Starting phenix.real_space_refine on Tue Jul 23 08:59:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui9_42289/07_2024/8ui9_42289_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui9_42289/07_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_42289/07_2024/8ui9_42289.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui9_42289/07_2024/8ui9_42289.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui9_42289/07_2024/8ui9_42289_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui9_42289/07_2024/8ui9_42289_neut.cif" } 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 11.82, per 1000 atoms: 0.54 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: 8.01 Conformation dependent library (CDL) restraints added in 5.2 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... Secondary structure from input PDB file: 113 helices and 15 sheets defined 49.9% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 890 through 895 removed outlier: 3.645A pdb=" N THR A 894 " --> pdb=" O CYS A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 955 Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 1053 through 1058 Processing helix chain 'A' and resid 1062 through 1066 Processing helix chain 'A' and resid 1069 through 1098 Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1163 through 1177 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 1316 through 1327 Processing helix chain 'A' and resid 1340 through 1345 Processing helix chain 'A' and resid 1358 through 1373 Processing helix chain 'A' and resid 1378 through 1389 removed outlier: 4.348A pdb=" N PHE A1382 " --> pdb=" O ASP A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1405 Processing helix chain 'A' and resid 1457 through 1463 removed outlier: 3.585A pdb=" N THR A1461 " --> pdb=" O GLY A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1474 through 1481 removed outlier: 3.585A pdb=" N HIS A1481 " --> pdb=" O SER A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1501 Processing helix chain 'A' and resid 1505 through 1510 Processing helix chain 'A' and resid 1510 through 1515 Processing helix chain 'A' and resid 1633 through 1662 Processing helix chain 'A' and resid 1699 through 1729 removed outlier: 4.010A pdb=" N GLN A1703 " --> pdb=" O GLY A1699 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A1705 " --> pdb=" O THR A1701 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1738 removed outlier: 3.665A pdb=" N CYS A1734 " --> pdb=" O THR A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1746 Processing helix chain 'A' and resid 1764 through 1779 removed outlier: 3.524A pdb=" N ALA A1768 " --> pdb=" O ASN A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1780 through 1781 No H-bonds generated for 'chain 'A' and resid 1780 through 1781' Processing helix chain 'A' and resid 1782 through 1787 removed outlier: 3.634A pdb=" N LEU A1785 " --> pdb=" O ARG A1782 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR A1786 " --> pdb=" O SER A1783 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A1787 " --> pdb=" O LEU A1784 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1782 through 1787' Processing helix chain 'A' and resid 1789 through 1814 Proline residue: A1799 - end of helix removed outlier: 3.530A pdb=" N GLY A1814 " --> pdb=" O LEU A1810 " (cutoff:3.500A) Processing helix chain 'A' and resid 1817 through 1822 removed outlier: 3.513A pdb=" N PHE A1820 " --> pdb=" O LYS A1817 " (cutoff:3.500A) Processing helix chain 'A' and resid 1832 through 1840 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.241A 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 146 Processing helix chain 'B' and resid 147 through 160 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) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.543A pdb=" N GLN B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 210 Processing helix chain 'B' and resid 214 through 225 Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.977A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 removed outlier: 3.565A pdb=" N GLY B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 350 removed outlier: 3.545A pdb=" N MET B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) 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 3 through 9 removed outlier: 4.289A pdb=" N LYS C 7 " --> pdb=" O THR C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 removed outlier: 3.904A pdb=" N TYR C 26 " --> pdb=" O TRP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 66 through 78 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.641A pdb=" N PHE C 83 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 removed outlier: 3.903A pdb=" N ARG C 102 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 131 through 145 removed outlier: 4.077A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 178 through 194 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 210 removed outlier: 3.835A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.547A pdb=" N GLN C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 289 removed outlier: 3.596A pdb=" N ILE C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 317 through 339 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 56 through 68 Processing helix chain 'D' and resid 83 through 96 Processing helix chain 'D' and resid 97 through 102 removed outlier: 4.399A pdb=" N ARG D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 129 removed outlier: 4.477A pdb=" N VAL D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 170 Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.718A pdb=" N ARG D 185 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 193 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'D' and resid 223 through 235 Processing helix chain 'D' and resid 237 through 252 Processing helix chain 'D' and resid 258 through 267 removed outlier: 3.744A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.687A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'D' and resid 320 through 341 Processing helix chain 'D' and resid 343 through 362 removed outlier: 4.369A pdb=" N ASN D 362 " --> pdb=" O GLN D 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.667A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 