Starting phenix.real_space_refine on Sun Aug 24 00:28:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bi4_44558/08_2025/9bi4_44558_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bi4_44558/08_2025/9bi4_44558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bi4_44558/08_2025/9bi4_44558_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bi4_44558/08_2025/9bi4_44558_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bi4_44558/08_2025/9bi4_44558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bi4_44558/08_2025/9bi4_44558.map" } resolution = 3.2 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= 0.001 sd= 0.086 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 50 5.49 5 Mg 2 5.21 5 S 75 5.16 5 C 9861 2.51 5 N 2729 2.21 5 O 3148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15869 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3620 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 443} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 3676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3676 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 449} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3748 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 28, 'TRANS': 447} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 462 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3855 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 28, 'TRANS': 464} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 440 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "C" 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: "D" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.13, per 1000 atoms: 0.20 Number of scatterers: 15869 At special positions: 0 Unit cell: (93.138, 100.719, 186.276, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 75 16.00 P 50 15.00 Mg 2 11.99 O 3148 8.00 N 2729 7.00 C 9861 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: 1.09 Conformation dependent library (CDL) restraints added in 667.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3582 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 17 sheets defined 42.2% alpha, 18.8% beta 17 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'C' and resid 39 through 52 removed outlier: 3.898A pdb=" N ILE C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.938A pdb=" N ALA C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Proline residue: C 140 - end of helix Processing helix chain 'C' and resid 146 through 153 removed outlier: 3.581A pdb=" N GLU C 151 " --> pdb=" O LYS C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.769A pdb=" N GLU C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 239 removed outlier: 3.604A pdb=" N LYS C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP C 197 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA C 221 " --> pdb=" O ASP C 217 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N MET C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 1090 through 1102 Processing helix chain 'C' and resid 1108 through 1145 removed outlier: 3.810A pdb=" N ASP C1125 " --> pdb=" O SER C1121 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C1138 " --> pdb=" O LEU C1134 " (cutoff:3.500A) Processing helix chain 'C' and resid 1146 through 1161 removed outlier: 3.555A pdb=" N ILE C1152 " --> pdb=" O ASP C1148 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU C1155 " --> pdb=" O ARG C1151 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C1159 " --> pdb=" O GLU C1155 " (cutoff:3.500A) Processing helix chain 'C' and resid 1205 through 1222 removed outlier: 3.581A pdb=" N GLU C1222 " --> pdb=" O LEU C1218 " (cutoff:3.500A) Processing helix chain 'C' and resid 1241 through 1259 Processing helix chain 'C' and resid 1273 through 1280 removed outlier: 4.199A pdb=" N LEU C1277 " --> pdb=" O ASP C1273 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY C1278 " --> pdb=" O GLU C1274 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS C1279 " --> pdb=" O LYS C1275 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET C1280 " --> pdb=" O PHE C1276 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1273 through 1280' Processing helix chain 'C' and resid 1281 through 1286 removed outlier: 3.561A pdb=" N PHE C1285 " --> pdb=" O ASN C1281 " (cutoff:3.500A) Processing helix chain 'C' and resid 1308 through 1310 No H-bonds generated for 'chain 'C' and resid 1308 through 1310' Processing helix chain 'D' and resid 39 through 52 removed outlier: 3.799A pdb=" N ILE D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 removed outlier: 3.918A pdb=" N THR D 71 " --> pdb=" O ASP D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.727A pdb=" N ALA D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Proline residue: D 140 - end of helix Processing helix chain 'D' and resid 146 through 153 removed outlier: 3.663A pdb=" N LEU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 166 removed outlier: 3.592A pdb=" N LEU D 165 " --> pdb=" O LEU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.738A pdb=" N GLU D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 218 removed outlier: 3.536A pdb=" N THR D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP D 197 " --> pdb=" O SER D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 239 Processing helix chain 'D' and resid 1090 through 1102 Processing helix chain 'D' and resid 1106 through 1135 removed outlier: 3.566A pdb=" N TYR D1110 " --> pdb=" O ILE D1106 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N HIS D1111 " --> pdb=" O GLU D1107 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR D1130 " --> pdb=" O ASP D1126 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D1133 " --> pdb=" O VAL D1129 " (cutoff:3.500A) Processing helix chain 'D' and resid 1135 through 1146 removed outlier: 3.932A pdb=" N TYR D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D1144 " --> pdb=" O LYS D1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 1147 through 1159 removed outlier: 3.567A pdb=" N ARG D1151 " --> pdb=" O GLN D1147 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D1152 " --> pdb=" O ASP D1148 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU D1155 " --> pdb=" O ARG D1151 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS D1158 " --> pdb=" O ASP D1154 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG D1159 " --> pdb=" O GLU D1155 " (cutoff:3.500A) Processing helix chain 'D' and resid 1207 through 1224 removed outlier: 3.595A pdb=" N GLU D1222 " --> pdb=" O LEU D1218 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR D1223 " --> pdb=" O ALA D1219 " (cutoff:3.500A) Processing helix chain 'D' and resid 1241 through 1261 removed outlier: 3.788A pdb=" N HIS D1261 " --> pdb=" O ASN D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1273 through 1281 removed outlier: 3.850A pdb=" N LEU D1277 " --> pdb=" O ASP D1273 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN D1281 " --> pdb=" O LEU D1277 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1285 Processing helix chain 'D' and resid 1308 through 1310 No H-bonds generated for 'chain 'D' and resid 1308 through 1310' Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.665A pdb=" N LYS B 44 " --> pdb=" O MET B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 79 removed outlier: 3.890A pdb=" N THR B 74 " --> pdb=" O GLN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 137 through 143 removed outlier: 3.927A pdb=" N THR B 143 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 191 removed outlier: 3.980A pdb=" N ASP B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.627A pdb=" N ALA B 275 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 276 " --> pdb=" O ALA B 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 276' Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.750A pdb=" N TYR B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 392 Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 446 through 451 Processing helix chain 'B' and resid 463 through 477 removed outlier: 3.509A pdb=" N PHE B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 500 Processing helix chain 'B' and resid 501 through 506 removed outlier: 3.581A pdb=" N LEU B 505 " --> pdb=" O GLU B 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.621A pdb=" N THR A 35 " --> pdb=" O ASP A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 78 Processing helix chain 'A' and resid 92 through 97 removed outlier: 4.182A pdb=" N VAL A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 135 through 143 removed outlier: 3.755A pdb=" N ILE A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 140 " --> pdb=" O PRO A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 191 removed outlier: 4.703A pdb=" N ARG A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 removed outlier: 4.094A pdb=" N GLN A 276 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 349 removed outlier: 3.612A pdb=" N GLU A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 340 " --> pdb=" O MET A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 393 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 449 through 458 removed outlier: 4.343A pdb=" N LEU A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 477 removed outlier: 3.518A pdb=" N PHE A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 491 removed outlier: 4.027A pdb=" N PHE A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 490 " --> pdb=" O PHE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.610A pdb=" N GLY A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.582A pdb=" N LEU A 505 " --> pdb=" O GLU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 522 Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 24 removed outlier: 6.536A pdb=" N ALA C 83 " --> pdb=" O TYR C 5 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU C 7 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS C 81 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE C 9 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN C 79 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 21 through 24 removed outlier: 6.536A pdb=" N ALA C 83 " --> pdb=" O TYR C 5 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU C 7 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS C 81 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE C 9 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN C 79 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN C 91 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU C 116 " --> pdb=" O LEU C 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 1230 through 1234 removed outlier: 6.351A pdb=" N THR C 30 " --> pdb=" O VAL C1269 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N HIS C1288 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU C 31 " --> pdb=" O HIS C1288 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 1230 through 1234 removed outlier: 6.351A pdb=" N THR C 30 " --> pdb=" O VAL C1269 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N HIS C1288 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU C 31 " --> pdb=" O HIS C1288 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1170 through 1173 Processing sheet with id=AA6, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.693A pdb=" N ALA D 83 " --> pdb=" O TYR D 5 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU D 7 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS D 81 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE D 9 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN D 79 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 76 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.693A pdb=" N ALA D 83 " --> pdb=" O TYR D 5 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU D 7 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS D 81 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE D 9 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN D 79 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 76 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU D 116 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 1230 through 1234 removed outlier: 6.283A pdb=" N THR D 30 " --> pdb=" O VAL D1269 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N LEU D 29 " --> pdb=" O HIS D1288 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N PHE D1290 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU D 31 " --> pdb=" O PHE D1290 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL D1292 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 33 " --> pdb=" O VAL