Starting phenix.real_space_refine on Mon Jul 22 21:13:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui8_42288/07_2024/8ui8_42288_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui8_42288/07_2024/8ui8_42288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui8_42288/07_2024/8ui8_42288.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui8_42288/07_2024/8ui8_42288.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui8_42288/07_2024/8ui8_42288_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui8_42288/07_2024/8ui8_42288_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 3 5.21 5 S 129 5.16 5 C 12489 2.51 5 N 3381 2.21 5 O 3807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 938": "OE1" <-> "OE2" Residue "A PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1065": "OE1" <-> "OE2" Residue "A ASP 1082": "OD1" <-> "OD2" Residue "A ASP 1181": "OD1" <-> "OD2" Residue "A GLU 1313": "OE1" <-> "OE2" Residue "A PHE 1324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1346": "OD1" <-> "OD2" Residue "A GLU 1350": "OE1" <-> "OE2" Residue "A GLU 1351": "OE1" <-> "OE2" Residue "A TYR 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1651": "OE1" <-> "OE2" Residue "A GLU 1691": "OE1" <-> "OE2" Residue "A GLU 1713": "OE1" <-> "OE2" Residue "A PHE 1758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1834": "OE1" <-> "OE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 125": "OD1" <-> "OD2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ASP 200": "OD1" <-> "OD2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 153": "OD1" <-> "OD2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D ASP 224": "OD1" <-> "OD2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D ASP 295": "OD1" <-> "OD2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "E ASP 34": "OD1" <-> "OD2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 99": "OD1" <-> "OD2" Residue "E TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E ASP 243": "OD1" <-> "OD2" Residue "E GLU 257": "OE1" <-> "OE2" Residue "E ASP 304": "OD1" <-> "OD2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 349": "OD1" <-> "OD2" Residue "F ASP 29": "OD1" <-> "OD2" Residue "F ASP 41": "OD1" <-> "OD2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F ASP 113": "OD1" <-> "OD2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 150": "OD1" <-> "OD2" Residue "F GLU 193": "OE1" <-> "OE2" Residue "F TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 232": "OD1" <-> "OD2" Residue "F ASP 243": "OD1" <-> "OD2" Residue "G ASP 21": "OD1" <-> "OD2" Residue "G ASP 113": "OD1" <-> "OD2" Residue "G TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 174": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 19822 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5134 Classifications: {'peptide': 643} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 5 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain: "C" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2697 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 13, 'TRANS': 325} Chain: "D" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2536 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 314} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "F" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.05, per 1000 atoms: 0.56 Number of scatterers: 19822 At special positions: 0 Unit cell: (107.64, 128.34, 141.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 129 16.00 P 13 15.00 Mg 3 11.99 O 3807 8.00 N 3381 7.00 C 12489 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 - 3.50 Amino acid : False - 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: 8.10 Conformation dependent library (CDL) restraints added in 3.5 seconds 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 12 sheets defined 55.3% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 940 through 955 Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 1053 through 1058 Processing helix chain 'A' and resid 1062 through 1066 Processing helix chain 'A' and resid 1069 through 1098 Processing helix chain 'A' and resid 1137 through 1150 Processing helix chain 'A' and resid 1163 through 1177 removed outlier: 6.241A pdb=" N GLU A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA A1174 " --> pdb=" O GLN A1170 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR A1175 " --> pdb=" O LEU A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1327 Processing helix chain 'A' and resid 1340 through 1345 Processing helix chain 'A' and resid 1358 through 1373 Processing helix chain 'A' and resid 1378 through 1389 removed outlier: 3.687A pdb=" N PHE A1382 " --> pdb=" O ASP A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1406 Processing helix chain 'A' and resid 1457 through 1463 removed outlier: 3.525A pdb=" N THR A1461 " --> pdb=" O GLY A1457 