33 removed outlier: 3.505A pdb=" N CYS E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 65 removed outlier: 4.093A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.916A pdb=" N ALA E 100 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY E 101 " --> pdb=" O SER E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 103 through 122 removed outlier: 4.413A pdb=" N VAL E 107 " --> pdb=" O SER E 103 " (cutoff:3.500A) 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 141 through 155 Processing helix chain 'E' and resid 172 through 177 removed outlier: 3.598A pdb=" N ARG E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 203 Processing helix chain 'E' and resid 208 through 219 removed outlier: 3.547A pdb=" N ALA E 212 " --> pdb=" O PRO E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.641A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 Processing helix chain 'E' and resid 287 through 300 removed outlier: 3.664A pdb=" N ILE E 291 " --> pdb=" O PRO E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 325 removed outlier: 4.591A pdb=" N GLU E 310 " --> pdb=" O GLN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 348 removed outlier: 4.349A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 79 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 155 Processing helix chain 'F' and resid 209 through 217 Processing helix chain 'G' and resid 9 through 18 Processing helix chain 'G' and resid 72 through 80 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 155 Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 222 Proline residue: G 220 - end of helix No H-bonds generated for 'chain 'G' and resid 217 through 222' Processing helix chain 'H' and resid 9 through 17 removed outlier: 4.020A pdb=" N LYS H 13 " --> pdb=" O GLY H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 21 removed outlier: 4.155A pdb=" N ASP H 21 " --> pdb=" O ALA H 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 18 through 21' Processing helix chain 'H' and resid 72 through 80 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) removed outlier: 3.599A pdb=" N LYS H 80 " --> pdb=" O SER H 76 " (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 217 removed outlier: 3.880A pdb=" N LYS H 217 " --> pdb=" O ASN H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 222 removed outlier: 3.762A pdb=" N SER H 222 " --> pdb=" O THR H 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1152 through 1156 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) removed outlier: 8.588A pdb=" N ILE A1333 " --> pdb=" O SER A1300 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A1302 " --> pdb=" O ILE A1333 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N THR A1335 " --> pdb=" O ILE A1302 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE A1304 " --> pdb=" O THR A1335 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR A1127 " --> pdb=" O GLU A1350 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE A1352 " --> pdb=" O THR A1127 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU A1129 " --> pdb=" O ILE A1352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1519 through 1521 removed outlier: 3.711A pdb=" N VAL A1749 " --> pdb=" O ASP A1520 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 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) removed outlier: 6.072A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N CYS B 171 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE B 74 " --> pdb=" O CYS B 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.279A pdb=" N LEU C 88 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ASP C 125 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU C 90 " --> pdb=" O ASP C 125 " (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) removed outlier: 6.530A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 196 through 197 removed outlier: 6.732A pdb=" N ASP C 196 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 105 through 109 removed outlier: 6.174A pdb=" N LEU D 106 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASP D 150 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU D 108 " --> pdb=" O ASP D 150 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 147 " --> pdb=" O ARG D 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 68 through 75 removed outlier: 6.616A pdb=" N LEU E 39 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 60 through 61 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=AA9, 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=AB1, first strand: chain 'F' and resid 166 through 171 removed outlier: 3.756A pdb=" N SER F 170 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU F 205 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing sheet with id=AB2, 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=AB3, 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=AB4, first strand: chain 'H' and resid 60 through 61 removed outlier: 3.600A pdb=" N GLU H 3 " --> pdb=" O ARG H 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing sheet with id=AB5, 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=AB6, first strand: chain 'H' and resid 178 through 183 1102 hydrogen bonds defined for protein. 