D1292 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ARG D1294 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D1305 " --> pdb=" O PHE D1289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 1170 through 1174 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.755A pdb=" N VAL B 118 " --> pdb=" O ASN B 147 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL B 51 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N MET B 50 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG B 10 " --> pdb=" O MET B 50 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL B 52 " --> pdb=" O ARG B 10 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU B 12 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS B 292 " --> pdb=" O ASP B 284 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AB3, first strand: chain 'B' and resid 163 through 167 removed outlier: 8.730A pdb=" N MET B 236 " --> pdb=" O TRP B 206 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN B 208 " --> pdb=" O MET B 236 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE B 238 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET B 210 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL B 237 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLN B 261 " --> pdb=" O ASN B 248 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN B 248 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 304 through 310 removed outlier: 7.809A pdb=" N GLN B 407 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B 367 " --> pdb=" O GLN B 407 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TYR B 409 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL B 369 " --> pdb=" O TYR B 409 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 50 through 53 removed outlier: 8.278A pdb=" N MET A 50 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ARG A 10 " --> pdb=" O MET A 50 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL A 52 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU A 12 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 88 through 89 removed outlier: 8.222A pdb=" N MET A 236 " --> pdb=" O TRP A 206 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN A 208 " --> pdb=" O MET A 236 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE A 238 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N MET A 210 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 257 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLN A 261 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN A 248 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 158 through 160 Processing sheet with id=AB8, first strand: chain 'A' and resid 304 through 310 667 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2628 1.29 - 1.42: 4121 1.42 - 1.55: 9241 1.55 - 1.68: 131 1.68 - 1.81: 128 Bond restraints: 16249 Sorted by residual: bond pdb=" CA LEU A 483 " pdb=" C LEU A 483 " ideal model delta sigma weight residual 1.524 1.428 0.096 1.29e-02 6.01e+03 5.59e+01 bond pdb=" C PHE A 486 " pdb=" O PHE A 486 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.18e-02 7.18e+03 3.97e+01 bond pdb=" CA GLU A 479 " pdb=" C GLU A 479 " ideal model delta sigma weight residual 1.526 1.453 0.073 1.20e-02 6.94e+03 3.68e+01 bond pdb=" C4 ATP C1401 " pdb=" C5 ATP C1401 " ideal model delta sigma weight residual 1.388 1.447 -0.059 1.00e-02 1.00e+04 3.52e+01 bond pdb=" C5 ATP C1401 " pdb=" N7 ATP C1401 " ideal model delta sigma weight residual 1.387 1.328 0.059 1.00e-02 1.00e+04 3.46e+01 ... (remaining 16244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 21884 3.93 - 7.87: 255 7.87 - 11.80: 14 11.80 - 15.73: 5 15.73 - 19.66: 1 Bond angle restraints: 22159 Sorted by residual: angle pdb=" PA ATP D1401 " pdb=" O3A ATP D1401 " pdb=" PB ATP D1401 " ideal model delta sigma weight residual 136.83 117.17 19.66 1.00e+00 1.00e+00 3.87e+02 angle pdb=" PB ATP D1401 " pdb=" O3B ATP D1401 " pdb=" PG ATP D1401 " ideal model delta sigma weight residual 139.87 124.24 15.63 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PB ATP C1401 " pdb=" O3B ATP C1401 " pdb=" PG ATP C1401 " ideal model delta sigma weight residual 139.87 124.95 14.92 1.00e+00 1.00e+00 2.23e+02 angle pdb=" PA ATP C1401 " pdb=" O3A ATP C1401 " pdb=" PB ATP C1401 " ideal model delta sigma weight residual 136.83 124.37 12.46 1.00e+00 1.00e+00 1.55e+02 angle pdb=" N HIS A 489 " pdb=" CA HIS A 489 " pdb=" C HIS A 489 " ideal model delta sigma weight residual 111.40 97.81 13.59 1.22e+00 6.72e-01 1.24e+02 ... (remaining 22154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 8422 17.80 - 35.59: 922 35.59 - 53.39: 381 53.39 - 71.18: 130 71.18 - 88.98: 30 Dihedral angle restraints: 9885 sinusoidal: 4384 harmonic: 5501 Sorted by residual: dihedral pdb=" N TRP B 33 " pdb=" C TRP B 33 " pdb=" CA TRP B 33 " pdb=" CB TRP B 33 " ideal model delta harmonic sigma weight residual 122.80 136.90 -14.10 0 2.50e+00 1.60e-01 3.18e+01 dihedral pdb=" C TRP B 33 " pdb=" N TRP B 33 " pdb=" CA TRP B 33 " pdb=" CB TRP B 33 " ideal model delta harmonic sigma weight residual -122.60 -136.41 13.81 0 2.50e+00 1.60e-01 3.05e+01 dihedral pdb=" C SER D 219 " pdb=" N SER D 219 " pdb=" CA SER D 219 " pdb=" CB SER D 219 " ideal model delta harmonic sigma weight residual -122.60 -134.10 11.50 0 2.50e+00 1.60e-01 2.12e+01 ... (remaining 9882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2375 0.117 - 0.234: 105 0.234 - 0.351: 18 0.351 - 0.468: 4 0.468 - 0.585: 1 Chirality restraints: 2503 Sorted by residual: chirality pdb=" CA TRP B 33 " pdb=" N TRP B 33 " pdb=" C TRP B 33 " pdb=" CB TRP B 33 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" CA ASP A 476 " pdb=" N ASP A 476 " pdb=" C ASP A 476 " pdb=" CB ASP A 476 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CA SER A 488 " pdb=" N SER A 488 " pdb=" C SER A 488 " pdb=" CB SER A 488 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 ... (remaining 2500 not shown) Planarity restraints: 2705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 486 " -0.084 2.00e-02 2.50e+03 5.17e-02 4.69e+01 pdb=" CG PHE B 486 " 0.082 2.00e-02 2.50e+03 pdb=" CD1 PHE B 486 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE B 486 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE B 486 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE B 486 