Starting phenix.real_space_refine on Sun Jun 30 17:26:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui9_42289/06_2024/8ui9_42289_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui9_42289/06_2024/8ui9_42289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui9_42289/06_2024/8ui9_42289.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui9_42289/06_2024/8ui9_42289.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui9_42289/06_2024/8ui9_42289_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui9_42289/06_2024/8ui9_42289_updated.pdb" } resolution = 3.5 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= 0.001 sd= 0.036 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 14 5.49 5 Mg 4 5.21 5 S 146 5.16 5 C 13746 2.51 5 N 3709 2.21 5 O 4217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 915": "OE1" <-> "OE2" Residue "A PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1181": "OD1" <-> "OD2" Residue "A PHE 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1306": "OE1" <-> "OE2" Residue "A ASP 1308": "OD1" <-> "OD2" Residue "A ASP 1346": "OD1" <-> "OD2" Residue "A PHE 1375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1460": "OE1" <-> "OE2" Residue "A PHE 1499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1713": "OE1" <-> "OE2" Residue "A PHE 1747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1766": "OD1" <-> "OD2" Residue "A PHE 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1834": "OE1" <-> "OE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 252": "OD1" <-> "OD2" Residue "C ASP 292": "OD1" <-> "OD2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C ASP 334": "OD1" <-> "OD2" Residue "D PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D ASP 153": "OD1" <-> "OD2" Residue "D ASP 237": "OD1" <-> "OD2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E ASP 99": "OD1" <-> "OD2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 243": "OD1" <-> "OD2" Residue "E GLU 248": "OE1" <-> "OE2" Residue "E ASP 250": "OD1" <-> "OD2" Residue "E GLU 289": "OE1" <-> "OE2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 115": "OE1" <-> "OE2" Residue "F PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 243": "OD1" <-> "OD2" Residue "G PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 210": "NH1" <-> "NH2" Residue "G ASP 232": "OD1" <-> "OD2" Residue "G TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 122": "OD1" <-> "OD2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "H PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 193": "OE1" <-> "OE2" Residue "H GLU 198": "OE1" <-> "OE2" Residue "H PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 21836 Number of models: 1 Model: "" Number of chains: 13 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: "H" 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: 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: "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: 10.52, per 1000 atoms: 0.48 Number of scatterers: 21836 At special positions: 0 Unit cell: (123.372, 129.168, 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 146 16.00 P 14 15.00 Mg 4 11.99 O 4217 8.00 N 3709 7.00 C 13746 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: 7.88 Conformation dependent library (CDL) restraints added in 3.8 seconds 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5252 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 17 sheets defined 43.8% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 891 through 894 No H-bonds generated for 'chain 'A' and resid 891 through 894' Processing helix chain 'A' and resid 941 through 954 Processing helix chain 'A' and resid 961 through 971 Proline residue: A 965 - end of helix Processing helix chain 'A' and resid 1054 through 1057 No H-bonds generated for 'chain 'A' and resid 1054 through 1057' Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1070 through 1097 Processing helix chain 'A' and resid 1138 through 1148 Processing helix chain 'A' and resid 1164 through 1176 removed outlier: 6.309A pdb=" N GLU A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ALA A1174 " --> pdb=" O GLN A1170 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A1175 " --> pdb=" O LEU A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1326 Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.608A pdb=" N SER A1342 " --> pdb=" O PRO A1339 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A1344 " --> pdb=" O PHE A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1372 Processing helix chain 'A' and resid 1379 through 1388 Processing helix chain 'A' and resid 1393 through 1404 Processing helix chain 'A' and resid 1458 through 1462 Processing helix chain 'A' and resid 1475 through 1480 Processing helix chain 'A' and resid 1486 through 1500 Processing helix chain 'A' and resid 1506 through 1509 No H-bonds generated for 'chain 'A' and resid 1506 through 1509' Processing helix chain 'A' and resid 1511 through 1514 No H-bonds generated for 'chain 'A' and resid 1511 through 1514' Processing helix chain 'A' and resid 1633 through 1661 Processing helix chain 'A' and resid 1700 through 1737 removed outlier: 3.787A pdb=" N SER A1705 " --> pdb=" O THR A1701 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A1730 " --> pdb=" O LYS A1726 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A1731 " --> pdb=" O ALA A1727 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN A1732 " --> pdb=" O LEU A1728 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N SER A1733 " --> pdb=" O GLU A1729 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS A1734 " --> pdb=" O THR A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1745 Processing helix chain 'A' and resid 1751 through 1754 No H-bonds generated for 'chain 'A' and resid 1751 through 1754' Processing helix chain 'A' and resid 1765 through 1780 Processing helix chain 'A' and resid 1783 through 1786 removed outlier: 3.994A pdb=" N TYR A1786 " --> pdb=" O SER A1783 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1783 