Starting phenix.real_space_refine on Sun Nov 17 21:18:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uhc_20770/11_2024/6uhc_20770_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uhc_20770/11_2024/6uhc_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uhc_20770/11_2024/6uhc_20770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uhc_20770/11_2024/6uhc_20770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uhc_20770/11_2024/6uhc_20770_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uhc_20770/11_2024/6uhc_20770_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} 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: {'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 5, 'GLU:plan': 15, 'ARG:plan': 9} 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: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 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, 'GLU:plan': 1, 'ASP: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: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 4} 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: 8.84, per 1000 atoms: 0.60 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: 3.24 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.86 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: 4.86 Time building geometry restraints manager: 3.76 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: 1.790 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.150 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.650 ------------------------------------------------------------------------------- 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= 0.612 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 : 12.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.003 TRP C 357 HIS 0.009 0.002 HIS C 151 PHE 0.023 0.003 PHE F 134 TYR 0.026 0.003 TYR D 250 ARG 0.007 0.001 ARG G 47 *********************** 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 : 1.629 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: 0.2926 time to fit residues: 227.2624 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 : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 173 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 HIS C 54 GLN C 65 ASN C 129 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 HIS D 254 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 14987 Z= 0.429 Angle : 0.789 8.910 20344 Z= 0.423 Chirality : 0.050 0.171 2286 Planarity : 0.006 0.058 2628 Dihedral : 6.395 85.634 2142 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.77 % Favored : 96.02 % Rotamer: Outliers : 5.27 % Allowed : 18.65 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.18), residues: 1908 helix: -0.57 (0.18), residues: 730 sheet: -0.67 (0.26), residues: 360 loop : -1.55 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 86 HIS 0.010 0.002 HIS A 108 PHE 0.024 0.003 PHE A 60 TYR 0.026 0.002 TYR C 172 ARG 0.009 0.001 ARG A 337 *********************** 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 328 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 252 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.7611 (t0) cc_final: 0.7338 (t0) REVERT: A 170 SER cc_start: 0.9354 (t) cc_final: 0.9139 (p) REVERT: A 260 ASN cc_start: 0.8140 (t0) cc_final: 0.7807 (t0) REVERT: A 310 ASP cc_start: 0.7278 (p0) cc_final: 0.7068 (t0) REVERT: B 272 ASN cc_start: 0.6885 (m-40) cc_final: 0.6610 (p0) REVERT: B 381 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7584 (mmmt) REVERT: C 11 ILE cc_start: 0.9153 (mm) cc_final: 0.8849 (mm) REVERT: C 14 HIS cc_start: 0.8495 (p-80) cc_final: 0.8058 (p-80) REVERT: C 79 TRP cc_start: 0.8692 (m100) cc_final: 0.8445 (m100) REVERT: C 211 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8488 (m) REVERT: C 223 ASP cc_start: 0.7857 (p0) cc_final: 0.7555 (p0) REVERT: C 348 THR cc_start: 0.9203 (p) cc_final: 0.8631 (p) REVERT: D 29 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7747 (mp0) REVERT: D 170 LYS cc_start: 0.8398 (tttt) cc_final: 0.8058 (ttpt) REVERT: D 182 MET cc_start: 0.8637 (mmm) cc_final: 0.8392 (mmm) REVERT: D 184 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8496 (mm-30) REVERT: E 40 ASP cc_start: 0.8128 (p0) cc_final: 0.7589 (p0) REVERT: E 43 ASP cc_start: 0.8280 (m-30) cc_final: 0.7767 (m-30) REVERT: E 74 TYR cc_start: 0.7304 (t80) cc_final: 0.7012 (t80) REVERT: E 126 ASP cc_start: 0.7400 (m-30) cc_final: 0.7153 (m-30) outliers start: 76 outliers final: 46 residues processed: 315 average time/residue: 0.2403 time to fit residues: 117.4765 Evaluate side-chains 234 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 192 HIS Chi-restraints excluded: chain A residue 208 LEU 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 351 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 182 LEU 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 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 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 116 LEU 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 16 ILE 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 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 