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE B 486 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 230 " -0.061 5.00e-02 4.00e+02 9.35e-02 1.40e+01 pdb=" N PRO B 231 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO B 231 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 231 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 202 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C ILE C 202 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE C 202 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS C 203 " -0.019 2.00e-02 2.50e+03 ... (remaining 2702 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 76 2.44 - 3.05: 9645 3.05 - 3.67: 23082 3.67 - 4.28: 35487 4.28 - 4.90: 59918 Nonbonded interactions: 128208 Sorted by model distance: nonbonded pdb=" O2B ATP D1401 " pdb="MG MG D1402 " model vdw 1.821 2.170 nonbonded pdb=" OG1 THR C 41 " pdb="MG MG C1402 " model vdw 1.858 2.170 nonbonded pdb=" OG1 THR D 41 " pdb="MG MG D1402 " model vdw 1.893 2.170 nonbonded pdb=" OD1 ASN B 124 " pdb="MN MN B1002 " model vdw 1.937 2.320 nonbonded pdb=" OD2 ASP B 56 " pdb="MN MN B1002 " model vdw 1.974 2.320 ... (remaining 128203 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 'A' and (resid 1 through 412 or resid 444 through 494 or (resid 495 and ( \ name N or name CA or name C or name O or name CB )) or resid 496 through 507 or \ resid 1001 through 1002)) selection = (chain 'B' and (resid 1 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 69 or (resid 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 137 or (resid 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB )) or resid 25 \ 6 through 306 or (resid 307 and (name N or name CA or name C or name O or name C \ B )) or resid 308 through 498 or (resid 499 and (name N or name CA or name C or \ name O or name CB )) or resid 500 through 503 or (resid 504 and (name N or name \ CA or name C or name O or name CB )) or resid 505 through 1002)) } ncs_group { reference = (chain 'C' and (resid 1 through 211 or (resid 212 and (name N or name CA or name \ C or name O or name CB )) or resid 213 through 1109 or (resid 1110 and (name N \ or name CA or name C or name O or name CB )) or resid 1111 through 1402)) selection = (chain 'D' and (resid 1 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 1102 or (resid 1103 and (name N or \ name CA or name C or name O or name CB )) or resid 1104 through 1119 or (resid 1 \ 120 and (name N or name CA or name C or name O or name CB )) or resid 1121 or (r \ esid 1122 and (name N or name CA or name C or name O or name CB )) or resid 1123 \ through 1174 or resid 1184 through 1402)) } 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 individual isotropic 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: 1.370 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.070 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 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 : 0.008 0.096 16249 Z= 0.498 Angle : 1.033 19.663 22159 Z= 0.714 Chirality : 0.063 0.585 2503 Planarity : 0.006 0.093 2705 Dihedral : 18.968 88.980 6303 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.43 % Favored : 94.14 % Rotamer: Outliers : 7.50 % Allowed : 12.52 % Favored : 79.99 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.18), residues: 1861 helix: -1.25 (0.18), residues: 672 sheet: -0.91 (0.28), residues: 363 loop : -1.68 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C1159 TYR 0.016 0.002 TYR D 236 PHE 0.084 0.003 PHE B 486 TRP 0.016 0.002 TRP A 33 HIS 0.017 0.001 HIS C1111 Details of bonding type rmsd covalent geometry : bond 0.00816 (16249) covalent geometry : angle 1.03330 (22159) hydrogen bonds : bond 0.21581 ( 663) hydrogen bonds : angle 8.16980 ( 1964) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 157 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: C 35 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7792 (mmp) REVERT: C 218 ARG cc_start: 0.5421 (OUTLIER) cc_final: 0.5104 (ttp80) REVERT: C 1132 LYS cc_start: 0.7700 (ttmt) cc_final: 0.7357 (mtpp) REVERT: D 177 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8274 (pt0) REVERT: D 1158 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7897 (mtmm) REVERT: B 16 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8375 (m-30) REVERT: B 191 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8184 (p0) REVERT: A 53 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.6727 (tt0) outliers start: 124 outliers final: 66 residues processed: 264 average time/residue: 0.1216 time to fit residues: 47.4335 Evaluate side-chains 201 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 128 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1124 THR Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1152 ILE Chi-restraints excluded: chain C residue 1156 LEU Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 1111 HIS Chi-restraints excluded: chain D residue 1112 LYS Chi-restraints excluded: chain D residue 1117 LEU Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1123 VAL Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1158 LYS Chi-restraints excluded: chain D residue 1159 ARG Chi-restraints excluded: chain D residue 1189 VAL Chi-restraints excluded: chain D residue 1310 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 497 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.0170 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN C 66 HIS C 97 ASN C 211 HIS C 225 ASN C 230 GLN C1261 HIS C1279 HIS D 36 ASN D 97 ASN D 207 GLN D 225 ASN D 230 GLN D1208 GLN D1239 ASN D1253 HIS B 125 HIS B 214 GLN B 261 GLN A 46 ASN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 HIS A 148 HIS A 320 HIS A 384 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.154614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113575 restraints weight = 20413.292| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.30 r_work: 0.3118 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16249 Z= 0.137 Angle : 0.555 7.272 22159 Z= 0.307 Chirality : 0.042 0.139 2503 Planarity : 0.004 0.060 2705 Dihedral : 18.182 89.684 2722 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.75 % Rotamer: Outliers : 4.05 % Allowed : 15.48 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.19), residues: 1861 helix: 