3201 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: 7.62 Time building geometry restraints manager: 8.84 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: 201 2.57 - 3.16: 16877 3.16 - 3.74: 35380 3.74 - 4.32: 46634 4.32 - 4.90: 78102 Nonbonded interactions: 177194 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 177189 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 60.540 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.890 ------------------------------------------------------------------------------- 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= 0.312 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 : 2.398 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: 0.3248 time to fit residues: 152.0576 Evaluate side-chains 276 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 266 time to evaluate : 2.499 ------------------------------------------------------------------------------- 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: 2.9990 chunk 70 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 213 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 129 optimal weight: 0.0770 chunk 158 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- 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** C 300 HIS ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22186 Z= 0.283 Angle : 0.604 7.900 29991 Z= 0.310 Chirality : 0.042 0.181 3481 Planarity : 0.004 0.072 3815 Dihedral : 8.011 161.615 3054 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.70 % Allowed : 23.25 % Favored : 73.05 % 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: -0.38 (0.16), residues: 2734 helix: 0.50 (0.14), residues: 1247 sheet: -0.46 (0.22), residues: 510 loop : -0.97 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1403 HIS 0.009 0.001 HIS G 153 PHE 0.034 0.002 PHE H 214 TYR 0.019 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 360 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 270 time to evaluate : 2.669 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: C 112 ARG cc_start: 0.8362 (mmt-90) cc_final: 0.8091 (mpt-90) REVERT: C 288 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.6910 (m) REVERT: D 194 CYS cc_start: 0.8330 (m) cc_final: 0.7773 (m) REVERT: E 275 ARG cc_start: 0.8777 (tmt90) cc_final: 0.8554 (ttt90) REVERT: F 139 MET cc_start: 0.6522 (ttt) cc_final: 0.6289 (ttt) REVERT: G 49 GLN cc_start: 0.6849 (tp40) cc_final: 0.6349 (tm-30) REVERT: H 146 ARG cc_start: 0.7874 (ptt-90) cc_final: 0.7421 (ptt-90) REVERT: H 169 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: H 254 LYS cc_start: 0.6774 (mttt) cc_final: 0.6085 (mtmm) outliers start: 90 outliers final: 55 residues processed: 338 average time/residue: 0.3220 time to fit residues: 171.5191 Evaluate side-chains 318 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 261 time to evaluate : 2.548 ------------------------------------------------------------------------------- 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 A residue 1787 VAL 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 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 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 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 157 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 ASP 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 151 THR 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 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 43 SER Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 219 THR 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 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: 20.0000 chunk 76 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 247 optimal weight: 7.9990 chunk 267 optimal weight: 6.9990 chunk 220 optimal weight: 20.0000 chunk 245 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 A1503 ASN A1669 GLN ** A1754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** 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 109 GLN H 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22186 Z= 0.263 Angle : 0.585 7.922 29991 Z= 0.299 Chirality : 0.042 0.200 3481 Planarity : 0.004 0.055 3815 Dihedral : 7.736 160.932 3046 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.64 % Allowed : 23.87 % Favored : 71.49 % 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: -0.11 (0.16), residues: 2734 helix: 0.82 (0.15), residues: 1247 sheet: -0.44 (0.22), residues: 501 loop : -0.91 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1403 HIS 0.011 0.001 HIS G 153 PHE 0.022 0.002 PHE H 215 TYR 0.015 0.002 TYR F 239 ARG 0.005 0.000 ARG H 146 *********************** 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 393 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 280 time to evaluate : 2.574 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 1172 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7319 (tptm) REVERT: A 1775 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7861 (mp) REVERT: A 1784 LEU cc_start: 0.8002 (mt) cc_final: 0.7333 (pp) REVERT: C 225 MET cc_start: 0.6568 (ppp) cc_final: 0.5907 (ppp) REVERT: C 286 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7409 (mp) REVERT: C 288 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.6976 (m) REVERT: D 137 ASP cc_start: 0.5091 (OUTLIER) cc_final: 0.4883 (m-30) REVERT: D 194 CYS cc_start: 0.8375 (m) cc_final: 0.7960 (m) REVERT: D 356 MET cc_start: 0.8589 (tmm) cc_final: 0.8347 (tmm) REVERT: F 139 MET cc_start: 0.6569 (ttt) cc_final: 0.6300 (ttt) REVERT: G 49 GLN cc_start: 0.6775 (tp40) cc_final: 0.6262 (tm-30) REVERT: G 154 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7382 (mt) REVERT: G 177 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7739 (p0) REVERT: G 184 GLN cc_start: 0.8276 (tp40) cc_final: 0.7954 (tp40) REVERT: H 146 ARG cc_start: 0.7816 (ptt-90) cc_final: 0.7531 (ptt-90) REVERT: H 164 LYS cc_start: 0.5693 (OUTLIER) cc_final: 0.5246 (mmmt) REVERT: H 229 MET cc_start: 0.6347 (tpp) cc_final: 0.6063 (tpt) REVERT: H 237 VAL cc_start: 0.7899 (t) cc_final: 0.7441 (p) REVERT: H 254 LYS cc_start: 0.6807 (mttt) cc_final: 0.6095 (mtmm) outliers start: 113 outliers final: 72 residues processed: 365 average time/residue: 0.3228 time to fit residues: 185.7863 Evaluate side-chains 345 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 265 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1387 THR Chi-restraints excluded: chain A residue 1403 TRP Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1669 GLN Chi-restraints excluded: chain A residue 1775 ILE 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 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 3 THR 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 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 D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 263 THR 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 347 GLN Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 93 LEU 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 151 THR 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 16 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 41 ASP 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 111 VAL 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 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 G residue 219 THR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 164 LYS Chi-restraints excluded: chain H residue 241 ILE 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: 0.8980 chunk 186 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 248 optimal weight: 30.0000 chunk 262 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 235 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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** ** A1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN B 272 ASN B 324 HIS ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 224 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 22186 Z= 0.420 Angle : 0.687 9.019 29991 Z= 0.353 Chirality : 0.045 0.203 3481 Planarity : 0.005 0.045 3815 Dihedral : 7.872 160.699 3045 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 6.04 % Allowed : 24.98 % Favored : 68.98 % 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: -0.48 (0.16), residues: 2734 helix: 0.51 (0.14), residues: 1264 sheet: -0.55 (0.22), residues: 491 loop : -1.16 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1403 HIS 0.010 0.002 HIS G 153 PHE 0.034 0.002 PHE H 215 TYR 0.022 0.003 TYR F 239 ARG 0.009 0.001 ARG A1394 *********************** 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 428 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 281 time to evaluate : 2.545 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: symmetry clash REVERT: A 1172 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7435 (tptm) REVERT: A 1386 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7409 (mm) REVERT: A 1644 HIS cc_start: 0.8118 (m90) cc_final: 0.7779 (m-70) REVERT: A 1775 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7888 (mp) REVERT: B 94 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7829 (mt) REVERT: C 263 TYR cc_start: 0.8030 (t80) cc_final: 0.7828 (t80) REVERT: C 286 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7456 (mp) REVERT: C 288 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8395 (p) REVERT: D 109 ASN cc_start: 0.6621 (OUTLIER) cc_final: 0.6419 (p0) REVERT: D 194 CYS cc_start: 0.8554 (m) cc_final: 0.8147 (m) REVERT: E 79 LYS cc_start: 0.6450 (mmtt) cc_final: 0.6145 (mmtt) REVERT: E 136 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7424 (tm-30) REVERT: E 256 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6554 (tmm-80) REVERT: E 260 ASN cc_start: 0.8171 (m-40) cc_final: 0.7686 (m-40) REVERT: E 275 ARG cc_start: 0.9026 (ttt90) cc_final: 0.8783 (ttt90) REVERT: F 139 MET cc_start: 0.6740 (ttt) cc_final: 0.6500 (ttt) REVERT: F 211 TYR cc_start: 0.8029 (m-80) cc_final: 0.7805 (m-10) REVERT: F 246 HIS cc_start: 0.6816 (p90) cc_final: 0.6615 (p90) REVERT: G 154 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7711 (mt) REVERT: G 177 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7735 (p0) REVERT: H 146 ARG cc_start: 0.7836 (ptt-90) cc_final: 0.7453 (ptt-90) REVERT: H 229 MET cc_start: 0.6531 (tpp) cc_final: 0.6173 (tpt) REVERT: H 237 VAL cc_start: 0.7990 (t) cc_final: 0.7484 (p) REVERT: H 254 LYS cc_start: 0.6766 (mttt) cc_final: 0.6036 (mtmm) outliers start: 147 outliers final: 93 residues processed: 397 average time/residue: 0.3278 time to fit residues: 204.5592 Evaluate side-chains 371 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 267 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1340 THR Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1386 LEU 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 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 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 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 98 ILE 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 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 227 ILE 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 314 VAL Chi-restraints excluded: chain D residue 347 GLN 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 52 ILE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 93 LEU 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 148 LEU 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 11 ILE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 41 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 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 121 LEU 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 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 159 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: 0.9990 chunk 149 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 134 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 ASN ** A1481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1754 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 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22186 Z= 0.265 Angle : 0.602 9.777 29991 Z= 0.305 Chirality : 0.042 0.196 3481 Planarity : 0.004 0.041 3815 Dihedral : 7.591 157.412 3044 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.38 % Allowed : 25.35 % Favored : 69.27 % 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: 1254 sheet: -0.56 (0.22), residues: 498 loop : -1.02 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1403 HIS 0.012 0.001 HIS G 153 PHE 0.034 0.002 PHE H 215 TYR 0.016 0.002 TYR F 133 ARG 0.005 0.000 ARG F 146 *********************** 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 417 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 286 time to evaluate : 2.646 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: symmetry clash REVERT: A 913 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6620 (mp) REVERT: A 1052 MET cc_start: 0.7115 (mmt) cc_final: 0.6852 (mtm) REVERT: A 1172 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7537 (tptm) REVERT: A 1325 MET cc_start: 0.7103 (mmt) cc_final: 0.6853 (mmm) REVERT: A 1386 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7340 (mm) REVERT: A 1644 HIS cc_start: 0.8127 (m90) cc_final: 0.7782 (m-70) REVERT: A 