through 1786' Processing helix chain 'A' and resid 1790 through 1813 Proline residue: A1799 - end of helix Processing helix chain 'A' and resid 1818 through 1821 Processing helix chain 'A' and resid 1833 through 1839 Processing helix chain 'B' and resid 38 through 41 No H-bonds generated for 'chain 'B' and resid 38 through 41' Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 82 through 101 Proline residue: B 96 - end of helix removed outlier: 5.336A pdb=" N LYS B 99 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ASP B 100 " --> pdb=" O PRO B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 removed outlier: 4.241A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 148 through 163 removed outlier: 4.970A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LYS B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 195 through 209 Processing helix chain 'B' and resid 215 through 224 Processing helix chain 'B' and resid 229 through 242 Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 292 through 304 Processing helix chain 'B' and resid 310 through 329 Processing helix chain 'B' and resid 334 through 349 removed outlier: 3.932A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 11 Processing helix chain 'C' and resid 22 through 25 No H-bonds generated for 'chain 'C' and resid 22 through 25' Processing helix chain 'C' and resid 38 through 49 Processing helix chain 'C' and resid 67 through 77 Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 99 through 102 No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 132 through 144 removed outlier: 4.077A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 179 through 193 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 199 through 209 Processing helix chain 'C' and resid 214 through 227 Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 259 through 273 Processing helix chain 'C' and resid 277 through 288 Processing helix chain 'C' and resid 295 through 311 Processing helix chain 'C' and resid 318 through 338 removed outlier: 3.737A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 98 through 104 removed outlier: 4.399A pdb=" N ARG D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LEU D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 224 through 234 Processing helix chain 'D' and resid 238 through 251 Processing helix chain 'D' and resid 259 through 266 Processing helix chain 'D' and resid 271 through 283 Processing helix chain 'D' and resid 286 through 298 Processing helix chain 'D' and resid 303 through 314 Processing helix chain 'D' and resid 321 through 340 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 20 through 32 removed outlier: 3.505A pdb=" N CYS E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 104 through 121 removed outlier: 4.389A pdb=" N MET E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 154 Processing helix chain 'E' and resid 173 through 176 No H-bonds generated for 'chain 'E' and resid 173 through 176' Processing helix chain 'E' and resid 189 through 202 Processing helix chain 'E' and resid 209 through 218 Processing helix chain 'E' and resid 223 through 236 Processing helix chain 'E' and resid 250 through 264 Processing helix chain 'E' and resid 268 through 284 removed outlier: 3.862A pdb=" N HIS E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 301 removed outlier: 4.038A pdb=" N HIS E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 324 removed outlier: 4.664A pdb=" N GLY E 309 " --> pdb=" O GLY E 305 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU E 310 " --> pdb=" O GLN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 347 Processing helix chain 'F' and resid 10 through 18 Processing helix chain 'F' and resid 54 through 56 No H-bonds generated for 'chain 'F' and resid 54 through 56' Processing helix chain 'F' and resid 72 through 79 removed outlier: 3.844A pdb=" N LEU F 79 " --> pdb=" O MET F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 154 Processing helix chain 'F' and resid 210 through 221 removed outlier: 4.228A pdb=" N ALA F 218 " --> pdb=" O PHE F 214 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THR F 219 " --> pdb=" O PHE F 215 " (cutoff:3.500A) Proline residue: F 220 - end of helix Processing helix chain 'G' and resid 10 through 19 removed outlier: 4.016A pdb=" N LEU G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 79 removed outlier: 3.764A pdb=" N LEU G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 154 Processing helix chain 'G' and resid 209 through 221 removed outlier: 4.757A pdb=" N ALA G 218 " --> pdb=" O PHE G 214 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR G 219 " --> pdb=" O PHE G 215 " (cutoff:3.500A) Proline residue: G 220 - end of helix Processing helix chain 'H' and resid 10 through 16 Processing helix chain 'H' and resid 18 through 20 No H-bonds generated for 'chain 'H' and resid 18 through 20' Processing helix chain 'H' and resid 72 through 79 removed outlier: 4.031A pdb=" N SER H 76 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE H 78 " --> pdb=" O SER H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 153 removed outlier: 4.226A pdb=" N HIS H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 221 removed outlier: 3.880A pdb=" N LYS H 217 " --> pdb=" O ASN H 213 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA H 218 " --> pdb=" O PHE H 214 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR H 219 " --> pdb=" O PHE H 215 " (cutoff:3.500A) Proline residue: H 220 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 1350 through 1354 removed outlier: 6.761A pdb=" N VAL A1332 " --> pdb=" O VAL A1128 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE A1130 " --> pdb=" O VAL A1332 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A1334 " --> pdb=" O ILE A1130 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLY A1132 " --> pdb=" O LEU A1334 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR A1336 " --> pdb=" O GLY A1132 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS A1152 " --> pdb=" O LEU A1301 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A1303 " --> pdb=" O LYS A1152 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N PHE A1154 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLU A1305 " --> pdb=" O PHE A1154 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A1156 " --> pdb=" O GLU A1305 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1519 through 1521 removed outlier: 5.614A pdb=" N PHE A1747 " --> pdb=" O ASP A1520 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 186 through 189 removed outlier: 6.166A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 170 through 174 removed outlier: 3.520A pdb=" N GLY C 60 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 195 through 199 removed outlier: 6.278A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 180 through 183 removed outlier: 5.972A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 68 through 75 Processing sheet with id= H, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.679A pdb=" N ILE F 87 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU F 104 " --> pdb=" O ILE F 87 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 66 through 71 removed outlier: 5.251A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 204 through 208 removed outlier: 3.811A pdb=" N LEU F 205 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 59 through 61 removed outlier: 4.082A pdb=" N THR G 59 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG G 61 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU G 3 " --> pdb=" O ARG G 61 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR G 114 " --> pdb=" O LEU G 101 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.525A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 203 through 208 Processing sheet with id= N, first strand: chain 'H' and resid 2 through 6 removed outlier: 3.811A pdb=" N ILE H 88 " --> pdb=" O LEU H 6 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 66 through 71 removed outlier: 6.329A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR H 249 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL H 237 " --> pdb=" O TYR H 249 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU H 251 " --> pdb=" O LEU H 235 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU H 235 " --> pdb=" O LEU H 251 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 157 through 162 Processing sheet with id= Q, first strand: chain 'H' and resid 166 through 171 970 hydrogen bonds defined for protein. 2823 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: 7.17 Time building geometry restraints manager: 8.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7249 1.36 - 1.50: 5539 1.50 - 1.65: 9181 1.65 - 1.80: 122 1.80 - 1.95: 95 Bond restraints: 22186 Sorted by residual: bond pdb=" C THR H 219 " pdb=" N PRO H 220 " ideal model delta sigma weight residual 1.334 1.376 -0.042 8.40e-03 1.42e+04 2.50e+01 bond pdb=" N ILE H 241 " pdb=" CA ILE H 241 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.33e+00 bond pdb=" N ASP F 243 " pdb=" CA ASP F 243 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.28e-02 6.10e+03 8.05e+00 bond pdb=" N ILE D 257 " pdb=" CA ILE D 257 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.22e-02 6.72e+03 7.81e+00 bond pdb=" N THR H 185 " pdb=" CA THR H 185 " ideal model delta sigma weight residual 1.452 1.487 -0.036 1.30e-02 5.92e+03 7.49e+00 ... (remaining 22181 not shown) Histogram of bond angle deviations from ideal: 94.12 - 102.58: 89 102.58 - 111.05: 8161 111.05 - 119.51: 11124 119.51 - 127.98: 10493 127.98 - 136.44: 124 Bond angle restraints: 29991 Sorted by residual: angle pdb=" CA LYS E 327 " pdb=" CB LYS E 327 " pdb=" CG LYS E 327 " ideal model delta sigma weight residual 114.10 124.26 -10.16 2.00e+00 2.50e-01 2.58e+01 angle pdb=" CA GLN G 204 " pdb=" CB GLN G 204 " pdb=" CG GLN G 204 " ideal model delta sigma weight residual 114.10 123.88 -9.78 2.00e+00 2.50e-01 2.39e+01 angle pdb=" CB GLU E 333 " pdb=" CG GLU E 333 " pdb=" CD GLU E 333 " ideal model delta sigma weight residual 112.60 120.10 -7.50 1.70e+00 3.46e-01 1.94e+01 angle pdb=" CA TRP A1679 " pdb=" CB TRP A1679 " pdb=" CG TRP A1679 " ideal model delta sigma weight residual 113.60 121.69 -8.09 1.90e+00 2.77e-01 1.81e+01 angle pdb=" CB GLN G 204 " pdb=" CG GLN G 204 " pdb=" CD GLN G 204 " ideal model delta sigma weight residual 112.60 119.71 -7.11 1.70e+00 3.46e-01 1.75e+01 ... (remaining 29986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.84: 13010 31.84 - 63.69: 621 63.69 - 95.53: 43 95.53 - 127.37: 1 127.37 - 159.22: 1 Dihedral angle restraints: 13676 sinusoidal: 5611 harmonic: 8065 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 300.00 140.78 159.22 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" CA GLU H 198 " pdb=" C GLU H 198 " pdb=" N MET H 199 " pdb=" CA MET H 199 " ideal model delta harmonic sigma weight residual -180.00 -150.72 -29.28 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ALA H 194 " pdb=" C ALA H 194 " pdb=" N VAL H 195 " pdb=" CA VAL H 195 " ideal model delta harmonic sigma weight residual 180.00 158.47 21.53 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 13673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3247 0.099 - 0.198: 222 0.198 - 0.296: 10 0.296 - 0.395: 1 0.395 - 0.494: 1 Chirality restraints: 3481 Sorted by residual: chirality pdb=" CB ILE B 73 " pdb=" CA ILE B 73 " pdb=" CG1 ILE B 73 " pdb=" CG2 ILE B 73 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CB ILE G 11 " pdb=" CA ILE G 11 " pdb=" CG1 ILE G 11 " pdb=" CG2 ILE G 11 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE G 160 " pdb=" CA ILE G 160 " pdb=" CG1 ILE G 160 " pdb=" CG2 ILE G 160 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 3478 not shown) Planarity restraints: 3815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1189 " -0.072 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO A1190 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO A1190 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A1190 