0.43 (0.20), residues: 700 sheet: -0.60 (0.28), residues: 336 loop : -1.40 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1120 TYR 0.012 0.001 TYR C 5 PHE 0.030 0.001 PHE B 257 TRP 0.018 0.002 TRP B 33 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00300 (16249) covalent geometry : angle 0.55529 (22159) hydrogen bonds : bond 0.05229 ( 663) hydrogen bonds : angle 4.73070 ( 1964) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 156 time to evaluate : 0.648 Fit side-chains REVERT: C 170 ASN cc_start: 0.8540 (t0) cc_final: 0.8027 (t0) REVERT: C 1132 LYS cc_start: 0.8438 (ttmt) cc_final: 0.8047 (mtpp) REVERT: C 1280 MET cc_start: 0.6485 (ttp) cc_final: 0.6200 (ttp) REVERT: D 1158 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8739 (mtpp) REVERT: D 1231 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8898 (tp) REVERT: D 1258 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8304 (tpt) REVERT: B 184 ARG cc_start: 0.7682 (tpp80) cc_final: 0.7393 (tpp80) REVERT: B 283 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8758 (tp) REVERT: B 320 HIS cc_start: 0.7722 (p-80) cc_final: 0.7275 (p-80) REVERT: A 53 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.6984 (tt0) REVERT: A 244 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: A 473 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8209 (mtmt) REVERT: A 478 ASP cc_start: 0.7801 (t0) cc_final: 0.7526 (t0) REVERT: A 485 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: A 489 HIS cc_start: 0.6918 (t-90) cc_final: 0.6671 (t-90) outliers start: 67 outliers final: 32 residues processed: 210 average time/residue: 0.1174 time to fit residues: 36.9077 Evaluate side-chains 182 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 1106 ILE Chi-restraints excluded: chain C residue 1145 LYS Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1261 HIS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1158 LYS Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1231 ILE Chi-restraints excluded: chain D residue 1258 MET Chi-restraints excluded: chain D residue 1267 LEU Chi-restraints excluded: chain D residue 1310 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 494 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 147 optimal weight: 0.1980 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1235 GLN C1254 ASN C1261 HIS D1257 ASN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.153134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111363 restraints weight = 20496.044| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.30 r_work: 0.3115 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16249 Z= 0.141 Angle : 0.527 7.217 22159 Z= 0.288 Chirality : 0.042 0.141 2503 Planarity : 0.003 0.045 2705 Dihedral : 17.432 88.472 2632 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.75 % Rotamer: Outliers : 3.57 % Allowed : 16.99 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.20), residues: 1861 helix: 1.10 (0.20), residues: 699 sheet: -0.51 (0.28), residues: 349 loop : -1.23 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1260 TYR 0.009 0.001 TYR A 279 PHE 0.025 0.001 PHE B 257 TRP 0.016 0.002 TRP B 33 HIS 0.024 0.001 HIS C1261 Details of bonding type rmsd covalent geometry : bond 0.00321 (16249) covalent geometry : angle 0.52717 (22159) hydrogen bonds : bond 0.04494 ( 663) hydrogen bonds : angle 4.27637 ( 1964) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 155 time to evaluate : 0.637 Fit side-chains REVERT: C 170 ASN cc_start: 0.8603 (t0) cc_final: 0.8073 (t0) REVERT: C 1132 LYS cc_start: 0.8514 (ttmt) cc_final: 0.8083 (mtpp) REVERT: C 1280 MET cc_start: 0.6624 (ttp) cc_final: 0.6374 (ttp) REVERT: D 1231 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8891 (tp) REVERT: D 1258 MET cc_start: 0.8527 (tpp) cc_final: 0.8275 (tpt) REVERT: D 1306 ASP cc_start: 0.8671 (t0) cc_final: 0.8159 (t0) REVERT: B 184 ARG cc_start: 0.7672 (tpp80) cc_final: 0.7322 (tpp80) REVERT: B 283 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8828 (tp) REVERT: B 320 HIS cc_start: 0.7763 (p-80) cc_final: 0.7313 (p-80) REVERT: B 348 LEU cc_start: 0.7746 (tt) cc_final: 0.7482 (tp) REVERT: A 53 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: A 244 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: A 478 ASP cc_start: 0.7664 (t0) cc_final: 0.7353 (t0) REVERT: A 489 HIS cc_start: 0.7189 (t-90) cc_final: 0.6979 (t-90) outliers start: 59 outliers final: 41 residues processed: 204 average time/residue: 0.1286 time to fit residues: 39.3282 Evaluate side-chains 186 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 1106 ILE Chi-restraints excluded: chain C residue 1124 THR Chi-restraints excluded: chain C residue 1139 MET Chi-restraints excluded: chain C residue 1145 LYS Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1231 ILE Chi-restraints excluded: chain D residue 1267 LEU Chi-restraints excluded: chain D residue 1310 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 494 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 150 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1098 GLN D1235 GLN B 61 ASN B 501 ASN A 214 GLN A 320 HIS A 501 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.149466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107662 restraints weight = 20458.139| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.24 r_work: 0.2898 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 16249 Z= 0.270 Angle : 0.607 6.982 22159 Z= 0.330 Chirality : 0.046 0.191 2503 Planarity : 0.004 0.040 2705 Dihedral : 17.432 87.631 2616 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.64 % Favored : 94.25 % Rotamer: Outliers : 5.08 % Allowed : 17.17 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.19), residues: 1861 helix: 1.04 (0.20), residues: 700 sheet: -0.58 (0.27), residues: 371 loop : -1.26 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1309 TYR 0.015 0.002 TYR C 5 PHE 0.031 0.002 PHE B 257 TRP 0.016 0.002 TRP A 33 HIS 0.007 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00652 (16249) covalent geometry : angle 0.60748 (22159) hydrogen bonds : bond 0.04900 ( 663) hydrogen bonds : angle 4.27390 ( 1964) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 147 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 198 MET cc_start: 