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 96 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 47 optimal weight: 40.0000 chunk 173 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 172 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN A 371 HIS B 267 GLN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14987 Z= 0.240 Angle : 0.618 7.767 20344 Z= 0.331 Chirality : 0.045 0.148 2286 Planarity : 0.005 0.060 2628 Dihedral : 5.734 75.812 2142 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.72 % Favored : 96.02 % Rotamer: Outliers : 4.79 % Allowed : 19.21 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.19), residues: 1908 helix: 0.22 (0.19), residues: 731 sheet: -0.63 (0.26), residues: 378 loop : -1.25 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 499 HIS 0.017 0.001 HIS A 192 PHE 0.022 0.002 PHE F 93 TYR 0.020 0.002 TYR C 172 ARG 0.006 0.001 ARG F 97 *********************** 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 283 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.7519 (t0) cc_final: 0.7260 (t0) REVERT: A 135 ASN cc_start: 0.7724 (t0) cc_final: 0.7452 (t0) REVERT: A 144 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7419 (mm-40) REVERT: A 260 ASN cc_start: 0.8128 (t0) cc_final: 0.7806 (t0) REVERT: B 272 ASN cc_start: 0.7087 (m-40) cc_final: 0.6805 (p0) REVERT: C 14 HIS cc_start: 0.8457 (p-80) cc_final: 0.7920 (p-80) REVERT: C 79 TRP cc_start: 0.8708 (m100) cc_final: 0.8346 (m100) REVERT: C 90 LEU cc_start: 0.7622 (tt) cc_final: 0.7418 (mt) REVERT: C 211 SER cc_start: 0.9076 (OUTLIER) cc_final: 0.8445 (m) REVERT: C 223 ASP cc_start: 0.7888 (p0) cc_final: 0.7540 (p0) REVERT: C 348 THR cc_start: 0.9044 (p) cc_final: 0.8678 (p) REVERT: D 29 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7814 (mp0) REVERT: D 37 ASP cc_start: 0.8025 (t70) cc_final: 0.7555 (t70) REVERT: D 121 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7692 (t80) REVERT: D 170 LYS cc_start: 0.8357 (ttpt) cc_final: 0.8026 (ttpt) REVERT: D 182 MET cc_start: 0.8610 (mmm) cc_final: 0.8304 (mmm) REVERT: E 40 ASP cc_start: 0.8209 (p0) cc_final: 0.7406 (p0) REVERT: E 43 ASP cc_start: 0.8296 (m-30) cc_final: 0.7695 (m-30) REVERT: E 126 ASP cc_start: 0.7576 (m-30) cc_final: 0.7240 (m-30) REVERT: G 60 LYS cc_start: 0.8685 (mtmt) cc_final: 0.8090 (mtmt) REVERT: G 61 ASN cc_start: 0.8313 (m-40) cc_final: 0.7694 (p0) REVERT: G 90 ASP cc_start: 0.8349 (t70) cc_final: 0.8074 (t70) outliers start: 69 outliers final: 41 residues processed: 272 average time/residue: 0.2231 time to fit residues: 96.6133 Evaluate side-chains 227 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 144 GLN 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 351 GLU 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 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 30 HIS Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 187 SER 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 285 LEU 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 121 PHE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 52 ASN 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 53 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain H residue 467 LEU Chi-restraints excluded: chain I residue 463 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 174 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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** B 267 GLN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 14987 Z= 0.164 Angle : 0.561 7.801 20344 Z= 0.297 Chirality : 0.043 0.169 2286 Planarity : 0.004 0.058 2628 Dihedral : 5.234 71.057 2142 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Rotamer: Outliers : 3.54 % Allowed : 21.08 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.19), residues: 1908 helix: 0.65 (0.19), residues: 734 sheet: -0.39 (0.26), residues: 363 loop : -1.06 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 499 HIS 0.003 0.001 HIS D 254 PHE 0.016 0.001 PHE F 90 TYR 0.025 0.001 TYR E 132 ARG 0.005 0.000 ARG E 137 *********************** 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 257 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 206 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.7575 (t0) cc_final: 0.7330 (t0) REVERT: A 192 HIS cc_start: 0.8355 (p-80) cc_final: 0.8140 (p90) REVERT: A 260 ASN cc_start: 0.8164 (t0) cc_final: 0.7836 (t0) REVERT: B 112 PRO cc_start: 0.7314 (Cg_exo) cc_final: 0.7103 (Cg_endo) REVERT: B 141 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8140 (tm-30) REVERT: B 272 ASN cc_start: 0.7060 (m-40) cc_final: 0.6810 (p0) REVERT: C 14 HIS cc_start: 0.8355 (p-80) cc_final: 0.7862 (p-80) REVERT: C 28 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8537 (t0) REVERT: C 79 TRP cc_start: 0.8639 (m100) cc_final: 0.8298 (m100) REVERT: C 211 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8418 (m) REVERT: C 223 ASP cc_start: 0.7851 (p0) cc_final: 0.7484 (p0) REVERT: C 348 THR cc_start: 0.9043 (p) cc_final: 0.8743 (p) REVERT: D 37 ASP cc_start: 0.7879 (t70) cc_final: 0.7586 (t70) REVERT: D 121 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7700 (t80) REVERT: D 170 LYS cc_start: 0.8361 (ttpt) cc_final: 0.7969 (ttpt) REVERT: D 182 MET cc_start: 0.8528 (mmm) cc_final: 0.8158 (mmm) REVERT: E 40 ASP cc_start: 0.8199 (p0) cc_final: 0.7459 (p0) REVERT: E 43 ASP cc_start: 0.8517 (m-30) cc_final: 0.7868 (m-30) REVERT: E 126 ASP cc_start: 0.7765 (m-30) cc_final: 0.7435 (m-30) REVERT: G 60 LYS cc_start: 0.8635 (mtmt) cc_final: 0.7962 (mtmt) REVERT: G 61 ASN cc_start: 0.8279 (m-40) cc_final: 0.7541 (p0) REVERT: G 90 ASP cc_start: 0.8448 (t70) cc_final: 0.8047 (t70) outliers start: 51 outliers final: 29 residues processed: 250 average time/residue: 0.2365 time to fit residues: 92.3007 Evaluate side-chains 208 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP 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 351 GLU Chi-restraints excluded: chain B residue 107 ILE 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 340 PHE Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 217 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 232 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 52 ASN 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 151 LEU 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 153 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 2 optimal weight: 0.0050 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.0270 chunk 157 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 165 optimal weight: 0.7980 chunk 46 optimal weight: 30.0000 overall best weight: 1.7656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN ** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14987 Z= 0.249 Angle : 0.587 9.226 20344 Z= 0.310 Chirality : 0.044 0.178 2286 Planarity : 0.004 0.059 2628 Dihedral : 5.210 69.304 2142 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.93 % Favored : 95.91 % Rotamer: Outliers : 4.51 % Allowed : 20.18 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 1908 helix: 0.81 (0.20), residues: 734 sheet: -0.31 (0.26), residues: 367 loop : -1.00 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 219 HIS 0.009 0.001 HIS C 30 PHE 0.039 0.002 PHE B 297 TYR 0.019 0.001 TYR B 222 ARG 0.009 0.001 ARG C 284 *********************** 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 248 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 183 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ASN cc_start: 0.8221 (t0) cc_final: 0.7933 (t0) REVERT: A 401 GLU cc_start: 0.7909 (pp20) cc_final: 0.7688 (pp20) REVERT: B 112 PRO cc_start: 0.7386 (Cg_exo) cc_final: 0.7161 (Cg_endo) REVERT: B 141 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8161 (tm-30) REVERT: B 272 ASN cc_start: 0.7168 (m-40) cc_final: 0.6901 (p0) REVERT: C 14 HIS cc_start: 0.8512 (p-80) cc_final: 0.8025 (p-80) REVERT: C 28 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8547 (t0) REVERT: C 79 TRP cc_start: 0.8696 (m100) cc_final: 0.8358 (m100) REVERT: C 211 SER cc_start: 0.9109 (OUTLIER) cc_final: 0.8537 (m) REVERT: C 223 ASP cc_start: 0.7930 (p0) cc_final: 0.7608 (p0) REVERT: C 348 THR cc_start: 0.9069 (p) cc_final: 0.8600 (p) REVERT: D 37 ASP cc_start: 0.7928 (t70) cc_final: 0.7683 (t70) REVERT: D 121 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7817 (t80) REVERT: D 170 LYS cc_start: 0.8435 (ttpt) cc_final: 0.8043 (ttpt) REVERT: D 182 MET cc_start: 0.8541 (mmm) cc_final: 0.8124 (mmm) REVERT: E 19 MET cc_start: 0.8227 (mpp) cc_final: 0.7746 (mpp) REVERT: E 40 ASP cc_start: 0.8182 (p0) cc_final: 0.7546 (p0) REVERT: E 43 ASP cc_start: 0.8523 (m-30) cc_final: 0.7969 (m-30) REVERT: E 126 ASP cc_start: 0.7959 (m-30) cc_final: 0.7610 (m-30) REVERT: G 26 ASP cc_start: 0.5457 (t0) cc_final: 0.5136 (t0) REVERT: G 48 GLN cc_start: 0.8475 (tp-100) cc_final: 0.8195 (tp-100) REVERT: G 60 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8091 (mtmt) REVERT: G 61 ASN cc_start: 0.8393 (m-40) cc_final: 0.7668 (p0) REVERT: G 90 ASP cc_start: 0.8492 (t70) cc_final: 0.8083 (t70) outliers start: 65 outliers final: 50 residues processed: 233 average time/residue: 0.2142 time to fit residues: 80.3016 Evaluate side-chains 228 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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 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 311 VAL Chi-restraints excluded: chain B residue 107 ILE 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 182 LEU Chi-restraints excluded: chain B residue 196 LEU 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 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 147 SER Chi-restraints excluded: chain C residue 163 ASP 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 271 THR Chi-restraints excluded: chain C residue 285 LEU 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 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 E residue 94 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 146 GLU 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 151 LEU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain H residue 464 VAL 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 62 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 184 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: