 (m) REVERT: E 40 ASP cc_start: 0.8064 (p0) cc_final: 0.7472 (p0) REVERT: E 43 ASP cc_start: 0.8158 (m-30) cc_final: 0.7684 (m-30) REVERT: E 126 ASP cc_start: 0.7673 (m-30) cc_final: 0.7451 (m-30) REVERT: E 167 GLN cc_start: 0.7247 (mt0) cc_final: 0.6931 (tt0) REVERT: G 48 GLN cc_start: 0.8091 (tp-100) cc_final: 0.7840 (tp-100) REVERT: G 60 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8158 (mtmt) REVERT: G 61 ASN cc_start: 0.8297 (m-40) cc_final: 0.7832 (p0) REVERT: G 74 ARG cc_start: 0.7577 (mtp-110) cc_final: 0.7375 (ptm-80) REVERT: I 468 MET cc_start: 0.7917 (mmm) cc_final: 0.7172 (mmt) outliers start: 86 outliers final: 52 residues processed: 275 average time/residue: 0.0983 time to fit residues: 43.0930 Evaluate side-chains 223 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 467 LEU Chi-restraints excluded: chain I residue 463 ILE Chi-restraints excluded: chain I residue 470 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 159 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 160 optimal weight: 0.0670 chunk 41 optimal weight: 50.0000 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN E 135 GLN F 167 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.089622 restraints weight = 28447.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.089853 restraints weight = 22807.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.090837 restraints weight = 18516.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.091505 restraints weight = 15670.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.091672 restraints weight = 13939.386| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.6130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 14987 Z= 0.199 Angle : 0.630 8.451 20344 Z= 0.335 Chirality : 0.046 0.192 2286 Planarity : 0.005 0.061 2628 Dihedral : 5.694 67.547 2142 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.88 % Favored : 95.96 % Rotamer: Outliers : 5.27 % Allowed : 20.87 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -0.73 (0.19), residues: 1908 helix: 0.54 (0.19), residues: 730 sheet: -0.65 (0.25), residues: 375 loop : -1.30 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 200 TYR 0.020 0.002 TYR B 222 PHE 0.018 0.002 PHE C 111 TRP 0.017 0.002 TRP H 499 HIS 0.010 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00467 (14987) covalent geometry : angle 0.62981 (20344) hydrogen bonds : bond 0.05187 ( 675) hydrogen bonds : angle 4.87791 ( 1863) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 178 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8678 (tpp) cc_final: 0.8254 (tpp) REVERT: A 198 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7333 (ttm170) REVERT: A 260 ASN cc_start: 0.8146 (t0) cc_final: 0.7739 (t0) REVERT: A 306 ASN cc_start: 0.8438 (t0) cc_final: 0.8210 (t0) REVERT: B 141 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8108 (tm-30) REVERT: B 272 ASN cc_start: 0.7349 (m-40) cc_final: 0.7091 (p0) REVERT: C 28 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8481 (t0) REVERT: C 79 TRP cc_start: 0.8646 (m100) cc_final: 0.8365 (m100) REVERT: C 211 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8595 (m) REVERT: D 121 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7879 (t80) REVERT: D 170 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7737 (ttpt) REVERT: D 182 MET cc_start: 0.7982 (mmm) cc_final: 0.7600 (mmm) REVERT: E 40 ASP cc_start: 0.7934 (p0) cc_final: 0.7727 (p0) REVERT: E 43 ASP cc_start: 0.8207 (m-30) cc_final: 0.7916 (m-30) REVERT: E 126 ASP cc_start: 0.7640 (m-30) cc_final: 0.7096 (m-30) REVERT: E 167 GLN cc_start: 0.7276 (mt0) cc_final: 0.7002 (tt0) REVERT: F 95 MET cc_start: 0.8124 (mtp) cc_final: 0.7918 (mtm) REVERT: G 43 ASP cc_start: 0.8500 (m-30) cc_final: 0.8266 (m-30) REVERT: G 48 GLN cc_start: 0.7941 (tp-100) cc_final: 0.7736 (tp-100) REVERT: G 60 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8301 (mtmt) REVERT: G 61 ASN cc_start: 0.8329 (m-40) cc_final: 0.7886 (p0) REVERT: I 468 MET cc_start: 0.7837 (mmm) cc_final: 0.7453 (mmt) outliers start: 76 outliers final: 54 residues processed: 242 average time/residue: 0.0928 time to fit residues: 35.9865 Evaluate side-chains 224 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 166 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain H residue 467 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 92 optimal weight: 0.0970 chunk 33 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 159 optimal weight: 0.0770 chunk 19 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 153 ASN ** 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 = 0.3675 r_free = 0.3675 target = 0.120097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.090247 restraints weight = 27994.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.092723 restraints weight = 18143.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094404 restraints weight = 13483.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.095569 restraints weight = 11044.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.096402 restraints weight = 9665.546| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14987 Z= 0.115 Angle : 0.559 7.318 20344 Z= 0.296 Chirality : 0.043 0.173 2286 Planarity : 0.004 0.058 2628 Dihedral : 5.355 64.953 2142 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.62 % Favored : 96.23 % Rotamer: Outliers : 4.23 % Allowed : 21.71 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -0.38 (0.19), residues: 1908 helix: 0.85 (0.20), residues: 728 sheet: -0.43 (0.26), residues: 377 loop : -1.14 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 284 TYR 0.018 0.001 TYR B 222 PHE 0.018 0.001 PHE F 90 TRP 0.012 0.001 TRP H 499 HIS 0.005 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00251 (14987) covalent geometry : angle 0.55948 (20344) hydrogen bonds : bond 0.04241 ( 675) hydrogen bonds : angle 4.57155 ( 1863) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8580 (tpp) cc_final: 0.8142 (tpp) REVERT: A 198 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7092 (ttm170) REVERT: A 260 ASN cc_start: 0.8140 (t0) cc_final: 0.7762 (t0) REVERT: B 272 ASN cc_start: 0.7377 (m-40) cc_final: 0.7099 (p0) REVERT: C 79 TRP cc_start: 0.8614 (m100) cc_final: 0.8339 (m100) REVERT: C 211 SER cc_start: 0.9028 (t) cc_final: 0.8718 (m) REVERT: D 121 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7943 (t80) REVERT: D 170 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7728 (ttpt) REVERT: D 182 MET cc_start: 0.8142 (mmm) cc_final: 0.7654 (mmm) REVERT: E 40 ASP cc_start: 0.7963 (p0) cc_final: 0.7713 (p0) REVERT: E 43 ASP cc_start: 0.8288 (m-30) cc_final: 0.7930 (m-30) REVERT: E 126 ASP cc_start: 0.7786 (m-30) cc_final: 0.7195 (m-30) REVERT: G 43 ASP cc_start: 0.8547 (m-30) cc_final: 0.8288 (m-30) REVERT: G 48 GLN cc_start: 0.7892 (tp-100) cc_final: 0.7581 (tp-100) REVERT: G 60 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8219 (mtmt) REVERT: G 61 ASN cc_start: 0.8367 (m-40) cc_final: 0.7778 (p0) REVERT: I 468 MET cc_start: 0.7908 (mmm) cc_final: 0.7444 (mmt) outliers start: 61 outliers final: 41 residues processed: 233 average time/residue: 0.0920 time to fit residues: 34.4662 Evaluate side-chains 211 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain H residue 463 ILE Chi-restraints excluded: chain H residue 467 LEU Chi-restraints excluded: chain I residue 463 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 177 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 183 optimal weight: 0.0370 chunk 7 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 170 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 47 optimal weight: 50.0000 chunk 129 optimal weight: 4.9990 overall best weight: 1.2660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN B 379 GLN C 28 ASN C 127 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.119192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.090451 restraints weight = 28299.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.092440 restraints weight = 19774.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.093800 restraints weight = 15512.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.094572 restraints weight = 13162.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095387 restraints weight = 11850.229| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14987 Z= 0.134 Angle : 0.566 7.233 20344 Z= 0.298 Chirality : 0.044 0.297 2286 Planarity : 0.004 0.057 2628 Dihedral : 5.236 64.193 2142 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.83 % Favored : 96.02 % Rotamer: Outliers : 4.65 % Allowed : 21.50 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -0.23 (0.19), residues: 1908 helix: 0.91 (0.20), residues: 732 sheet: -0.38 (0.26), residues: 377 loop : -0.96 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 284 TYR 0.017 0.001 TYR B 222 PHE 0.018 0.001 PHE F 90 TRP 0.010 0.001 TRP C 104 HIS 0.006 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00310 (14987) covalent geometry : angle 0.56634 (20344) hydrogen bonds : bond 0.04267 ( 675) hydrogen bonds : angle 4.51127 ( 1863) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 179 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8674 (tpp) cc_final: 0.8146 (tpp) REVERT: A 260 ASN cc_start: 0.8028 (t0) cc_final: 0.7694 (t0) REVERT: B 117 THR cc_start: 0.7754 (p) cc_final: 0.7430 (t) REVERT: B 141 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8057 (tm-30) REVERT: C 28 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8490 (t0) REVERT: C 211 SER cc_start: 0.8899 (t) cc_final: 0.8638 (m) REVERT: D 121 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7874 (t80) REVERT: D 170 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7616 (ttpt) REVERT: D 182 MET cc_start: 0.7954 (mmm) cc_final: 0.7436 (mmm) REVERT: E 40 ASP cc_start: 0.7722 (p0) cc_final: 0.7484 (p0) REVERT: E 43 ASP cc_start: 0.8111 (m-30) cc_final: 0.7819 (m-30) REVERT: E 126 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: G 48 GLN cc_start: 0.7700 (tp-100) cc_final: 0.7411 (tp-100) REVERT: G 60 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8330 (mtmt) REVERT: G 61 ASN cc_start: 0.8200 (m-40) cc_final: 0.7765 (p0) REVERT: I 468 MET cc_start: 0.7802 (mmm) cc_final: 0.7476 (mmt) outliers start: 67 outliers final: 44 residues processed: 231 average time/residue: 0.0936 time to fit residues: 35.1427 Evaluate side-chains 210 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain H residue 463 ILE Chi-restraints excluded: chain H residue 467 LEU Chi-restraints excluded: chain I residue 463 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 40.0000 chunk 115 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 63 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN B 272 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.119580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.092408 restraints weight = 28232.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.092520 restraints weight = 22693.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.093062 restraints weight = 18320.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094031 restraints weight = 16699.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094121 restraints weight = 14384.249| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.6617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14987 Z= 0.126 Angle : 0.565 8.734 20344 Z= 0.298 Chirality : 0.044 0.235 2286 Planarity : 0.004 0.056 2628 Dihedral : 5.166 62.981 2142 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.62 % Favored : 96.23 % Rotamer: Outliers : 4.65 % Allowed : 21.84 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -0.08 (0.19), residues: 1908 helix: 1.01 (0.20), residues: 726 sheet: -0.31 (0.26), residues: 377 loop : -0.84 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 74 TYR 0.016 0.001 TYR B 222 PHE 0.019 0.001 PHE F 90 TRP 0.033 0.001 TRP C 79 HIS 0.005 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00285 (14987) covalent geometry : angle 0.56502 (20344) hydrogen bonds : bond 0.04062 ( 675) hydrogen bonds : angle 4.41946 ( 1863) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 171 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8699 (tpp) cc_final: 0.8179 (tpp) REVERT: A 260 ASN cc_start: 0.8157 (t0) cc_final: 0.7732 (t0) REVERT: B 117 THR cc_start: 0.7767 (p) cc_final: 0.7452 (t) REVERT: B 141 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8047 (tm-30) REVERT: C 211 SER cc_start: 0.8881 (t) cc_final: 0.8668 (m) REVERT: C 239 THR cc_start: 0.8820 (t) cc_final: 0.8554 (p) REVERT: D 121 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7889 (t80) REVERT: D 170 LYS cc_start: 0.7918 (ttpt) cc_final: 0.7542 (ttpt) REVERT: D 182 MET cc_start: 0.7891 (mmm) cc_final: 0.7452 (mmm) REVERT: E 43 ASP cc_start: 0.8147 (m-30) cc_final: 0.7917 (m-30) REVERT: E 124 GLN cc_start: 0.8933 (mp10) cc_final: 0.8732 (pm20) REVERT: E 126 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7248 (m-30) REVERT: G 48 GLN cc_start: 0.7867 (tp-100) cc_final: 0.7563 (tp-100) REVERT: G 60 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8253 (mtmt) REVERT: G 61 ASN cc_start: 0.8220 (m-40) cc_final: 0.7744 (p0) REVERT: G 107 MET cc_start: 0.8633 (mmt) cc_final: 0.8204 (mmt) REVERT: I 468 MET cc_start: 0.7817 (mmm) cc_final: 0.7146 (mmt) outliers start: 67 outliers final: 48 residues processed: 223 average time/residue: 0.0940 time to fit residues: 33.9373 Evaluate side-chains 216 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 273 PHE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain H residue 463 ILE Chi-restraints excluded: chain H residue 467 LEU Chi-restraints excluded: chain I residue 463 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 160 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 159 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 188 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.118185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.090909 restraints weight = 28343.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.091413 restraints weight = 20901.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.092036 restraints weight = 17261.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.092729 restraints weight = 15413.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.092765 restraints weight = 13735.207| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.6770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14987 Z= 0.143 Angle : 0.572 7.964 20344 Z= 0.302 Chirality : 0.045 0.219 2286 Planarity : 0.004 0.058 2628 Dihedral : 5.195 61.860 2142 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.72 % Favored : 96.12 % Rotamer: Outliers : 4.23 % Allowed : 22.88 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -0.06 (0.20), residues: 1908 helix: 0.99 (0.20), residues: 737 sheet: -0.26 (0.26), residues: 376 loop : -0.83 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 74 TYR 0.016 0.001 TYR B 222 PHE 0.019 0.001 PHE F 90 TRP 0.027 0.002 TRP C 79 HIS 0.006 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00333 (14987) covalent geometry : angle 0.57244 (20344) hydrogen bonds : bond 0.04183 ( 675) hydrogen bonds : angle 4.41144 ( 1863) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 173 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8778 (tpp) cc_final: 0.8301 (tpp) REVERT: A 260 ASN cc_start: 0.8173 (t0) cc_final: 0.7798 (t0) REVERT: B 117 THR cc_start: 0.7839 (p) cc_final: 0.7520 (t) REVERT: B 141 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8111 (tm-30) REVERT: C 211 SER cc_start: 0.8908 (t) cc_final: 0.8684 (m) REVERT: C 239 THR cc_start: 0.8837 (t) cc_final: 0.8577 (p) REVERT: D 121 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7895 (t80) REVERT: D 182 MET cc_start: 0.7894 (mmm) cc_final: 0.7552 (mmm) REVERT: E 40 ASP cc_start: 0.7810 (p0) cc_final: 0.6921 (p0) REVERT: E 43 ASP cc_start: 0.8292 (m-30) cc_final: 0.7773 (m-30) REVERT: F 17 GLN cc_start: 0.8398 (tp40) cc_final: 0.8133 (tt0) REVERT: F 95 MET cc_start: 0.8673 (ttm) cc_final: 0.8281 (mtp) REVERT: G 60 LYS cc_start: 0.8607 (mtmt) cc_final: 0.7987 (mtmt) REVERT: G 61 ASN cc_start: 0.8316 (m-40) cc_final: 0.7854 (p0) REVERT: I 468 MET cc_start: 0.7886 (mmm) cc_final: 0.7192 (mmt) outliers start: 61 outliers final: 48 residues processed: 218 average time/residue: 0.0920 time to fit residues: 32.4359 Evaluate side-chains 215 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain H residue 467 LEU Chi-restraints excluded: chain I residue 463 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 57 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 184 optimal weight: 0.2980 chunk 168 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.120201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.093789 restraints weight = 28138.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.093299 restraints weight = 22780.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.094652 restraints weight = 17778.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.095004 restraints weight = 15442.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095272 restraints weight = 13883.544| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14987 Z= 0.149 Angle : 0.591 8.224 20344 Z= 0.311 Chirality : 0.045 0.218 2286 Planarity : 0.004 0.059 2628 Dihedral : 5.248 60.198 2142 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.09 % Favored : 95.75 % Rotamer: Outliers : 4.23 % Allowed : 23.09 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.01 (0.20), residues: 1908 helix: 1.05 (0.20), residues: 729 sheet: -0.22 (0.26), residues: 376 loop : -0.78 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 74 TYR 0.016 0.001 TYR B 222 PHE 0.018 0.001 PHE F 90 TRP 0.026 0.002 TRP C 79 HIS 0.005 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00350 (14987) covalent geometry : angle 0.59090 (20344) hydrogen bonds : bond 0.04258 ( 675) hydrogen bonds : angle 4.43130 ( 1863) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8774 (tpp) cc_final: 0.8321 (tpp) REVERT: A 260 ASN cc_start: 0.8144 (t0) cc_final: 0.7783 (t0) REVERT: B 117 THR cc_start: 0.7917 (p) cc_final: 0.7603 (t) REVERT: B 141 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8167 (tm-30) REVERT: C 239 THR cc_start: 0.8828 (t) cc_final: 0.8540 (p) REVERT: D 121 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.7906 (t80) REVERT: D 182 MET cc_start: 0.7863 (mmm) cc_final: 0.7520 (mmm) REVERT: E 40 ASP cc_start: 0.7817 (p0) cc_final: 0.7355 (p0) REVERT: E 43 ASP cc_start: 0.8278 (m-30) cc_final: 0.7915 (m-30) REVERT: F 95 MET cc_start: 0.8679 (ttm) cc_final: 0.8258 (mtp) REVERT: G 60 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8012 (mtmt) REVERT: G 61 ASN cc_start: 0.8264 (m-40) cc_final: 0.7916 (p0) REVERT: G 107 MET cc_start: 0.8676 (mmt) cc_final: 0.8359 (mmt) REVERT: I 468 MET cc_start: 0.7799 (mmm) cc_final: 0.7089 (mmt) outliers start: 61 outliers final: 51 residues processed: 216 average time/residue: 0.0860 time to fit residues: 30.5695 Evaluate side-chains 220 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 273 PHE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain H residue 467 LEU Chi-restraints excluded: chain I residue 463 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 140 optimal weight: 30.0000 chunk 9 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 64 optimal weight: 0.0770 chunk 71 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 106 optimal weight: 40.0000 chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 overall best weight: 2.