0.6609 (ttm) cc_final: 0.6312 (ttm) REVERT: C 1132 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7861 (mtpp) REVERT: C 1172 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7848 (ptm-80) REVERT: D 1306 ASP cc_start: 0.8589 (t0) cc_final: 0.8024 (t0) REVERT: B 184 ARG cc_start: 0.7524 (tpp80) cc_final: 0.7282 (tpp80) REVERT: B 191 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8321 (p0) REVERT: B 201 MET cc_start: 0.7031 (pmm) cc_final: 0.6810 (pmm) REVERT: B 320 HIS cc_start: 0.7708 (p-80) cc_final: 0.7350 (p-80) REVERT: A 53 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: A 244 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: A 478 ASP cc_start: 0.7668 (t0) cc_final: 0.7363 (t0) outliers start: 84 outliers final: 64 residues processed: 216 average time/residue: 0.1321 time to fit residues: 42.9146 Evaluate side-chains 211 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 143 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 1106 ILE Chi-restraints excluded: chain C residue 1124 THR Chi-restraints excluded: chain C residue 1139 MET Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1155 GLU Chi-restraints excluded: chain C residue 1172 ARG Chi-restraints excluded: chain C residue 1189 VAL Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1267 LEU Chi-restraints excluded: chain D residue 1292 VAL Chi-restraints excluded: chain D residue 1310 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 494 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 7 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 chunk 121 optimal weight: 0.0050 chunk 138 optimal weight: 4.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.152930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110133 restraints weight = 20195.892| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.30 r_work: 0.3081 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16249 Z= 0.113 Angle : 0.488 6.360 22159 Z= 0.269 Chirality : 0.041 0.161 2503 Planarity : 0.003 0.034 2705 Dihedral : 16.761 89.510 2611 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.87 % Favored : 96.02 % Rotamer: Outliers : 3.02 % Allowed : 19.29 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.20), residues: 1861 helix: 1.55 (0.20), residues: 696 sheet: -0.36 (0.27), residues: 380 loop : -1.05 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 187 TYR 0.008 0.001 TYR A 279 PHE 0.016 0.001 PHE A 257 TRP 0.018 0.002 TRP B 33 HIS 0.007 0.001 HIS C1253 Details of bonding type rmsd covalent geometry : bond 0.00248 (16249) covalent geometry : angle 0.48770 (22159) hydrogen bonds : bond 0.03862 ( 663) hydrogen bonds : angle 3.95133 ( 1964) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 159 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: C 170 ASN cc_start: 0.8534 (t0) cc_final: 0.8084 (t0) REVERT: C 1132 LYS cc_start: 0.8374 (ttmt) cc_final: 0.7984 (mtpp) REVERT: D 1231 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8859 (tp) REVERT: D 1306 ASP cc_start: 0.8509 (t0) cc_final: 0.8212 (t0) REVERT: B 191 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8466 (p0) REVERT: B 320 HIS cc_start: 0.7711 (p-80) cc_final: 0.7404 (p-80) REVERT: A 53 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: A 116 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8942 (mt) REVERT: A 477 LYS cc_start: 0.8370 (mptt) cc_final: 0.8026 (mmtm) REVERT: A 478 ASP cc_start: 0.7778 (t0) cc_final: 0.7479 (t0) REVERT: A 489 HIS cc_start: 0.7074 (t-90) cc_final: 0.6854 (t-90) outliers start: 50 outliers final: 27 residues processed: 202 average time/residue: 0.1254 time to fit residues: 38.5497 Evaluate side-chains 179 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 1139 MET Chi-restraints excluded: chain C residue 1145 LYS Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1155 GLU Chi-restraints excluded: chain C residue 1189 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1147 GLN Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1231 ILE Chi-restraints excluded: chain D residue 1310 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 494 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 12 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 181 optimal weight: 40.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.149963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107234 restraints weight = 20348.975| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.20 r_work: 0.3022 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16249 Z= 0.240 Angle : 0.583 7.545 22159 Z= 0.314 Chirality : 0.045 0.165 2503 Planarity : 0.004 0.041 2705 Dihedral : 17.019 89.389 2609 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.27 % Favored : 94.68 % Rotamer: Outliers : 4.78 % Allowed : 18.08 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.20), residues: 1861 helix: 1.38 (0.20), residues: 700 sheet: -0.48 (0.27), residues: 377 loop : -1.07 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 184 TYR 0.013 0.002 TYR B 279 PHE 0.027 0.002 PHE B 257 TRP 0.015 0.002 TRP B 33 HIS 0.008 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00584 (16249) covalent geometry : angle 0.58304 (22159) hydrogen bonds : bond 0.04499 ( 663) hydrogen bonds : angle 4.07972 ( 1964) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 143 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1132 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7978 (mtpp) REVERT: C 1172 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7911 (ptm-80) REVERT: D 1306 ASP cc_start: 0.8522 (t0) cc_final: 0.8248 (t0) REVERT: B 184 ARG cc_start: 0.7736 (tpp80) cc_final: 0.7382 (tpp80) REVERT: B 191 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8381 (p0) REVERT: B 306 MET cc_start: 0.9242 (tpt) cc_final: 0.8778 (tpt) REVERT: B 320 HIS cc_start: 0.7748 (p-80) cc_final: 0.7431 (p-80) REVERT: A 53 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7122 (tt0) REVERT: A 244 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: A 477 LYS cc_start: 0.8442 (mptt) cc_final: 0.8120 (mmtm) REVERT: A 478 ASP cc_start: 0.7796 (t0) cc_final: 0.7521 (t0) REVERT: A 484 LYS cc_start: 0.7793 (tptp) cc_final: 0.7573 (tptp) outliers start: 79 outliers final: 59 residues processed: 211 average time/residue: 0.1132 time to fit