1775 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7878 (mp) REVERT: B 94 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7891 (mt) REVERT: C 286 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7416 (mp) REVERT: C 288 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8350 (p) REVERT: D 356 MET cc_start: 0.8631 (tmm) cc_final: 0.8364 (tmm) REVERT: E 79 LYS cc_start: 0.6385 (mmtt) cc_final: 0.6095 (mmtt) REVERT: E 136 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: E 256 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6591 (tmm-80) REVERT: E 260 ASN cc_start: 0.8074 (m-40) cc_final: 0.7849 (m-40) REVERT: E 338 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8474 (mtmt) REVERT: F 25 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7835 (pp20) REVERT: F 139 MET cc_start: 0.6839 (ttt) cc_final: 0.6620 (ttt) REVERT: F 211 TYR cc_start: 0.7996 (m-80) cc_final: 0.7724 (m-10) REVERT: F 246 HIS cc_start: 0.6771 (p90) cc_final: 0.6552 (p90) REVERT: G 139 MET cc_start: 0.7731 (tpp) cc_final: 0.7517 (ttm) REVERT: G 154 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7492 (mt) REVERT: G 177 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7779 (p0) REVERT: G 199 MET cc_start: 0.6939 (tmm) cc_final: 0.6602 (tmm) REVERT: H 119 MET cc_start: 0.6706 (mpp) cc_final: 0.6219 (mpp) REVERT: H 146 ARG cc_start: 0.7850 (ptt-90) cc_final: 0.7458 (ptt-90) REVERT: H 169 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7949 (t80) REVERT: H 237 VAL cc_start: 0.7934 (t) cc_final: 0.7435 (p) outliers start: 131 outliers final: 87 residues processed: 385 average time/residue: 0.3213 time to fit residues: 194.9790 Evaluate side-chains 371 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 270 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 913 LEU 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 1340 THR Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1468 ILE 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 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 146 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 282 LEU 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 98 ILE Chi-restraints excluded: chain C residue 105 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 D residue 41 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 347 GLN 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 93 LEU 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 338 LYS 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 25 GLU 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 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 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 187 ASN Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 169 PHE 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: 0.3980 chunk 236 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 263 optimal weight: 40.0000 chunk 218 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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** B 125 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22186 Z= 0.215 Angle : 0.584 9.899 29991 Z= 0.295 Chirality : 0.042 0.220 3481 Planarity : 0.004 0.040 3815 Dihedral : 7.326 154.585 3040 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.34 % Allowed : 25.97 % Favored : 68.69 % 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: -0.03 (0.16), residues: 2734 helix: 0.99 (0.15), residues: 1258 sheet: -0.54 (0.22), residues: 499 loop : -0.98 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1403 HIS 0.013 0.001 HIS G 153 PHE 0.028 0.001 PHE H 215 TYR 0.018 0.002 TYR G 250 ARG 0.008 0.000 ARG E 105 *********************** 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 414 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 284 time to evaluate : 2.540 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: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.7106 (mmt) cc_final: 0.6828 (mtm) REVERT: A 1386 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7327 (mm) REVERT: A 1461 THR cc_start: 0.5891 (OUTLIER) cc_final: 0.5678 (m) REVERT: A 1644 HIS cc_start: 0.8080 (m90) cc_final: 0.7758 (m-70) REVERT: A 1775 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7865 (mp) REVERT: A 1818 ARG cc_start: 0.3918 (OUTLIER) cc_final: 0.2889 (mmp-170) REVERT: A 1823 TYR cc_start: 0.6865 (t80) cc_final: 0.6033 (t80) REVERT: C 286 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7396 (mp) REVERT: C 288 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8305 (p) REVERT: D 190 LEU cc_start: 0.8697 (mt) cc_final: 0.8447 (mt) REVERT: D 194 CYS cc_start: 0.8477 (m) cc_final: 0.8042 (m) REVERT: E 256 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6597 (tmm-80) REVERT: E 260 ASN cc_start: 0.8225 (m-40) cc_final: 0.7695 (m-40) REVERT: E 333 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6740 (tm-30) REVERT: F 25 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7796 (pp20) REVERT: F 211 TYR cc_start: 0.7890 (m-80) cc_final: 0.7642 (m-10) REVERT: G 139 MET cc_start: 0.7722 (tpp) cc_final: 0.7520 (ttm) REVERT: G 199 MET cc_start: 0.6922 (tmm) cc_final: 0.6651 (tmm) REVERT: H 119 MET cc_start: 0.6753 (mpp) cc_final: 0.6345 (mpp) REVERT: H 146 ARG cc_start: 0.7794 (ptt-90) cc_final: 0.7255 (ptt-90) REVERT: H 229 MET cc_start: 0.6374 (tpp) cc_final: 0.6111 (tpt) outliers start: 130 outliers final: 87 residues processed: 386 average time/residue: 0.3391 time to fit residues: 206.7006 Evaluate side-chains 370 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 275 time to evaluate : 2.683 ------------------------------------------------------------------------------- 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 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 1386 LEU Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1468 ILE 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 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 315 GLU 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 287 PHE Chi-restraints excluded: chain C residue 288 VAL 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 227 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 ASP 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 314 VAL Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 93 LEU 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 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 25 GLU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 41 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 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 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 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 137 VAL Chi-restraints excluded: chain G residue 187 ASN Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 116 MET 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: 4.9990 chunk 29 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 262 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 125 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 HIS ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN C 265 ASN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 22186 Z= 0.393 Angle : 0.686 10.811 29991 Z= 0.350 Chirality : 0.046 0.300 3481 Planarity : 0.004 0.043 3815 Dihedral : 7.531 153.793 3040 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 6.20 % Allowed : 25.18 % Favored : 68.61 % 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: -0.37 (0.16), residues: 2734 helix: 0.66 (0.15), residues: 1256 sheet: -0.65 (0.22), residues: 506 loop : -1.09 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1403 HIS 0.019 0.002 HIS B 287 PHE 0.024 0.002 PHE H 215 TYR 0.020 0.002 TYR F 239 ARG 0.009 0.001 ARG H 91 *********************** 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 435 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 284 time to evaluate : 2.498 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 1052 MET cc_start: 0.7169 (mmt) cc_final: 0.6868 (mtm) REVERT: A 1172 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7583 (tptm) REVERT: A 1325 MET cc_start: 0.7027 (mmt) cc_final: 0.6773 (mmm) REVERT: A 1344 MET cc_start: 0.8249 (mmm) cc_final: 0.7905 (mmt) REVERT: A 1386 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7363 (mm) REVERT: A 1644 HIS cc_start: 0.8130 (m90) cc_final: 0.7817 (m-70) REVERT: A 1775 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7848 (mp) REVERT: A 1818 ARG cc_start: 0.4070 (OUTLIER) cc_final: 0.2973 (mmp-170) REVERT: C 286 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7434 (mp) REVERT: C 288 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8276 (t) REVERT: D 109 ASN cc_start: 0.6532 (OUTLIER) cc_final: 0.6316 (p0) REVERT: D 194 CYS cc_start: 0.8620 (m) cc_final: 0.7886 (t) REVERT: E 79 LYS cc_start: 0.6429 (mmtt) cc_final: 0.6155 (mmtt) REVERT: E 256 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6408 (tmm-80) REVERT: E 260 ASN cc_start: 0.8148 (m-40) cc_final: 0.7882 (m-40) REVERT: E 318 TYR cc_start: 0.7968 (m-80) cc_final: 0.7392 (m-10) REVERT: E 338 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8512 (mtmt) REVERT: F 148 CYS cc_start: 0.6294 (m) cc_final: 0.5996 (m) REVERT: F 211 TYR cc_start: 0.8040 (m-80) cc_final: 0.7809 (m-10) REVERT: F 246 HIS cc_start: 0.6970 (p90) cc_final: 0.6756 (p90) REVERT: G 177 ASN cc_start: 0.7993 (OUTLIER) cc_final: 0.7775 (p0) REVERT: G 199 MET cc_start: 0.6920 (tmm) cc_final: 0.6571 (tmm) REVERT: G 232 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7888 (p0) REVERT: G 251 LEU cc_start: 0.9038 (tp) cc_final: 0.8833 (tp) REVERT: H 119 MET cc_start: 0.6718 (mpp) cc_final: 0.6344 (mpp) REVERT: H 146 ARG cc_start: 0.7737 (ptt-90) cc_final: 0.7102 (ptt-90) REVERT: H 229 MET cc_start: 0.6513 (tpp) cc_final: 0.6191 (tpt) outliers start: 151 outliers final: 102 residues processed: 402 average time/residue: 0.3155 time to fit residues: 199.8292 Evaluate side-chains 387 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 274 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1062 THR 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 1189 LYS 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 1386 LEU 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 1787 VAL 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 118 ASN 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 187 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 287 HIS 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 220 LEU 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 227 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 ASP 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 314 VAL Chi-restraints excluded: chain D residue 347 GLN 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 76 THR Chi-restraints excluded: chain E residue 93 LEU 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 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 338 LYS 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 41 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 99 LEU Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 113 ASP 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 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 137 VAL Chi-restraints excluded: chain G residue 160 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 219 THR Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 116 MET 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: 5.9990 chunk 104 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 129 optimal weight: 0.0870 chunk 24 optimal weight: 0.6980 chunk 206 optimal weight: 7.