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A1463 " --> pdb=" O ALA A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1468 Processing helix chain 'A' and resid 1474 through 1481 removed outlier: 3.663A pdb=" N HIS A1481 " --> pdb=" O SER A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1501 Processing helix chain 'A' and resid 1505 through 1510 Processing helix chain 'A' and resid 1510 through 1515 Processing helix chain 'A' and resid 1633 through 1663 removed outlier: 3.574A pdb=" N LEU A1663 " --> pdb=" O LEU A1659 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1730 removed outlier: 4.316A pdb=" N SER A1705 " --> pdb=" O THR A1701 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A1707 " --> pdb=" O GLN A1703 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A1730 " --> pdb=" O LYS A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1738 removed outlier: 3.605A pdb=" N CYS A1734 " --> pdb=" O THR A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1742 through 1746 Processing helix chain 'A' and resid 1750 through 1755 Processing helix chain 'A' and resid 1764 through 1780 Processing helix chain 'A' and resid 1781 through 1787 removed outlier: 3.546A pdb=" N LEU A1785 " --> pdb=" O ARG A1782 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR A1786 " --> pdb=" O SER A1783 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A1787 " --> pdb=" O LEU A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1814 Proline residue: A1799 - end of helix Processing helix chain 'A' and resid 1817 through 1822 Processing helix chain 'A' and resid 1824 through 1828 Processing helix chain 'A' and resid 1832 through 1840 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.838A pdb=" N ILE B 50 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.067A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 removed outlier: 4.934A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 194 through 207 Processing helix chain 'B' and resid 214 through 225 Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 291 through 305 removed outlier: 4.025A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 Processing helix chain 'B' and resid 333 through 350 removed outlier: 3.562A pdb=" N MET B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 11 Processing helix chain 'C' and resid 21 through 26 removed outlier: 3.973A pdb=" N TYR C 26 " --> pdb=" O TRP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 50 removed outlier: 3.947A pdb=" N GLU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.792A pdb=" N MET C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 86' Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.020A pdb=" N ARG C 102 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 127 through 130 Processing helix chain 'C' and resid 131 through 145 removed outlier: 3.795A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.580A pdb=" N LYS C 160 " --> pdb=" O TYR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 removed outlier: 3.624A pdb=" N CYS C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 194 removed outlier: 3.707A pdb=" N MET C 182 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 183 " --> pdb=" O PRO C 179 " (cutoff:3.500A) Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 210 removed outlier: 3.985A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 228 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.545A pdb=" N GLN C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 274 removed outlier: 3.504A pdb=" N ALA C 262 " --> pdb=" O ASP C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 289 removed outlier: 3.867A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 314 removed outlier: 3.805A pdb=" N VAL C 314 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 339 removed outlier: 3.698A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 56 through 68 removed outlier: 3.903A pdb=" N GLY D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 96 Processing helix chain 'D' and resid 97 through 104 removed outlier: 4.018A pdb=" N ARG D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.843A pdb=" N LEU D 129 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 removed outlier: 3.877A pdb=" N MET D 155 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 170 Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.771A pdb=" N ARG D 185 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 Processing helix chain 'D' and resid 203 through 219 Processing helix chain 'D' and resid 223 through 235 Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.505A pdb=" N GLY D 253 " --> pdb=" O THR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 267 Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.667A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 298 removed outlier: 3.604A pdb=" N LEU