residues: 36.3175 Evaluate side-chains 203 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 140 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 1139 MET Chi-restraints excluded: chain C residue 1145 LYS Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1155 GLU Chi-restraints excluded: chain C residue 1156 LEU Chi-restraints excluded: chain C residue 1172 ARG Chi-restraints excluded: chain C residue 1189 VAL Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1292 VAL Chi-restraints excluded: chain D residue 1310 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 513 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 84 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.150233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106575 restraints weight = 20176.869| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.22 r_work: 0.2975 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16249 Z= 0.175 Angle : 0.532 6.929 22159 Z= 0.290 Chirality : 0.043 0.156 2503 Planarity : 0.003 0.044 2705 Dihedral : 16.856 89.495 2607 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer: Outliers : 4.11 % Allowed : 19.04 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.20), residues: 1861 helix: 1.57 (0.20), residues: 696 sheet: -0.43 (0.27), residues: 377 loop : -1.00 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.011 0.001 TYR A 279 PHE 0.020 0.002 PHE B 257 TRP 0.017 0.002 TRP B 33 HIS 0.008 0.001 HIS C1253 Details of bonding type rmsd covalent geometry : bond 0.00422 (16249) covalent geometry : angle 0.53210 (22159) hydrogen bonds : bond 0.04100 ( 663) hydrogen bonds : angle 3.99667 ( 1964) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 151 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: C 170 ASN cc_start: 0.8591 (t0) cc_final: 0.8038 (t0) REVERT: C 1132 LYS cc_start: 0.8300 (ttmt) cc_final: 0.7891 (mtpp) REVERT: C 1172 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7907 (ptm-80) REVERT: D 1306 ASP cc_start: 0.8487 (t0) cc_final: 0.8172 (t0) REVERT: B 184 ARG cc_start: 0.7555 (tpp80) cc_final: 0.7119 (tpp80) REVERT: B 191 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8421 (p0) REVERT: B 306 MET cc_start: 0.9281 (tpt) cc_final: 0.8802 (tpt) REVERT: B 320 HIS cc_start: 0.7697 (p-80) cc_final: 0.7395 (p-80) REVERT: A 53 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: A 244 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: A 477 LYS cc_start: 0.8424 (mptt) cc_final: 0.8100 (mmtm) REVERT: A 478 ASP cc_start: 0.7788 (t0) cc_final: 0.7580 (t0) outliers start: 68 outliers final: 60 residues processed: 206 average time/residue: 0.1276 time to fit residues: 40.3123 Evaluate side-chains 209 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 145 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 1106 ILE Chi-restraints excluded: chain C residue 1128 ASP Chi-restraints excluded: chain C residue 1139 MET Chi-restraints excluded: chain C residue 1145 LYS Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1155 GLU Chi-restraints excluded: chain C residue 1156 LEU Chi-restraints excluded: chain C residue 1172 ARG Chi-restraints excluded: chain C residue 1189 VAL Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1292 VAL Chi-restraints excluded: chain D residue 1310 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 513 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 53 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.152005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108957 restraints weight = 20277.522| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.38 r_work: 0.3074 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16249 Z= 0.126 Angle : 0.499 8.669 22159 Z= 0.272 Chirality : 0.041 0.152 2503 Planarity : 0.003 0.045 2705 Dihedral : 16.631 88.356 2605 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.30 % Favored : 95.65 % Rotamer: Outliers : 3.51 % Allowed : 20.07 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.20), residues: 1861 helix: 1.76 (0.20), residues: 697 sheet: -0.23 (0.27), residues: 380 loop : -0.96 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.009 0.001 TYR B 107 PHE 0.018 0.001 PHE A 474 TRP 0.018 0.002 TRP B 33 HIS 0.006 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00293 (16249) covalent geometry : angle 0.49854 (22159) hydrogen bonds : bond 0.03719 ( 663) hydrogen bonds : angle 3.88067 ( 1964) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 5 TYR cc_start: 0.8900 (t80) cc_final: 0.8695 (t80) REVERT: C 170 ASN cc_start: 0.8594 (t0) cc_final: 0.8031 (t0) REVERT: C 1172 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7932 (ptm-80) REVERT: D 1306 ASP cc_start: 0.8425 (t0) cc_final: 0.8201 (t0) REVERT: B 184 ARG cc_start: 0.7660 (tpp80) cc_final: 0.7263 (tpp80) REVERT: B 191 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8469 (p0) REVERT: B 306 MET cc_start: 0.9265 (tpt) cc_final: 0.8809 (tpt) REVERT: B 320 HIS cc_start: 0.7737 (p-80) cc_final: 0.7442 (p-80) REVERT: A 53 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: A 244 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: A 477 LYS cc_start: 0.8367 (mptt) cc_final: 0.8041 (mmtm) outliers start: 58 outliers final: 47 residues processed: 208 average time/residue: 0.1293 time to fit residues: 40.9023 Evaluate side-chains 201 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 1128 ASP Chi-restraints excluded: chain C residue 1139 MET Chi-restraints excluded: chain C residue 1145 LYS Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1155 GLU Chi-restraints excluded: chain C residue 1156 LEU Chi-restraints excluded: chain C residue 1172 ARG Chi-restraints excluded: chain C residue 1189 VAL Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1292 VAL Chi-restraints excluded: chain D residue 1310 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 513 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 99 optimal weight: 0.0570 chunk 82 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.152343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109140 restraints weight = 20122.341| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.15 r_work: 0.3061 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16249 Z= 0.124 Angle : 0.496 7.183 22159 Z= 0.271 Chirality : 0.041 