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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** A1147 GLN ** A1467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 HIS ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2936 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= 0.169 Angle : 0.598 11.285 29991 Z= 0.302 Chirality : 0.042 0.226 3481 Planarity : 0.004 0.042 3815 Dihedral : 7.219 149.051 3040 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.70 % Allowed : 27.86 % Favored : 68.45 % 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: 0.02 (0.16), residues: 2734 helix: 1.05 (0.15), residues: 1251 sheet: -0.60 (0.23), residues: 501 loop : -0.89 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1403 HIS 0.013 0.001 HIS G 153 PHE 0.023 0.001 PHE H 215 TYR 0.013 0.001 TYR A1399 ARG 0.009 0.000 ARG H 91 *********************** 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 394 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 304 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.7184 (mmt) cc_final: 0.6882 (mtm) REVERT: A 1325 MET cc_start: 0.6885 (mmt) cc_final: 0.6616 (mmm) REVERT: A 1344 MET cc_start: 0.8254 (mmm) cc_final: 0.7912 (mmt) REVERT: A 1386 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7300 (mm) REVERT: A 1644 HIS cc_start: 0.8113 (m90) cc_final: 0.7826 (m-70) REVERT: A 1707 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6932 (mm-30) REVERT: A 1775 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7859 (mp) REVERT: A 1818 ARG cc_start: 0.3974 (OUTLIER) cc_final: 0.2905 (mmp-170) REVERT: B 62 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8365 (t) REVERT: C 112 ARG cc_start: 0.8132 (mpt-90) cc_final: 0.7885 (mpt180) REVERT: C 225 MET cc_start: 0.6453 (ppp) cc_final: 0.5899 (ppp) REVERT: E 149 ARG cc_start: 0.8863 (ptm-80) cc_final: 0.8657 (ptm-80) REVERT: E 256 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6513 (tmm-80) REVERT: E 260 ASN cc_start: 0.8283 (m-40) cc_final: 0.7781 (m-40) REVERT: E 333 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6783 (tm-30) REVERT: F 25 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7602 (pp20) REVERT: F 211 TYR cc_start: 0.7857 (m-80) cc_final: 0.7628 (m-10) REVERT: G 251 LEU cc_start: 0.8942 (tp) cc_final: 0.8580 (tp) REVERT: H 119 MET cc_start: 0.6751 (mpp) cc_final: 0.6395 (mpp) REVERT: H 146 ARG cc_start: 0.7695 (ptt-90) cc_final: 0.7287 (ptt-90) REVERT: H 229 MET cc_start: 0.6652 (tpp) cc_final: 0.6428 (tpt) outliers start: 90 outliers final: 63 residues processed: 367 average time/residue: 0.3296 time to fit residues: 189.6660 Evaluate side-chains 351 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 282 time to evaluate : 2.490 ------------------------------------------------------------------------------- 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 1188 GLN Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1468 ILE 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 39 VAL Chi-restraints excluded: chain B residue 62 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 195 ASP Chi-restraints excluded: chain C residue 3 THR 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 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 265 ILE Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 128 ASP 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 279 TYR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 29 ASP 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 97 ASP Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 113 ASP 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 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 72 LEU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 87 ILE 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: 7.9990 chunk 251 optimal weight: 8.9990 chunk 229 optimal weight: 20.0000 chunk 244 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 106 optimal weight: 0.0060 chunk 191 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 chunk 243 optimal weight: 0.6980 overall best weight: 2.7402 ------------------------------------------------------------------------------- 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** B 125 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22186 Z= 0.301 Angle : 0.644 12.112 29991 Z= 0.326 Chirality : 0.044 0.318 3481 Planarity : 0.004 0.042 3815 Dihedral : 7.197 149.937 3038 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.66 % Allowed : 27.81 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2734 helix: 0.90 (0.15), residues: 1255 sheet: -0.69 (0.22), residues: 503 loop : -0.98 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A1403 HIS 0.013 0.001 HIS G 153 PHE 0.021 0.002 PHE H 215 TYR 0.019 0.002 TYR E 318 ARG 0.011 0.001 ARG F 146 *********************** 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 368 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 279 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.7195 (mmt) cc_final: 0.6862 (mtm) REVERT: A 1172 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7604 (tptm) REVERT: A 1325 MET cc_start: 0.7051 (mmt) cc_final: 0.6820 (mmm) REVERT: A 1344 MET cc_start: 0.8311 (mmm) cc_final: 0.7968 (mmt) REVERT: A 1386 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7285 (mm) REVERT: A 1644 HIS cc_start: 0.8130 (m90) cc_final: 0.7811 (m-70) REVERT: A 1660 ASP cc_start: 0.7495 (t0) cc_final: 0.7270 (t0) REVERT: A 1775 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7848 (mp) REVERT: A 1818 ARG cc_start: 0.4035 (OUTLIER) cc_final: 0.2965 (mmp-170) REVERT: C 288 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8281 (p) REVERT: E 79 LYS cc_start: 0.6434 (mmtt) cc_final: 0.6155 (mmtt) REVERT: E 256 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6456 (tmm-80) REVERT: E 260 ASN cc_start: 0.8167 (m-40) cc_final: 0.7908 (m-40) REVERT: F 25 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7875 (pp20) REVERT: F 211 TYR cc_start: 0.7993 (m-80) cc_final: 0.7763 (m-10) REVERT: F 246 HIS cc_start: 0.6835 (p90) cc_final: 0.6620 (p90) REVERT: G 210 ARG cc_start: 0.7022 (tpm170) cc_final: 0.6700 (tpm170) REVERT: G 251 LEU cc_start: 0.9059 (tp) cc_final: 0.8752 (tp) REVERT: H 75 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6376 (pmm) REVERT: H 119 MET cc_start: 0.6789 (mpp) cc_final: 0.6454 (mpp) REVERT: H 146 ARG cc_start: 0.7742 (ptt-90) cc_final: 0.7339 (ptt-90) outliers start: 89 outliers final: 73 residues processed: 345 average time/residue: 0.3215 time to fit residues: 176.2045 Evaluate side-chains 356 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 275 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1062 THR 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 1369 ILE Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1386 LEU 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 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 73 ILE 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 