D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 361 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.742A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.795A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 66 removed outlier: 3.889A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS E 66 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 102 removed outlier: 3.592A pdb=" N GLY E 101 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 122 removed outlier: 4.258A pdb=" N GLU E 110 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 155 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 188 through 204 Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.830A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 304 through 325 removed outlier: 4.299A pdb=" N GLY E 309 " --> pdb=" O GLY E 305 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU E 310 " --> pdb=" O GLN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 349 removed outlier: 4.308A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP E 349 " --> pdb=" O LYS E 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 79 Processing helix chain 'F' and resid 141 through 155 Processing helix chain 'F' and resid 208 through 217 removed outlier: 3.578A pdb=" N LEU F 212 " --> pdb=" O ALA F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 222 removed outlier: 3.646A pdb=" N LEU F 221 " --> pdb=" O ALA F 218 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER F 222 " --> pdb=" O THR F 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 218 through 222' Processing helix chain 'G' and resid 8 through 19 removed outlier: 4.055A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 153 Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'G' and resid 218 through 222 removed outlier: 3.904A pdb=" N LEU G 221 " --> pdb=" O ALA G 218 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER G 222 " --> pdb=" O THR G 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 218 through 222' Processing sheet with id=AA1, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.294A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU D 74 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N CYS D 180 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N PHE D 76 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1151 through 1156 removed outlier: 5.774A pdb=" N LYS A1152 " --> pdb=" O LEU A1301 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A1303 " --> pdb=" O LYS A1152 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N PHE A1154 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLU A1305 " --> pdb=" O PHE A1154 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL A1156 " --> pdb=" O GLU A1305 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N ILE A1333 " --> pdb=" O SER A1300 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE A1302 " --> pdb=" O ILE A1333 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR A1335 " --> pdb=" O ILE A1302 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE A1304 " --> pdb=" O THR A1335 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR A1127 " --> pdb=" O GLU A1350 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE A1352 " --> pdb=" O THR A1127 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU A1129 " --> pdb=" O ILE A1352 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1519 through 1521 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.154A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N CYS B 171 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE B 74 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE B 73 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 91 removed outlier: 6.439A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 196 through 197 removed outlier: 6.716A pdb=" N ASP C 196 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 68 through 74 removed outlier: 6.655A pdb=" N LEU E 93 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N THR E 135 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL E 95 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N CYS E 165 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL E 40 " --> pdb=" O CYS E 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 60 through 62 removed outlier: 3.601A pdb=" N ILE F 87 " --> pdb=" O GLU F 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 66 through 71 removed outlier: 5.371A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR F 196 " --> pdb=" O LYS F 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 177 through 180 Processing sheet with id=AB2, first strand: chain 'G' and resid 61 through 62 removed outlier: 3.514A pdb=" N GLU G 3 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.417A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 3003 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.50 Time building geometry restraints manager: 8.