0.150 2503 Planarity : 0.003 0.045 2705 Dihedral : 16.569 89.615 2603 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.35 % Favored : 95.59 % Rotamer: Outliers : 3.33 % Allowed : 20.07 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.20), residues: 1861 helix: 1.89 (0.20), residues: 697 sheet: -0.15 (0.26), residues: 387 loop : -0.90 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.010 0.001 TYR B 107 PHE 0.017 0.001 PHE A 257 TRP 0.018 0.002 TRP B 33 HIS 0.008 0.001 HIS C1253 Details of bonding type rmsd covalent geometry : bond 0.00286 (16249) covalent geometry : angle 0.49646 (22159) hydrogen bonds : bond 0.03656 ( 663) hydrogen bonds : angle 3.82148 ( 1964) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 151 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: C 170 ASN cc_start: 0.8545 (t0) cc_final: 0.8007 (t0) REVERT: C 1128 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7183 (m-30) REVERT: C 1172 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7917 (ptm-80) REVERT: D 1306 ASP cc_start: 0.8383 (t0) cc_final: 0.8175 (t0) REVERT: B 184 ARG cc_start: 0.7728 (tpp80) cc_final: 0.7270 (tpp80) REVERT: B 191 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8449 (p0) REVERT: B 306 MET cc_start: 0.9221 (tpt) cc_final: 0.8844 (tpt) REVERT: B 320 HIS cc_start: 0.7733 (p-80) cc_final: 0.7473 (p-80) REVERT: A 53 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7097 (tt0) REVERT: A 244 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: A 477 LYS cc_start: 0.8424 (mptt) cc_final: 0.8102 (mmtm) outliers start: 55 outliers final: 46 residues processed: 194 average time/residue: 0.1373 time to fit residues: 40.0173 Evaluate side-chains 199 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 148 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 1128 ASP Chi-restraints excluded: chain C residue 1139 MET Chi-restraints excluded: chain C residue 1145 LYS Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1155 GLU Chi-restraints excluded: chain C residue 1156 LEU Chi-restraints excluded: chain C residue 1172 ARG Chi-restraints excluded: chain C residue 1189 VAL Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain D residue 1164 THR Chi-restraints excluded: chain D residue 1292 VAL Chi-restraints excluded: chain D residue 1310 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 513 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 174 optimal weight: 0.0470 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 114 optimal weight: 0.0370 chunk 7 optimal weight: 0.2980 chunk 57 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 92 optimal weight: 0.0060 chunk 81 optimal weight: 0.6980 chunk 86 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 overall best weight: 0.0972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.156182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113668 restraints weight = 20178.840| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.35 r_work: 0.3135 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16249 Z= 0.098 Angle : 0.483 10.762 22159 Z= 0.262 Chirality : 0.040 0.185 2503 Planarity : 0.003 0.045 2705 Dihedral : 16.258 84.080 2600 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.82 % Favored : 96.13 % Rotamer: Outliers : 2.00 % Allowed : 21.83 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.20), residues: 1861 helix: 2.03 (0.20), residues: 706 sheet: -0.02 (0.27), residues: 385 loop : -0.84 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 187 TYR 0.010 0.001 TYR B 107 PHE 0.015 0.001 PHE A 486 TRP 0.019 0.002 TRP B 33 HIS 0.006 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00205 (16249) covalent geometry : angle 0.48319 (22159) hydrogen bonds : bond 0.03308 ( 663) hydrogen bonds : angle 3.72223 ( 1964) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: C 170 ASN cc_start: 0.8505 (t0) cc_final: 0.8024 (t0) REVERT: C 1128 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7074 (m-30) REVERT: D 1 MET cc_start: 0.5503 (mtp) cc_final: 0.5218 (mtm) REVERT: B 184 ARG cc_start: 0.7749 (tpp80) cc_final: 0.7332 (tpp80) REVERT: B 283 LEU cc_start: 0.8971 (mt) cc_final: 0.8639 (tp) REVERT: B 306 MET cc_start: 0.9223 (tpt) cc_final: 0.8775 (tpt) REVERT: B 320 HIS cc_start: 0.7716 (p-80) cc_final: 0.7478 (p-80) REVERT: A 244 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: A 477 LYS cc_start: 0.8391 (mptt) cc_final: 0.8141 (mmtm) outliers start: 33 outliers final: 24 residues processed: 193 average time/residue: 0.1286 time to fit residues: 37.8653 Evaluate side-chains 185 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 1128 ASP Chi-restraints excluded: chain C residue 1145 LYS Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1155 GLU Chi-restraints excluded: chain C residue 1156 LEU Chi-restraints excluded: chain C residue 1238 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 1124 THR Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 179 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 174 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 145 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1253 HIS A 320 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.152303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109325 restraints weight = 20087.588| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.28 r_work: 0.3058 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16249 Z= 0.148 Angle : 0.523 10.652 22159 Z= 0.281 Chirality : 0.042 0.151 2503 Planarity : 0.003 0.047 2705 Dihedral : 16.438 89.371 2593 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.92 % Rotamer: Outliers : 2.12 % Allowed : 21.64 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.20), residues: 1861 helix: 1.98 (0.20), residues: 697 sheet: -0.01 (0.26), residues: 388 loop : -0.81 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 187 TYR 0.030 0.001 TYR B 107 PHE 0.021 0.001 PHE B 474 TRP 0.016 0.002 TRP B 33 HIS 0.009 0.001 HIS C1253 Details of bonding type rmsd covalent geometry : bond 0.00351 (16249) covalent geometry : angle 0.52330 (22159) hydrogen bonds : bond 0.03739 ( 663) hydrogen bonds : angle 3.78388 ( 1964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4214.66 seconds wall clock time: 73 minutes 10.14 seconds (4390.14 seconds total)