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 212 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 280 ILE 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 D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 128 ASP 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 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 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 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 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 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 72 LEU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 87 ILE 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 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: 4.9990 chunk 258 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 270 optimal weight: 40.0000 chunk 249 optimal weight: 30.0000 chunk 215 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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** ** A1467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 126 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 22186 Z= 0.405 Angle : 0.729 12.937 29991 Z= 0.370 Chirality : 0.046 0.350 3481 Planarity : 0.005 0.047 3815 Dihedral : 7.551 147.979 3038 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.86 % Allowed : 28.10 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2734 helix: 0.53 (0.15), residues: 1258 sheet: -0.73 (0.23), residues: 493 loop : -1.13 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP A1403 HIS 0.016 0.002 HIS G 153 PHE 0.021 0.002 PHE H 215 TYR 0.019 0.002 TYR F 239 ARG 0.013 0.001 ARG H 91 ********************** 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 371 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 277 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.7299 (mmt) cc_final: 0.6972 (mtm) REVERT: A 1172 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7635 (tptm) REVERT: A 1344 MET cc_start: 0.8400 (mmm) cc_final: 0.8078 (mmt) REVERT: A 1386 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7292 (mm) REVERT: A 1644 HIS cc_start: 0.8193 (m90) cc_final: 0.7864 (m-70) REVERT: A 1775 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7841 (mp) REVERT: A 1818 ARG cc_start: 0.4290 (OUTLIER) cc_final: 0.3182 (mmp-170) REVERT: B 282 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8102 (tt) REVERT: C 288 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8292 (t) REVERT: D 194 CYS cc_start: 0.8627 (m) cc_final: 0.7941 (t) REVERT: E 79 LYS cc_start: 0.6436 (mmtt) cc_final: 0.6185 (mmtt) REVERT: E 256 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6404 (tmm-80) REVERT: E 260 ASN cc_start: 0.8265 (m-40) cc_final: 0.7803 (m-40) REVERT: E 280 GLU cc_start: 0.7520 (tp30) cc_final: 0.7201 (tp30) REVERT: F 25 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8019 (pp20) REVERT: F 246 HIS cc_start: 0.7127 (p90) cc_final: 0.6899 (p90) REVERT: G 210 ARG cc_start: 0.7041 (tpm170) cc_final: 0.6731 (tpm170) REVERT: G 251 LEU cc_start: 0.9168 (tp) cc_final: 0.8947 (tp) REVERT: H 75 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6511 (pmm) REVERT: H 119 MET cc_start: 0.6906 (mpp) cc_final: 0.6544 (mpp) REVERT: H 146 ARG cc_start: 0.7725 (ptt-90) cc_final: 0.7348 (ptt-90) outliers start: 94 outliers final: 77 residues processed: 348 average time/residue: 0.3233 time to fit residues: 175.5871 Evaluate side-chains 349 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 263 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1062 THR 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 1377 THR Chi-restraints excluded: chain A residue 1386 LEU 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 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 69 VAL Chi-restraints excluded: chain B residue 73 ILE 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 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 130 MET 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 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 D residue 41 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 93 LEU 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 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 283 THR 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 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 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 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 30 ILE 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 160 ILE Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 87 ILE 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 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: 0.0570 chunk 66 optimal weight: 1.9990 chunk 198 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 216 optimal weight: 0.2980 chunk 90 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 20.0000 overall best weight: 0.5900 ------------------------------------------------------------------------------- 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** B 172 ASN B 235 ASN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.170782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.129866 restraints weight = 43235.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.130348 restraints weight = 30253.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.130961 restraints weight = 23264.822| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3377 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= 0.179 Angle : 0.622 12.210 29991 Z= 0.313 Chirality : 0.042 0.260 3481 Planarity : 0.004 0.048 3815 Dihedral : 7.213 142.092 3038 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.29 % Allowed : 28.84 % Favored : 67.87 % 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: -0.05 (0.16), residues: 2734 helix: 0.98 (0.15), residues: 1253 sheet: -0.60 (0.23), residues: 486 loop : -0.93 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A1403 HIS 0.013 0.001 HIS G 153 PHE 0.021 0.001 PHE H 215 TYR 0.024 0.002 TYR A1508 ARG 0.019 0.001 ARG E 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4514.01 seconds wall clock time: 82 minutes 27.28 seconds (4947.28 seconds total)