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 6505 1.34 - 1.49: 4824 1.49 - 1.65: 8628 1.65 - 1.80: 90 1.80 - 1.95: 100 Bond restraints: 20147 Sorted by residual: bond pdb=" CA ALA B 342 " pdb=" CB ALA B 342 " ideal model delta sigma weight residual 1.528 1.461 0.067 1.56e-02 4.11e+03 1.87e+01 bond pdb=" C LEU B 341 " pdb=" O LEU B 341 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.15e-02 7.56e+03 1.52e+01 bond pdb=" C LEU B 340 " pdb=" O LEU B 340 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.16e-02 7.43e+03 1.18e+01 bond pdb=" C ALA B 342 " pdb=" O ALA B 342 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.17e-02 7.31e+03 9.34e+00 bond pdb=" N LEU F 209 " pdb=" CA LEU F 209 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.20e-02 6.94e+03 9.04e+00 ... (remaining 20142 not shown) Histogram of bond angle deviations from ideal: 96.59 - 104.45: 287 104.45 - 112.30: 10347 112.30 - 120.16: 8134 120.16 - 128.01: 8345 128.01 - 135.87: 122 Bond angle restraints: 27235 Sorted by residual: angle pdb=" C GLU C 2 " pdb=" CA GLU C 2 " pdb=" CB GLU C 2 " ideal model delta sigma weight residual 116.54 108.92 7.62 1.15e+00 7.56e-01 4.39e+01 angle pdb=" N LEU B 341 " pdb=" CA LEU B 341 " pdb=" C LEU B 341 " ideal model delta sigma weight residual 111.11 104.56 6.55 1.20e+00 6.94e-01 2.98e+01 angle pdb=" N PRO G 234 " pdb=" CA PRO G 234 " pdb=" C PRO G 234 " ideal model delta sigma weight residual 110.40 118.86 -8.46 1.61e+00 3.86e-01 2.76e+01 angle pdb=" CA GLU C 50 " pdb=" CB GLU C 50 " pdb=" CG GLU C 50 " ideal model delta sigma weight residual 114.10 124.21 -10.11 2.00e+00 2.50e-01 2.56e+01 angle pdb=" N ILE C 17 " pdb=" CA ILE C 17 " pdb=" C ILE C 17 " ideal model delta sigma weight residual 113.71 108.97 4.74 9.50e-01 1.11e+00 2.49e+01 ... (remaining 27230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.40: 11827 33.40 - 66.80: 546 66.80 - 100.20: 34 100.20 - 133.60: 0 133.60 - 167.00: 2 Dihedral angle restraints: 12409 sinusoidal: 5105 harmonic: 7304 Sorted by residual: dihedral pdb=" O2A ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PA ADP E2000 " pdb=" PB ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 133.00 167.00 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O2A ADP D2000 " pdb=" O3A ADP D2000 " pdb=" PA ADP D2000 " pdb=" PB ADP D2000 " ideal model delta sinusoidal sigma weight residual -60.00 75.29 -135.29 1 2.00e+01 2.50e-03 4.11e+01 dihedral pdb=" CA LEU G 247 " pdb=" C LEU G 247 " pdb=" N LYS G 248 " pdb=" CA LYS G 248 " ideal model delta harmonic sigma weight residual -180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 12406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2238 0.046 - 0.092: 686 0.092 - 0.139: 189 0.139 - 0.185: 39 0.185 - 0.231: 4 Chirality restraints: 3156 Sorted by residual: chirality pdb=" CA ALA G 242 " pdb=" N ALA G 242 " pdb=" C ALA G 242 " pdb=" CB ALA G 242 " both_signs ideal model delta sigma weight residual False 2.48 2.72 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE G 87 " pdb=" CA ILE G 87 " pdb=" CG1 ILE G 87 " pdb=" CG2 ILE G 87 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA LYS G 248 " pdb=" N LYS G 248 " pdb=" C LYS G 248 " pdb=" CB LYS G 248 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.45e-01 ... (remaining 3153 not shown) Planarity restraints: 3459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 215 " 0.013 2.00e-02 2.50e+03 2.56e-02 1.15e+01 pdb=" CG PHE F 215 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE F 215 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 PHE F 215 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 215 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE F 215 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE F 215 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 249 " -0.035 2.00e-02 2.50e+03 2.29e-02 1.04e+01 pdb=" CG TYR F 249 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR F 249 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR F 249 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR F 249 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR F 249 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR F 249 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 249 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A1082 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.58e+00 pdb=" CG ASP A1082 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP A1082 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP A1082 " -0.019 2.00e-02 2.50e+03 ... (remaining 3456 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 203 2.58 - 3.16: 15618 3.16 - 3.74: 32055 3.74 - 4.32: 42842 4.32 - 4.90: 71795 Nonbonded interactions: 162513 Sorted by model distance: nonbonded pdb=" OE2 GLU A1305 " pdb="MG MG A2001 " model vdw 2.003 