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 252 " -0.066 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO H 253 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO H 253 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO H 253 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 138 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C LYS H 138 " -0.067 2.00e-02 2.50e+03 pdb=" O LYS H 138 " 0.026 2.00e-02 2.50e+03 pdb=" N MET H 139 " 0.023 2.00e-02 2.50e+03 ... (remaining 3812 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 203 2.57 - 3.16: 16937 3.16 - 3.74: 35501 3.74 - 4.32: 46913 4.32 - 4.90: 78168 Nonbonded interactions: 177722 Sorted by model distance: nonbonded pdb=" OE2 GLU A1305 " pdb="MG MG A2001 " model vdw 1.992 2.170 nonbonded pdb="MG MG A2001 " pdb=" O3G AGS A2002 " model vdw 1.994 2.170 nonbonded pdb="MG MG C 401 " pdb=" O2G AGS C 402 " model vdw 2.029 2.170 nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.039 2.170 nonbonded pdb="MG MG A2001 " pdb=" O1B AGS A2002 " model vdw 2.053 2.170 ... (remaining 177717 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' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.390 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 54.790 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.120 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 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 0.097 22186 Z= 0.314 Angle : 0.883 12.050 29991 Z= 0.470 Chirality : 0.052 0.494 3481 Planarity : 0.006 0.110 3815 Dihedral : 17.195 159.218 8424 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.78 % Rotamer: Outliers : 0.78 % Allowed : 24.77 % Favored : 74.45 % 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: -1.22 (0.15), residues: 2734 helix: -0.44 (0.13), residues: 1243 sheet: -0.52 (0.23), residues: 493 loop : -1.24 (0.17), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A1403 HIS 0.023 0.001 HIS G 153 PHE 0.056 0.002 PHE E 335 TYR 0.030 0.002 TYR G 249 ARG 0.018 0.001 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 288 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1344 MET cc_start: 0.8071 (mmm) cc_final: 0.7766 (mmt) REVERT: A 1784 LEU cc_start: 0.7889 (mt) cc_final: 0.7237 (pp) REVERT: D 194 CYS cc_start: 0.8257 (m) cc_final: 0.7656 (m) REVERT: E 83 GLU cc_start: 0.7215 (pp20) cc_final: 0.6866 (pm20) REVERT: F 64 ARG cc_start: 0.8136 (tmt170) cc_final: 0.7898 (tmt170) REVERT: H 71 ASN cc_start: 0.7069 (m-40) cc_final: 0.6861 (p0) outliers start: 19 outliers final: 10 residues processed: 299 average time/residue: 0.3211 time to fit residues: 150.3413 Evaluate side-chains 276 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 266 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 20.0000 chunk 206 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 110 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 129 optimal weight: 0.0770 chunk 158 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22186 Z= 0.268 Angle : 0.586 8.523 29991 Z= 0.299 Chirality : 0.042 0.201 3481 Planarity : 0.004 0.070 3815 Dihedral : 7.958 161.524 3054 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.66 % Allowed : 23.09 % Favored : 73.25 % 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: -0.47 (0.16), residues: 2734 helix: 0.40 (0.14), residues: 1252 sheet: -0.47 (0.22), residues: 513 loop : -1.00 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1403 HIS 0.010 0.001 HIS G 153 PHE 0.035 0.002 PHE H 214 TYR 0.018 0.002 TYR F 239 ARG 0.007 0.001 ARG A1790 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 279 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 ARG cc_start: 0.8439 (mmt-90) cc_final: 0.8193 (mpt-90) REVERT: C 288 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.6983 (m) REVERT: E 231 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8404 (mt-10) REVERT: E 275 ARG cc_start: 0.8774 (tmt90) cc_final: 0.8533 (ttt90) REVERT: F 139 MET cc_start: 0.6513 (ttt) cc_final: 0.6259 (ttt) REVERT: G 49 GLN cc_start: 0.6865 (tp40) cc_final: 0.6292 (tm-30) REVERT: G 177 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7757 (p0) REVERT: H 146 ARG cc_start: 0.7909 (ptt-90) cc_final: 0.7469 (ptt-90) REVERT: H 169 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8285 (m-80) REVERT: H 254 LYS cc_start: 0.6769 (mttt) cc_final: 0.6081 (mtmm) outliers start: 89 outliers final: 54 residues processed: 346 average time/residue: 0.3106 time to fit residues: 170.0627 Evaluate side-chains 319 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 261 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 164 LYS Chi-restraints excluded: chain H residue 169 PHE Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 267 optimal weight: 7.9990 chunk 220 optimal weight: 20.0000 chunk 245 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1166 GLN ** A1467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 224 ASN C 300 HIS ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN F 71 ASN F 179 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 22186 Z= 0.378 Angle : 0.670 8.282 29991 Z= 0.341 Chirality : 0.044 0.197 3481 Planarity : 0.005 0.055 3815 Dihedral : 7.943 161.785 3044 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.92 % Allowed : 23.62 % Favored : 70.46 % 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: -0.61 (0.16), residues: 2734 helix: 0.36 (0.14), residues: 1274 sheet: -0.56 (0.23), residues: 496 loop : -1.20 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1403 HIS 0.012 0.002 HIS G 153 PHE 0.022 0.002 PHE G 169 TYR 0.022 0.002 TYR F 239 ARG 0.011 0.001 ARG A1394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 275 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1172 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7493 (tptp) REVERT: A 1394 ARG cc_start: 0.6288 (ttt90) cc_final: 0.4836 (mtp85) REVERT: A 1644 HIS cc_start: 0.8141 (m90) cc_final: 0.7776 (m-70) REVERT: A 1775 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7928 (mp) REVERT: A 1784 LEU cc_start: 0.8199 (mt) cc_final: 0.7520 (pp) REVERT: B 94 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7764 (mt) REVERT: C 126 GLU cc_start: 0.8033 (tp30) cc_final: 0.7783 (tp30) REVERT: C 225 MET cc_start: 0.6714 (ppp) cc_final: 0.5840 (ppp) REVERT: C 286 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7389 (mp) REVERT: C 288 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.7140 (m) REVERT: E 79 LYS cc_start: 0.6301 (mmtt) cc_final: 0.5999 (mmtt) REVERT: E 136 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: E 256 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6664 (tmm-80) REVERT: F 139 MET cc_start: 0.6727 (ttt) cc_final: 0.6477 (ttt) REVERT: F 211 TYR cc_start: 0.7948 (m-80) cc_final: 0.7721 (m-10) REVERT: F 246 HIS cc_start: 0.6945 (p90) cc_final: 0.6712 (p90) REVERT: G 49 GLN cc_start: 0.6821 (tp40) cc_final: 0.6369 (tm-30) REVERT: G 139 MET cc_start: 0.7763 (tpp) cc_final: 0.7484 (ttm) REVERT: G 154 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7647 (mt) REVERT: G 177 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7815 (p0) REVERT: G 199 MET cc_start: 0.7104 (tmm) cc_final: 0.6745 (tmm) REVERT: H 146 ARG cc_start: 0.7757 (ptt-90) cc_final: 0.7393 (ptt-90) REVERT: H 164 LYS cc_start: 0.5657 (OUTLIER) cc_final: 0.5144 (mmmt) REVERT: H 229 MET cc_start: 0.6567 (tpp) cc_final: 0.6206 (tpt) REVERT: H 254 LYS cc_start: 0.6636 (mttt) cc_final: 0.5983 (mtmm) outliers start: 144 outliers final: 89 residues processed: 387 average time/residue: 0.3145 time to fit residues: 191.7358 Evaluate side-chains 360 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 261 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1172 LYS Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1384 THR Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1775 ILE Chi-restraints excluded: chain A residue 1779 PHE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 164 LYS Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 262 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 ASN ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN B 324 HIS ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN F 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22186 Z= 0.383 Angle : 0.663 9.344 29991 Z= 0.338 Chirality : 0.045 0.202 3481 Planarity : 0.004 0.066 3815 Dihedral : 7.890 159.549 3043 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 6.00 % Allowed : 24.98 % Favored : 69.02 % 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: -0.70 (0.16), residues: 2734 helix: 0.32 (0.15), residues: 1267 sheet: -0.73 (0.22), residues: 498 loop : -1.23 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1403 HIS 0.012 0.002 HIS G 153 PHE 0.039 0.002 PHE H 215 TYR 0.021 0.003 TYR A1058 ARG 0.008 0.001 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 284 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1172 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7479 (tptp) REVERT: A 1394 ARG cc_start: 0.6332 (ttt90) cc_final: 0.5201 (mtp85) REVERT: A 1515 LEU cc_start: 0.5547 (mt) cc_final: 0.5267 (mt) REVERT: A 1644 HIS cc_start: 0.8135 (m90) cc_final: 0.7788 (m-70) REVERT: A 1775 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7907 (mp) REVERT: A 1818 ARG cc_start: 0.3999 (OUTLIER) cc_final: 0.2913 (mmp-170) REVERT: C 286 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7404 (mp) REVERT: C 288 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.7271 (m) REVERT: D 194 CYS cc_start: 0.8490 (m) cc_final: 0.7966 (m) REVERT: E 79 LYS cc_start: 0.6378 (mmtt) cc_final: 0.6087 (mmtt) REVERT: E 256 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6635 (tmm-80) REVERT: E 260 ASN cc_start: 0.8256 (m-40) cc_final: 0.7804 (m-40) REVERT: E 282 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8596 (tt) REVERT: F 139 MET cc_start: 0.6818 (ttt) cc_final: 0.6583 (ttt) REVERT: F 211 TYR cc_start: 0.7986 (m-80) cc_final: 0.7749 (m-10) REVERT: F 246 HIS cc_start: 0.6890 (p90) cc_final: 0.6673 (p90) REVERT: G 154 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7705 (mt) REVERT: G 177 ASN cc_start: 0.8064 (OUTLIER) cc_final: 0.7848 (p0) REVERT: G 199 MET cc_start: 0.7164 (tmm) cc_final: 0.6820 (tmm) REVERT: H 146 ARG cc_start: 0.7834 (ptt-90) cc_final: 0.7425 (ptt-90) REVERT: H 169 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.8078 (t80) REVERT: H 229 MET cc_start: 0.6747 (tpp) cc_final: 0.6447 (tpt) REVERT: H 254 LYS cc_start: 0.6695 (mttt) cc_final: 0.5977 (mtmm) outliers start: 146 outliers final: 93 residues processed: 404 average time/residue: 0.3240 time to fit residues: 204.9508 Evaluate side-chains 372 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 269 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain A residue 1172 LYS Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1303 LEU 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 1384 THR Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1688 LEU Chi-restraints excluded: chain A residue 1775 ILE Chi-restraints excluded: chain A residue 1779 PHE Chi-restraints excluded: chain A residue 1793 SER Chi-restraints excluded: chain A residue 1818 ARG Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 169 PHE Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 108 optimal weight: 0.1980 chunk 224 optimal weight: 0.9990 chunk 181 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 134 optimal weight: 10.0000 chunk 235 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 ASN ** A1481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN B 235 ASN ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN G 213 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22186 Z= 0.214 Angle : 0.570 9.545 29991 Z= 0.289 Chirality : 0.042 0.186 3481 Planarity : 0.004 0.042 3815 Dihedral : 7.455 156.009 3039 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.97 % Allowed : 26.09 % Favored : 68.94 % 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: -0.36 (0.16), residues: 2734 helix: 0.67 (0.15), residues: 1267 sheet: -0.66 (0.22), residues: 512 loop : -1.08 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1403 HIS 0.013 0.001 HIS G 153 PHE 0.030 0.001 PHE H 215 TYR 0.015 0.002 TYR E 318 ARG 0.006 0.000 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 276 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1515 LEU cc_start: 0.5554 (mt) cc_final: 0.5328 (mt) REVERT: A 1644 HIS cc_start: 0.8106 (m90) cc_final: 0.7769 (m-70) REVERT: A 1775 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7909 (mp) REVERT: C 286 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7350 (mp) REVERT: D 109 ASN cc_start: 0.6534 (OUTLIER) cc_final: 0.6290 (p0) REVERT: D 194 CYS cc_start: 0.8444 (m) cc_final: 0.7894 (m) REVERT: D 356 MET cc_start: 0.8593 (tmm) cc_final: 0.8331 (tmm) REVERT: E 79 LYS cc_start: 0.6369 (mmtt) cc_final: 0.6073 (mmtt) REVERT: E 136 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: E 256 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6595 (tmm-80) REVERT: E 260 ASN cc_start: 0.8147 (m-40) cc_final: 0.7917 (m-40) REVERT: E 282 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8569 (tt) REVERT: G 154 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7427 (mt) REVERT: G 199 MET cc_start: 0.7088 (tmm) cc_final: 0.6862 (tmm) REVERT: G 251 LEU cc_start: 0.9034 (tp) cc_final: 0.8825 (tp) REVERT: H 146 ARG cc_start: 0.7821 (ptt-90) cc_final: 0.7396 (ptt-90) REVERT: H 229 MET cc_start: 0.6995 (tpp) cc_final: 0.6783 (tpt) REVERT: H 254 LYS cc_start: 0.6644 (mttt) cc_final: 0.5934 (mtmm) outliers start: 121 outliers final: 77 residues processed: 372 average time/residue: 0.3226 time to fit residues: 188.5337 Evaluate side-chains 349 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 265 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1186 ASN Chi-restraints excluded: chain A residue 1188 GLN 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 1387 THR Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1766 ASP Chi-restraints excluded: chain A residue 1775 ILE Chi-restraints excluded: chain A residue 1779 PHE Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 263 optimal weight: 20.0000 chunk 218 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN B 287 HIS C 9 GLN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22186 Z= 0.340 Angle : 0.637 10.106 29991 Z= 0.324 Chirality : 0.044 0.236 3481 Planarity : 0.004 0.041 3815 Dihedral : 7.486 155.237 3039 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.59 % Allowed : 25.84 % Favored : 68.57 % 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: -0.55 (0.16), residues: 2734 helix: 0.50 (0.15), residues: 1264 sheet: -0.76 (0.22), residues: 506 loop : -1.17 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1403 HIS 0.018 0.002 HIS B 287 PHE 0.025 0.002 PHE H 215 TYR 0.020 0.002 TYR G 250 ARG 0.011 0.001 ARG A1394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 277 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1067 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7345 (mt) REVERT: A 1515 LEU cc_start: 0.5539 (mt) cc_final: 0.5269 (mt) REVERT: A 1644 HIS cc_start: 0.8124 (m90) cc_final: 0.7803 (m-70) REVERT: A 1775 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7890 (mp) REVERT: A 1818 ARG cc_start: 0.4101 (OUTLIER) cc_final: 0.3005 (mmp-170) REVERT: C 112 ARG cc_start: 0.8537 (mmt-90) cc_final: 0.8033 (mpt180) REVERT: C 286 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7342 (mp) REVERT: C 288 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8428 (p) REVERT: D 356 MET cc_start: 0.8604 (tmm) cc_final: 0.8388 (tmm) REVERT: E 79 LYS cc_start: 0.6427 (mmtt) cc_final: 0.6135 (mmtt) REVERT: E 136 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7427 (tm-30) REVERT: E 256 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6538 (tmm-80) REVERT: E 260 ASN cc_start: 0.8224 (m-40) cc_final: 0.7700 (m-40) REVERT: E 282 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8663 (tt) REVERT: E 318 TYR cc_start: 0.7955 (m-80) cc_final: 0.7395 (m-10) REVERT: E 333 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6804 (tm-30) REVERT: E 338 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8532 (mtmt) REVERT: F 25 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.7914 (pp20) REVERT: F 139 MET cc_start: 0.6950 (ttt) cc_final: 0.6558 (ttt) REVERT: F 211 TYR cc_start: 0.7806 (m-80) cc_final: 0.7577 (m-10) REVERT: G 154 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7671 (mt) REVERT: G 199 MET cc_start: 0.7098 (tmm) cc_final: 0.6814 (tmm) REVERT: H 146 ARG cc_start: 0.7797 (ptt-90) cc_final: 0.7091 (ptt-90) REVERT: H 169 PHE cc_start: 0.8324 (t80) cc_final: 0.8037 (t80) outliers start: 136 outliers final: 90 residues processed: 388 average time/residue: 0.3175 time to fit residues: 194.3756 Evaluate side-chains 369 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 268 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1188 GLN 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 1387 THR Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1766 ASP Chi-restraints excluded: chain A residue 1775 ILE Chi-restraints excluded: chain A residue 1779 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1793 SER Chi-restraints excluded: chain A residue 1818 ARG Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 149 optimal weight: 0.5980 chunk 192 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 221 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 164 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN C 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22186 Z= 0.168 Angle : 0.566 10.214 29991 Z= 0.286 Chirality : 0.041 0.178 3481 Planarity : 0.004 0.043 3815 Dihedral : 7.164 151.594 3039 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.19 % Allowed : 27.44 % Favored : 68.36 % 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: -0.10 (0.16), residues: 2734 helix: 0.89 (0.15), residues: 1258 sheet: -0.63 (0.22), residues: 520 loop : -0.90 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1403 HIS 0.014 0.001 HIS G 153 PHE 0.023 0.001 PHE H 215 TYR 0.017 0.001 TYR G 250 ARG 0.009 0.000 ARG F 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 293 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1325 MET cc_start: 0.7128 (mmt) cc_final: 0.6773 (mmm) REVERT: A 1515 LEU cc_start: 0.5584 (mt) cc_final: 0.5360 (mt) REVERT: A 1644 HIS cc_start: 0.8116 (m90) cc_final: 0.7814 (m-70) REVERT: A 1707 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6802 (mm-30) REVERT: A 1818 ARG cc_start: 0.3937 (OUTLIER) cc_final: 0.2842 (mmp-170) REVERT: B 154 LEU cc_start: 0.8735 (tp) cc_final: 0.8429 (tt) REVERT: C 112 ARG cc_start: 0.8394 (mmt-90) cc_final: 0.7970 (mpt180) REVERT: C 286 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7317 (mp) REVERT: C 288 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.6950 (m) REVERT: D 194 CYS cc_start: 0.8417 (m) cc_final: 0.8014 (m) REVERT: E 156 MET cc_start: 0.5943 (ppp) cc_final: 0.5554 (ppp) REVERT: E 256 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6569 (tmm-80) REVERT: E 260 ASN cc_start: 0.8184 (m-40) cc_final: 0.7780 (m-40) REVERT: E 282 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8601 (tt) REVERT: E 318 TYR cc_start: 0.7786 (m-80) cc_final: 0.7072 (m-80) REVERT: E 338 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8387 (mtmt) REVERT: F 25 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7722 (pp20) REVERT: F 139 MET cc_start: 0.6864 (ttt) cc_final: 0.6521 (ttt) REVERT: G 122 ASP cc_start: 0.6537 (p0) cc_final: 0.5958 (p0) REVERT: H 146 ARG cc_start: 0.7761 (ptt-90) cc_final: 0.7333 (ptt-90) REVERT: H 169 PHE cc_start: 0.8251 (t80) cc_final: 0.8040 (t80) REVERT: H 229 MET cc_start: 0.6484 (tpp) cc_final: 0.6112 (tpt) outliers start: 102 outliers final: 67 residues processed: 372 average time/residue: 0.3296 time to fit residues: 191.7513 Evaluate side-chains 347 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 273 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1650 SER Chi-restraints excluded: chain A residue 1766 ASP Chi-restraints excluded: chain A residue 1818 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 206 optimal weight: 0.0170 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1147 GLN ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22186 Z= 0.213 Angle : 0.587 12.413 29991 Z= 0.295 Chirality : 0.042 0.268 3481 Planarity : 0.004 0.042 3815 Dihedral : 7.030 151.709 3037 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.44 % Allowed : 27.20 % Favored : 68.36 % 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: -0.08 (0.16), residues: 2734 helix: 0.93 (0.15), residues: 1257 sheet: -0.63 (0.23), residues: 516 loop : -0.91 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A1403 HIS 0.015 0.001 HIS G 153 PHE 0.021 0.001 PHE H 215 TYR 0.018 0.002 TYR G 250 ARG 0.009 0.000 ARG F 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 272 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1515 LEU cc_start: 0.5594 (mt) cc_final: 0.5358 (mt) REVERT: A 1644 HIS cc_start: 0.8122 (m90) cc_final: 0.7814 (m-70) REVERT: A 1646 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8237 (tt) REVERT: A 1707 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6844 (mm-30) REVERT: A 1818 ARG cc_start: 0.3979 (OUTLIER) cc_final: 0.2926 (mmp-170) REVERT: C 112 ARG cc_start: 0.8429 (mmt-90) cc_final: 0.8022 (mpt180) REVERT: C 286 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7319 (mp) REVERT: C 288 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.7007 (m) REVERT: D 109 ASN cc_start: 0.6413 (OUTLIER) cc_final: 0.6149 (p0) REVERT: D 194 CYS cc_start: 0.8367 (m) cc_final: 0.7988 (m) REVERT: E 136 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: E 156 MET cc_start: 0.5902 (ppp) cc_final: 0.5500 (ppp) REVERT: E 256 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6610 (tmm-80) REVERT: E 260 ASN cc_start: 0.8160 (m-40) cc_final: 0.7738 (m-40) REVERT: E 282 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8626 (tt) REVERT: F 25 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7801 (pp20) REVERT: F 139 MET cc_start: 0.6921 (ttt) cc_final: 0.6505 (ttt) REVERT: G 122 ASP cc_start: 0.6552 (p0) cc_final: 0.6001 (p0) REVERT: G 251 LEU cc_start: 0.8985 (tp) cc_final: 0.8745 (tp) REVERT: H 169 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.8072 (t80) REVERT: H 229 MET cc_start: 0.6665 (tpp) cc_final: 0.6343 (tpt) outliers start: 108 outliers final: 78 residues processed: 362 average time/residue: 0.3091 time to fit residues: 175.3899 Evaluate side-chains 348 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 260 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1650 SER Chi-restraints excluded: chain A residue 1766 ASP Chi-restraints excluded: chain A residue 1818 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 169 PHE Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 229 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 231 optimal weight: 7.9990 chunk 243 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 266 GLN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22186 Z= 0.280 Angle : 0.625 11.827 29991 Z= 0.316 Chirality : 0.043 0.290 3481 Planarity : 0.004 0.047 3815 Dihedral : 7.109 151.388 3036 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.31 % Allowed : 27.40 % Favored : 68.28 % 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: -0.22 (0.16), residues: 2734 helix: 0.78 (0.15), residues: 1259 sheet: -0.67 (0.23), residues: 508 loop : -0.95 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A1403 HIS 0.016 0.001 HIS G 153 PHE 0.020 0.002 PHE H 215 TYR 0.019 0.002 TYR G 250 ARG 0.010 0.000 ARG H 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 266 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1325 MET cc_start: 0.7205 (mmt) cc_final: 0.6849 (mmm) REVERT: A 1515 LEU cc_start: 0.5762 (mt) cc_final: 0.5529 (mt) REVERT: A 1644 HIS cc_start: 0.8140 (m90) cc_final: 0.7830 (m-70) REVERT: A 1646 