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.118988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.091756 restraints weight = 28360.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.091941 restraints weight = 20800.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.092787 restraints weight = 17553.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.094073 restraints weight = 14996.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.093831 restraints weight = 13075.663| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.7057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14987 Z= 0.182 Angle : 0.623 8.893 20344 Z= 0.329 Chirality : 0.046 0.206 2286 Planarity : 0.004 0.060 2628 Dihedral : 5.356 59.805 2142 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.44 % Rotamer: Outliers : 3.88 % Allowed : 23.58 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: -0.08 (0.20), residues: 1908 helix: 0.96 (0.20), residues: 733 sheet: -0.22 (0.26), residues: 376 loop : -0.84 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 74 TYR 0.016 0.001 TYR B 222 PHE 0.021 0.002 PHE E 103 TRP 0.025 0.002 TRP C 79 HIS 0.006 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00428 (14987) covalent geometry : angle 0.62336 (20344) hydrogen bonds : bond 0.04532 ( 675) hydrogen bonds : angle 4.48840 ( 1863) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8858 (tpp) cc_final: 0.8356 (tpp) REVERT: A 260 ASN cc_start: 0.8169 (t0) cc_final: 0.7724 (t0) REVERT: B 117 THR cc_start: 0.7966 (p) cc_final: 0.7632 (t) REVERT: B 141 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8199 (tm-30) REVERT: B 257 GLU cc_start: 0.7458 (pm20) cc_final: 0.7206 (pm20) REVERT: D 121 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7952 (t80) REVERT: D 170 LYS cc_start: 0.7727 (ttpp) cc_final: 0.7429 (ttpt) REVERT: D 182 MET cc_start: 0.7914 (mmm) cc_final: 0.7682 (mmm) REVERT: E 40 ASP cc_start: 0.7954 (p0) cc_final: 0.7651 (p0) REVERT: E 43 ASP cc_start: 0.8353 (m-30) cc_final: 0.8010 (m-30) REVERT: F 95 MET cc_start: 0.8641 (ttm) cc_final: 0.8281 (mtp) REVERT: G 60 LYS cc_start: 0.8650 (mtmt) cc_final: 0.8051 (mtmt) REVERT: G 61 ASN cc_start: 0.8318 (m-40) cc_final: 0.7987 (p0) REVERT: G 107 MET cc_start: 0.8734 (mmt) cc_final: 0.8458 (mmt) REVERT: I 468 MET cc_start: 0.7813 (mmm) cc_final: 0.7026 (mmt) outliers start: 56 outliers final: 52 residues processed: 214 average time/residue: 0.0927 time to fit residues: 32.3253 Evaluate side-chains 215 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 162 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 34 CYS Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 227 CYS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 245 HIS Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 273 PHE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain H residue 467 LEU Chi-restraints excluded: chain I residue 463 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 4 optimal weight: 0.2980 chunk 53 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 15 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 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 = 0.3699 r_free = 0.3699 target = 0.121650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.092640 restraints weight = 27757.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.094852 restraints weight = 18628.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.096430 restraints weight = 14245.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.097474 restraints weight = 11850.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.097824 restraints weight = 10517.817| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.7099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14987 Z= 0.119 Angle : 0.586 8.611 20344 Z= 0.309 Chirality : 0.044 0.207 2286 Planarity : 0.004 0.058 2628 Dihedral : 5.220 58.412 2142 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.56 % Favored : 96.28 % Rotamer: Outliers : 2.77 % Allowed : 24.90 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.03 (0.20), residues: 1908 helix: 0.94 (0.20), residues: 733 sheet: -0.13 (0.27), residues: 376 loop : -0.69 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 137 TYR 0.018 0.001 TYR G 109 PHE 0.020 0.001 PHE F 90 TRP 0.022 0.001 TRP C 79 HIS 0.014 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00265 (14987) covalent geometry : angle 0.58579 (20344) hydrogen bonds : bond 0.03899 ( 675) hydrogen bonds : angle 4.37278 ( 1863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2223.36 seconds wall clock time: 39 minutes 14.60 seconds (2354.60 seconds total)