2.170 nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.018 2.170 nonbonded pdb=" OG1 THR A1139 " pdb="MG MG A2001 " model vdw 2.042 2.170 nonbonded pdb="MG MG A2001 " pdb=" O1B AGS A2002 " model vdw 2.057 2.170 nonbonded pdb="MG MG C 401 " pdb=" O1B AGS C 402 " model vdw 2.062 2.170 ... (remaining 162508 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'G' } 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 55.520 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 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 : 0.005 0.067 20147 Z= 0.324 Angle : 0.851 13.407 27235 Z= 0.463 Chirality : 0.049 0.231 3156 Planarity : 0.006 0.073 3459 Dihedral : 17.828 166.999 7651 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.91 % Allowed : 25.48 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.16), residues: 2475 helix: -0.33 (0.13), residues: 1235 sheet: -0.65 (0.25), residues: 379 loop : -1.03 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1769 HIS 0.013 0.002 HIS E 301 PHE 0.043 0.002 PHE F 215 TYR 0.052 0.003 TYR F 249 ARG 0.011 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 315 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 923 LEU cc_start: 0.4495 (OUTLIER) cc_final: 0.4267 (mt) REVERT: A 1375 PHE cc_start: 0.7822 (m-80) cc_final: 0.7618 (m-80) REVERT: F 84 ASN cc_start: 0.7351 (m-40) cc_final: 0.6841 (p0) REVERT: G 72 LEU cc_start: 0.7707 (pt) cc_final: 0.7218 (mt) outliers start: 20 outliers final: 10 residues processed: 326 average time/residue: 0.3239 time to fit residues: 159.9648 Evaluate side-chains 307 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 296 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1694 LEU Chi-restraints excluded: chain A residue 1793 SER Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 125 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 223 optimal weight: 20.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS A1147 GLN A1490 HIS ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20147 Z= 0.270 Angle : 0.575 8.268 27235 Z= 0.296 Chirality : 0.041 0.239 3156 Planarity : 0.004 0.064 3459 Dihedral : 8.327 167.233 2771 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.67 % Allowed : 23.16 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.17), residues: 2475 helix: 0.75 (0.15), residues: 1235 sheet: -0.46 (0.25), residues: 381 loop : -0.72 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 28 HIS 0.005 0.001 HIS A1490 PHE 0.020 0.001 PHE F 214 TYR 0.039 0.002 TYR F 249 ARG 0.007 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 304 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1324 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8170 (t80) REVERT: B 40 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7739 (mm-30) REVERT: F 199 MET cc_start: 0.5497 (tmm) cc_final: 0.5167 (tmm) outliers start: 81 outliers final: 45 residues processed: 355 average time/residue: 0.3148 time to fit residues: 171.6256 Evaluate side-chains 336 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 289 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1694 LEU Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1793 SER Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 152 optimal weight: 0.4980 chunk 61 optimal weight: 7.9990 chunk 223 optimal weight: 20.0000 chunk 241 optimal weight: 0.9980 chunk 199 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS A1490 HIS ** A1751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN E 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20147 Z= 0.240 Angle : 0.546 7.424 27235 Z= 0.278 Chirality : 0.041 0.153 3156 Planarity : 0.004 0.064 3459 Dihedral : 7.929 168.224 2761 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.31 % Allowed : 23.62 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2475 helix: 1.04 (0.15), residues: 1245 sheet: -0.37 (0.26), residues: 381 loop : -0.64 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 PHE 0.042 0.001 PHE F 214 TYR 0.018 0.002 TYR F 249 ARG 0.005 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 313 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 202 MET cc_start: 0.8916 (tpp) cc_final: 0.8698 (tpp) REVERT: C 212 ASP cc_start: 0.8198 (t0) cc_final: 0.7987 (t0) REVERT: F 238 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7037 (mm-30) REVERT: G 72 LEU cc_start: 0.7745 (pt) cc_final: 0.7147 (mt) outliers start: 73 outliers final: 52 residues processed: 355 average time/residue: 0.3095 time to fit residues: 169.4767 Evaluate side-chains 353 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 300 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1694 LEU Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1709 LYS Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 20.0000 chunk 168 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 212 