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8185 (tt) REVERT: A 1707 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6825 (mm-30) REVERT: A 1818 ARG cc_start: 0.3987 (OUTLIER) cc_final: 0.2943 (mmp-170) REVERT: C 112 ARG cc_start: 0.8475 (mmt-90) cc_final: 0.8069 (mpt180) REVERT: C 286 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7358 (mp) REVERT: C 288 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8349 (p) REVERT: D 109 ASN cc_start: 0.6387 (OUTLIER) cc_final: 0.6106 (p0) REVERT: E 79 LYS cc_start: 0.6444 (mmtt) cc_final: 0.6162 (mmtt) REVERT: E 136 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7519 (tm-30) REVERT: E 156 MET cc_start: 0.5986 (ppp) cc_final: 0.5561 (ppp) REVERT: E 256 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6543 (tmm-80) REVERT: E 260 ASN cc_start: 0.8195 (m-40) cc_final: 0.7771 (m-40) REVERT: E 282 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8635 (tt) REVERT: G 122 ASP cc_start: 0.6542 (p0) cc_final: 0.5998 (p0) REVERT: G 210 ARG cc_start: 0.6947 (tpm170) cc_final: 0.6681 (tpm170) REVERT: G 251 LEU cc_start: 0.9068 (tp) cc_final: 0.8828 (tp) REVERT: H 146 ARG cc_start: 0.7713 (ptt-90) cc_final: 0.7420 (ptt-90) REVERT: H 169 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.8070 (t80) REVERT: H 229 MET cc_start: 0.6771 (tpp) cc_final: 0.6490 (tpt) outliers start: 105 outliers final: 82 residues processed: 353 average time/residue: 0.3223 time to fit residues: 177.8443 Evaluate side-chains 350 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 259 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1650 SER Chi-restraints excluded: chain A residue 1766 ASP Chi-restraints excluded: chain A residue 1779 PHE Chi-restraints excluded: chain A residue 1793 SER Chi-restraints excluded: chain A residue 1818 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 169 PHE Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 270 optimal weight: 7.9990 chunk 249 optimal weight: 20.0000 chunk 215 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 132 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22186 Z= 0.189 Angle : 0.606 12.658 29991 Z= 0.304 Chirality : 0.042 0.280 3481 Planarity : 0.004 0.046 3815 Dihedral : 6.987 149.564 3036 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.70 % Allowed : 28.06 % Favored : 68.24 % 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: -0.08 (0.16), residues: 2734 helix: 0.89 (0.15), residues: 1258 sheet: -0.59 (0.23), residues: 506 loop : -0.88 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1403 HIS 0.015 0.001 HIS G 153 PHE 0.020 0.001 PHE H 215 TYR 0.021 0.002 TYR E 318 ARG 0.012 0.000 ARG F 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 271 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1325 MET cc_start: 0.7058 (mmt) cc_final: 0.6717 (mmm) REVERT: A 1515 LEU cc_start: 0.5746 (mt) cc_final: 0.5527 (mt) REVERT: A 1644 HIS cc_start: 0.8125 (m90) cc_final: 0.7825 (m-70) REVERT: A 1646 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8208 (tt) REVERT: A 1818 ARG cc_start: 0.3958 (OUTLIER) cc_final: 0.2964 (mmp-170) REVERT: C 98 ILE cc_start: 0.6693 (OUTLIER) cc_final: 0.6230 (pt) REVERT: C 112 ARG cc_start: 0.8407 (mmt-90) cc_final: 0.7857 (mpt180) REVERT: C 213 MET cc_start: 0.7878 (tpp) cc_final: 0.7517 (mpp) REVERT: C 286 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7289 (mp) REVERT: C 288 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.6982 (m) REVERT: E 136 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7456 (tm-30) REVERT: E 156 MET cc_start: 0.5877 (ppp) cc_final: 0.5482 (ppp) REVERT: E 256 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6600 (tmm-80) REVERT: E 260 ASN cc_start: 0.8183 (m-40) cc_final: 0.7771 (m-40) REVERT: E 282 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8628 (tt) REVERT: F 25 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7645 (pp20) REVERT: G 122 ASP cc_start: 0.6394 (p0) cc_final: 0.5882 (p0) REVERT: G 210 ARG cc_start: 0.6841 (tpm170) cc_final: 0.6539 (tpm170) REVERT: G 251 LEU cc_start: 0.8969 (tp) cc_final: 0.8579 (tp) REVERT: H 146 ARG cc_start: 0.7712 (ptt-90) cc_final: 0.7417 (ptt-90) REVERT: H 229 MET cc_start: 0.6858 (tpp) cc_final: 0.6612 (tpt) outliers start: 90 outliers final: 74 residues processed: 344 average time/residue: 0.3187 time to fit residues: 172.5250 Evaluate side-chains 339 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 256 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1650 SER Chi-restraints excluded: chain A residue 1766 ASP Chi-restraints excluded: chain A residue 1779 PHE Chi-restraints excluded: chain A residue 1793 SER Chi-restraints excluded: chain A residue 1818 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 4.9990 chunk 229 optimal weight: 0.0970 chunk 66 optimal weight: 5.9990 chunk 198 optimal weight: 0.0980 chunk 31 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 216 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 221 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.172652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.131353 restraints weight = 43236.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.131756 restraints weight = 28425.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.132522 restraints weight = 22297.131| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22186 Z= 0.156 Angle : 0.597 12.561 29991 Z= 0.298 Chirality : 0.041 0.173 3481 Planarity : 0.004 0.044 3815 Dihedral : 6.758 147.233 3036 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.00 % Allowed : 28.72 % Favored : 68.28 % 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: 0.16 (0.16), residues: 2734 helix: 1.11 (0.15), residues: 1251 sheet: -0.46 (0.23), residues: 510 loop : -0.79 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A1403 HIS 0.015 0.001 HIS G 153 PHE 0.027 0.001 PHE H 215 TYR 0.021 0.001 TYR E 318 ARG 0.011 0.000 ARG F 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4300.17 seconds wall clock time: 78 minutes 21.25 seconds (4701.25 seconds total)