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS A 955 ASN A1490 HIS ** A1751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN E 109 GLN E 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20147 Z= 0.210 Angle : 0.531 10.394 27235 Z= 0.269 Chirality : 0.041 0.292 3156 Planarity : 0.004 0.063 3459 Dihedral : 7.658 168.919 2757 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.85 % Allowed : 23.03 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2475 helix: 1.26 (0.15), residues: 1243 sheet: -0.37 (0.26), residues: 380 loop : -0.58 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 PHE 0.039 0.001 PHE F 214 TYR 0.016 0.001 TYR A1399 ARG 0.012 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 316 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1488 GLU cc_start: 0.7763 (pm20) cc_final: 0.7292 (pm20) REVERT: B 40 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7707 (mm-30) REVERT: C 202 MET cc_start: 0.8905 (tpp) cc_final: 0.8691 (tpp) REVERT: D 102 ARG cc_start: 0.8274 (mmt180) cc_final: 0.7576 (tmm160) REVERT: E 333 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: F 238 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6956 (mm-30) REVERT: G 72 LEU cc_start: 0.7732 (pt) cc_final: 0.7178 (mt) outliers start: 85 outliers final: 61 residues processed: 369 average time/residue: 0.3551 time to fit residues: 201.9193 Evaluate side-chains 365 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 301 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1694 LEU Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1709 LYS Chi-restraints excluded: chain A residue 1772 ILE Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 98 optimal weight: 0.1980 chunk 202 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 0.0870 chunk 213 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1490 HIS ** A1751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 : 0.002 0.042 20147 Z= 0.156 Angle : 0.522 12.878 27235 Z= 0.262 Chirality : 0.040 0.323 3156 Planarity : 0.004 0.065 3459 Dihedral : 7.505 169.986 2757 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.22 % Allowed : 24.39 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2475 helix: 1.38 (0.15), residues: 1249 sheet: -0.34 (0.26), residues: 381 loop : -0.48 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 PHE 0.017 0.001 PHE A1758 TYR 0.029 0.001 TYR F 249 ARG 0.006 0.000 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 328 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1368 MET cc_start: 0.7808 (mmm) cc_final: 0.7334 (mmm) REVERT: A 1488 GLU cc_start: 0.7774 (pm20) cc_final: 0.7412 (pm20) REVERT: B 40 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: B 91 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7908 (ttm110) REVERT: B 296 ILE cc_start: 0.9471 (tp) cc_final: 0.9263 (tp) REVERT: C 202 MET cc_start: 0.8889 (tpp) cc_final: 0.8676 (tpp) REVERT: F 49 GLN cc_start: 0.7193 (tm130) cc_final: 0.6960 (tm130) REVERT: F 238 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6922 (mm-30) REVERT: G 72 LEU cc_start: 0.7651 (pt) cc_final: 0.7133 (mt) outliers start: 71 outliers final: 48 residues processed: 374 average time/residue: 0.3185 time to fit residues: 180.5141 Evaluate side-chains 359 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 309 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1709 LYS Chi-restraints excluded: chain A residue 1772 ILE Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.7980 chunk 214 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 58 optimal weight: 0.0670 chunk 238 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 124 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1490 HIS ** A1751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN E 90 ASN E 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN F 204 GLN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20147 Z= 0.149 Angle : 0.519 13.570 27235 Z= 0.259 Chirality : 0.040 0.340 3156 Planarity : 0.004 0.067 3459 Dihedral : 7.344 171.463 2755 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.13 % Allowed : 24.80 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.17), residues: 2475 helix: 1.50 (0.15), residues: 1252 sheet: -0.21 (0.26), residues: 371 loop : -0.45 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 28 HIS 0.005 0.001 HIS A1490 PHE 0.041 0.001 PHE F 214 TYR 0.021 0.001 TYR F 249 ARG 0.007 0.000 ARG E 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 320 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.7923 (ttm110) REVERT: F 179 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7550 (m-40) REVERT: F 238 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6949 (mm-30) REVERT: G 16 LEU cc_start: 0.8152 (tt) cc_final: 0.7759 (tt) REVERT: G 68 MET cc_start: 0.6923 (ptp) cc_final: 0.6445 (ptp) REVERT: G 72 LEU cc_start: 0.7644 (pt) cc_final: 0.7259 (mt) outliers start: 69 outliers final: 54 residues processed: 361 average time/residue: 0.3240 time to fit residues: 176.9871 Evaluate side-chains 359 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 303 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1485 MET Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1709 LYS Chi-restraints excluded: chain A residue 1772 ILE Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain A residue 1830 ASP Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 20.0000 chunk 26 optimal weight: 0.2980 chunk 135 optimal weight: 9.9990 chunk 173 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 200 optimal weight: 0.1980 chunk 132 optimal weight: 0.0040 chunk 237 optimal weight: 7.9990 chunk 148 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1490 HIS A1644 HIS ** A1751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20147 Z= 0.141 Angle : 0.524 13.979 27235 Z= 0.260 Chirality : 0.040 0.345 3156 Planarity : 0.004 0.069 3459 Dihedral : 7.271 172.014 2755 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.35 % Allowed : 24.84 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2475 helix: 1.57 (0.15), residues: 1250 sheet: -0.21 (0.26), residues: 381 loop : -0.39 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 PHE 0.017 0.001 PHE D 101 TYR 0.020 0.001 TYR F 249 ARG 0.007 0.000 ARG E 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 311 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1368 MET cc_start: 0.7862 (mmm) cc_final: 0.7314 (mmm) REVERT: B 91 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.7917 (ttm110) REVERT: D 318 ASN cc_start: 0.8146 (p0) cc_final: 0.7885 (p0) REVERT: F 49 GLN cc_start: 0.7192 (tm130) cc_final: 0.6932 (tm130) REVERT: F 179 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7655 (m-40) REVERT: F 238 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: G 68 MET cc_start: 0.6906 (ptp) cc_final: 0.6418 (ptp) REVERT: G 72 LEU cc_start: 0.7685 (pt) cc_final: 0.7274 (mt) outliers start: 74 outliers final: 56 residues processed: 360 average time/residue: 0.3547 time to fit residues: 196.4580 Evaluate side-chains 369 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 311 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1772 ILE Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain A residue 1830 ASP Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 179 ASN Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS A1490 HIS A1644 HIS ** A1751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN E 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20147 Z= 0.243 Angle : 0.562 13.621 27235 Z= 0.280 Chirality : 0.041 0.346 3156 Planarity : 0.004 0.070 3459 Dihedral : 7.394 169.707 2755 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.94 % Allowed : 24.61 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.17), residues: 2475 helix: 1.51 (0.15), residues: 1245 sheet: -0.15 (0.26), residues: 380 loop : -0.39 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 28 HIS 0.005 0.001 HIS A1490 PHE 0.020 0.001 PHE A1758 TYR 0.026 0.002 TYR F 249 ARG 0.004 0.000 ARG A1092 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 309 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 ILE cc_start: 0.8867 (pt) cc_final: 0.8616 (mm) REVERT: A 1368 MET cc_start: 0.7869 (mmm) cc_final: 0.7418 (mmm) REVERT: A 1498 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: B 91 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7935 (ttm110) REVERT: D 102 ARG cc_start: 0.8283 (mmt180) cc_final: 0.7615 (tmm160) REVERT: D 318 ASN cc_start: 0.8203 (p0) cc_final: 0.7930 (p0) REVERT: E 51 ARG cc_start: 0.9419 (OUTLIER) cc_final: 0.7343 (mtt90) REVERT: F 238 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7002 (mm-30) REVERT: G 68 MET cc_start: 0.6951 (ptp) cc_final: 0.6408 (ptp) REVERT: G 72 LEU cc_start: 0.7731 (pt) cc_final: 0.7394 (mt) REVERT: G 101 LEU cc_start: 0.7560 (mm) cc_final: 0.6933 (pp) REVERT: G 154 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7397 (mt) outliers start: 87 outliers final: 65 residues processed: 364 average time/residue: 0.3270 time to fit residues: 179.9186 Evaluate side-chains 362 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 293 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1772 ILE Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 7.9990 chunk 227 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 220 optimal weight: 30.0000 chunk 132 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 chunk 208 optimal weight: 0.5980 chunk 145 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1490 HIS A1644 HIS ** A1751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN E 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20147 Z= 0.241 Angle : 0.575 13.626 27235 Z= 0.285 Chirality : 0.041 0.359 3156 Planarity : 0.004 0.072 3459 Dihedral : 7.425 169.791 2755 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.54 % Allowed : 24.93 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.17), residues: 2475 helix: 1.49 (0.15), residues: 1246 sheet: -0.16 (0.26), residues: 380 loop : -0.37 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 28 HIS 0.005 0.001 HIS A1490 PHE 0.039 0.001 PHE F 214 TYR 0.025 0.002 TYR F 249 ARG 0.014 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 316 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 ILE cc_start: 0.8865 (pt) cc_final: 0.8620 (mm) REVERT: A 1498 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: B 91 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7934 (ttm110) REVERT: C 212 ASP cc_start: 0.8047 (t70) cc_final: 0.7625 (t0) REVERT: D 102 ARG cc_start: 0.8293 (mmt180) cc_final: 0.7633 (tmm160) REVERT: D 318 ASN cc_start: 0.8216 (p0) cc_final: 0.7950 (p0) REVERT: E 51 ARG cc_start: 0.9406 (OUTLIER) cc_final: 0.7302 (mtt90) REVERT: E 99 ASP cc_start: 0.7830 (m-30) cc_final: 0.7629 (m-30) REVERT: F 238 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6888 (mm-30) REVERT: G 68 MET cc_start: 0.6937 (ptp) cc_final: 0.6424 (ptp) REVERT: G 72 LEU cc_start: 0.7851 (pt) cc_final: 0.7460 (mt) outliers start: 78 outliers final: 67 residues processed: 369 average time/residue: 0.3122 time to fit residues: 175.8937 Evaluate side-chains 360 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 290 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1772 ILE Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS A1490 HIS A1644 HIS ** A1751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN E 92 HIS E 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20147 Z= 0.302 Angle : 0.604 13.358 27235 Z= 0.301 Chirality : 0.043 0.354 3156 Planarity : 0.004 0.070 3459 Dihedral : 7.536 168.388 2755 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.67 % Allowed : 25.07 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.17), residues: 2475 helix: 1.41 (0.15), residues: 1239 sheet: -0.19 (0.26), residues: 382 loop : -0.36 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 28 HIS 0.005 0.001 HIS A1490 PHE 0.048 0.002 PHE F 214 TYR 0.043 0.002 TYR F 249 ARG 0.011 0.000 ARG B 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 293 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 ILE cc_start: 0.8889 (pt) cc_final: 0.8625 (mm) REVERT: A 1498 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: B 91 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.7936 (ttm110) REVERT: B 158 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8545 (ttp) REVERT: C 182 MET cc_start: 0.7524 (tpp) cc_final: 0.7322 (tpp) REVERT: C 202 MET cc_start: 0.8757 (tpp) cc_final: 0.8526 (tpp) REVERT: D 102 ARG cc_start: 0.8297 (mmt180) cc_final: 0.7683 (tmm160) REVERT: D 318 ASN cc_start: 0.8237 (p0) cc_final: 0.7962 (p0) REVERT: E 51 ARG cc_start: 0.9426 (OUTLIER) cc_final: 0.7350 (mtt90) REVERT: F 214 PHE cc_start: 0.8771 (m-80) cc_final: 0.8519 (m-80) REVERT: F 238 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6866 (mm-30) REVERT: G 68 MET cc_start: 0.7000 (ptp) cc_final: 0.6486 (ptp) REVERT: G 72 LEU cc_start: 0.7833 (pt) cc_final: 0.7429 (mt) REVERT: G 101 LEU cc_start: 0.7592 (mm) cc_final: 0.7077 (pp) REVERT: G 154 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7448 (mt) outliers start: 81 outliers final: 67 residues processed: 347 average time/residue: 0.3247 time to fit residues: 170.6555 Evaluate side-chains 357 residues out of total 2206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 285 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1772 ILE Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain A residue 1830 ASP Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1490 HIS A1644 HIS ** A1751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN E 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** G 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.166379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121631 restraints weight = 30616.048| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.93 r_work: 0.3220 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20147 Z= 0.182 Angle : 0.568 14.029 27235 Z= 0.282 Chirality : 0.041 0.356 3156 Planarity : 0.004 0.070 3459 Dihedral : 7.381 169.737 2755 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.40 % Allowed : 25.52 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2475 helix: 1.55 (0.15), residues: 1241 sheet: -0.19 (0.26), residues: 391 loop : -0.33 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 28 HIS 0.005 0.001 HIS A1490 PHE 0.040 0.001 PHE F 214 TYR 0.026 0.001 TYR F 249 ARG 0.011 0.000 ARG B 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4462.02 seconds wall clock time: 80 minutes 36.14 seconds (4836.14 seconds total)