Starting phenix.real_space_refine on Thu Aug 8 03:51:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui7_42287/08_2024/8ui7_42287.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui7_42287/08_2024/8ui7_42287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui7_42287/08_2024/8ui7_42287.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui7_42287/08_2024/8ui7_42287.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui7_42287/08_2024/8ui7_42287.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui7_42287/08_2024/8ui7_42287.cif" } resolution = 4.2 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 3 5.21 5 S 145 5.16 5 C 13746 2.51 5 N 3709 2.21 5 O 4215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1056": "OE1" <-> "OE2" Residue "A GLU 1120": "OE1" <-> "OE2" Residue "A TYR 1143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1173": "OE1" <-> "OE2" Residue "A ASP 1308": "OD1" <-> "OD2" Residue "A GLU 1313": "OE1" <-> "OE2" Residue "A PHE 1341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1351": "OE1" <-> "OE2" Residue "A PHE 1677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1834": "OE1" <-> "OE2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 95": "OD1" <-> "OD2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 272": "OE1" <-> "OE2" Residue "E ASP 6": "OD1" <-> "OD2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 99": "OD1" <-> "OD2" Residue "E TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 174": "OE1" <-> "OE2" Residue "G PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 21831 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.34, per 1000 atoms: 0.52 Number of scatterers: 21831 At special positions: 0 Unit cell: (137.448, 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 145 16.00 P 13 15.00 Mg 3 11.99 O 4215 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: 8.31 Conformation dependent library (CDL) restraints added in 3.7 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: 118 helices and 14 sheets defined 51.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 940 through 955 Processing helix chain 'A' and resid 959 through 972 removed outlier: 4.172A pdb=" N TYR A 963 " --> pdb=" O SER A 959 " (cutoff:3.500A) Proline residue: A 965 - end of helix 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 1176 removed outlier: 6.204A pdb=" N GLU A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA A1174 " --> pdb=" O GLN A1170 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR A1175 " --> pdb=" O LEU A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1328 Processing helix chain 'A' and resid 1340 through 1345 Processing helix chain 'A' and resid 1358 through 1373 Processing helix chain 'A' and resid 1378 through 1389 removed outlier: 3.955A pdb=" N PHE A1382 " --> pdb=" O ASP A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1406 Processing helix chain 'A' and resid 1457 through 1463 removed outlier: 3.648A pdb=" N THR A1461 " --> pdb=" O GLY A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1468 Processing helix chain 'A' and resid 1474 through 1481 removed outlier: 3.669A pdb=" N HIS A1481 " --> pdb=" O SER A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1502 removed outlier: 4.125A pdb=" N ARG A1502 " --> pdb=" O GLU A1498 " (cutoff:3.500A) 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 1730 removed outlier: 4.165A pdb=" N SER A1705 " --> pdb=" O THR A1701 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A1707 " --> pdb=" O GLN A1703 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR A1730 " --> pdb=" O LYS A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1737 Processing helix chain 'A' and resid 1740 through 1745 removed outlier: 4.328A pdb=" N ASN A1743 " --> pdb=" O ASP A1740 " (cutoff:3.500A) Processing helix chain 'A' and resid 1750 through 1755 Processing helix chain 'A' and resid 1764 through 1779 Processing helix chain 'A' and resid 1789 through 1814 Proline residue: A1799 - end of helix Processing helix chain 'A' and resid 1817 through 1822 Processing helix chain 'A' and resid 1824 through 1828 Processing helix chain 'A' and resid 1832 through 1840 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 53 through 66 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 96 through 100 removed outlier: 4.270A pdb=" N LYS B 99 " --> pdb=" O PRO B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.995A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 147 through 161 removed outlier: 4.723A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.599A 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 224 Processing helix chain 'B' and resid 228 through 243 removed outlier: 3.629A pdb=" N ALA B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) 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 289 removed outlier: 3.916A pdb=" N ALA B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.524A pdb=" N ILE B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 Processing helix chain 'B' and resid 333 through 350 removed outlier: 3.860A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 removed outlier: 3.660A pdb=" N LYS C 7 " --> pdb=" O THR C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 removed outlier: 3.767A 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 65 through 78 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.608A pdb=" N MET C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 86' Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 131 through 144 removed outlier: 4.079A 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 Processing helix chain 'C' and resid 212 through 228 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 289 removed outlier: 3.634A pdb=" N ILE C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 315 removed outlier: 3.603A pdb=" N SER C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 314 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 339 removed outlier: 3.823A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 56 through 68 Processing helix chain 'D' and resid 83 through 96 Processing helix chain 'D' and resid 97 through 104 removed outlier: 4.094A pdb=" N ARG D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 129 removed outlier: 4.236A 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: 3.726A pdb=" N ARG D 185 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.538A pdb=" N THR D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 218 removed outlier: 3.809A pdb=" N GLN D 207 " --> pdb=" O SER D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 235 Processing helix chain 'D' and resid 237 through 253 Processing helix chain 'D' and resid 258 through 264 removed outlier: 3.676A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.670A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.986A 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 316 removed outlier: 3.957A pdb=" N GLU D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 363 removed outlier: 4.144A pdb=" N ASN D 362 " --> pdb=" O GLN D 358 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS D 363 " --> pdb=" O LEU D 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 19 through 33 removed outlier: 3.612A pdb=" N ALA E 23 " --> pdb=" O HIS E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 66 removed outlier: 3.613A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS E 66 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 102 removed outlier: 4.113A pdb=" N ASP E 99 " --> pdb=" O ASN E 96 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 122 removed outlier: 3.671A pdb=" N GLN E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU E 110 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N MET E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 153 Processing helix chain 'E' and resid 172 through 179 removed outlier: 3.576A pdb=" N ARG E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS E 179 " --> pdb=" O ILE E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 203 Processing helix chain 'E' and resid 208 through 220 removed outlier: 3.521A 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: 3.695A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 304 through 325 removed outlier: 4.004A pdb=" N GLY E 309 " --> pdb=" O GLY E 305 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU E 310 " --> pdb=" O GLN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 348 removed outlier: 4.442A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 79 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.535A pdb=" N ALA F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 217 Processing helix chain 'F' and resid 218 through 222 removed outlier: 3.872A pdb=" N LEU F 221 " --> pdb=" O ALA F 218 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER F 222 " --> pdb=" O THR F 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 218 through 222' Processing helix chain 'G' and resid 8 through 19 removed outlier: 4.213A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 155 removed outlier: 4.025A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'G' and resid 218 through 222 removed outlier: 3.632A pdb=" N LEU G 221 " --> pdb=" O ALA G 218 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER G 222 " --> pdb=" O THR G 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 218 through 222' Processing helix chain 'H' and resid 11 through 19 removed outlier: 4.038A pdb=" N GLU H 17 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 209 through 216 Processing helix chain 'H' and resid 217 through 222 Proline residue: H 220 - end of helix No H-bonds generated for 'chain 'H' and resid 217 through 222' Processing sheet with id=AA1, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.284A pdb=" N LEU D 74 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N CYS D 180 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N PHE D 76 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1151 through 1156 removed outlier: 5.685A pdb=" N LYS A1152 " --> pdb=" O LEU A1301 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A1303 " --> pdb=" O LYS A1152 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PHE A1154 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU A1305 " --> pdb=" O PHE A1154 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A1156 " --> pdb=" O GLU A1305 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ILE A1333 " --> pdb=" O SER A1300 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A1302 " --> pdb=" O ILE A1333 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR A1335 " --> pdb=" O ILE A1302 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A1304 " --> pdb=" O THR A1335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1519 through 1521 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.634A pdb=" N LEU B 103 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE B 73 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.142A pdb=" N LEU C 88 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 68 through 74 Processing sheet with id=AA7, first strand: chain 'F' and resid 60 through 62 removed outlier: 4.659A pdb=" N ILE F 87 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU F 104 " --> pdb=" O ILE F 87 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.308A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 177 through 183 removed outlier: 4.976A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 60 through 62 Processing sheet with id=AB2, first strand: chain 'G' and resid 66 through 71 removed outlier: 7.397A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY G 245 " --> pdb=" O ILE G 241 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS G 138 " --> pdb=" O THR G 196 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR G 196 " --> pdb=" O LYS G 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 60 through 61 removed outlier: 3.592A pdb=" N ARG H 61 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU H 3 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 66 through 71 removed outlier: 6.352A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR H 51 " --> pdb=" O HIS H 246 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS H 246 " --> pdb=" O THR H 51 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR H 196 " --> pdb=" O LYS H 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 178 through 182 removed outlier: 3.827A pdb=" N GLY H 178 " --> pdb=" O ALA H 171 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA H 171 " --> pdb=" O GLY H 178 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL H 167 " --> pdb=" O LEU H 182 " (cutoff:3.500A) 1148 hydrogen bonds defined for protein. 3276 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: 7.48 Time building geometry restraints manager: 9.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7201 1.35 - 1.50: 5441 1.50 - 1.65: 9324 1.65 - 1.80: 115 1.80 - 1.95: 101 Bond restraints: 22182 Sorted by residual: bond pdb=" N MET F 139 " pdb=" CA MET F 139 " ideal model delta sigma weight residual 1.453 1.486 -0.033 9.20e-03 1.18e+04 1.29e+01 bond pdb=" N ARG B 155 " pdb=" CA ARG B 155 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.17e-02 7.31e+03 9.32e+00 bond pdb=" N ASP D 50 " pdb=" CA ASP D 50 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.62e+00 bond pdb=" N MET E 229 " pdb=" CA MET E 229 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.79e+00 bond pdb=" C VAL C 183 " pdb=" N PRO C 184 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.55e+00 ... (remaining 22177 not shown) Histogram of bond angle deviations from ideal: 94.85 - 103.12: 152 103.12 - 111.38: 9261 111.38 - 119.65: 10107 119.65 - 127.92: 10332 127.92 - 136.18: 132 Bond angle restraints: 29984 Sorted by residual: angle pdb=" N LEU E 161 " pdb=" CA LEU E 161 " pdb=" C LEU E 161 " ideal model delta sigma weight residual 108.13 118.01 -9.88 1.72e+00 3.38e-01 3.30e+01 angle pdb=" N GLN E 313 " pdb=" CA GLN E 313 " pdb=" CB GLN E 313 " ideal model delta sigma weight residual 110.28 118.97 -8.69 1.55e+00 4.16e-01 3.14e+01 angle pdb=" C ASN H 107 " pdb=" N GLN H 108 " pdb=" CA GLN H 108 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.21e+01 angle pdb=" CB MET A1656 " pdb=" CG MET A1656 " pdb=" SD MET A1656 " ideal model delta sigma weight residual 112.70 125.74 -13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" CA GLN E 313 " pdb=" CB GLN E 313 " pdb=" CG GLN E 313 " ideal model delta sigma weight residual 114.10 122.40 -8.30 2.00e+00 2.50e-01 1.72e+01 ... (remaining 29979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.08: 13195 29.08 - 58.15: 433 58.15 - 87.23: 36 87.23 - 116.30: 1 116.30 - 145.38: 2 Dihedral angle restraints: 13667 sinusoidal: 5602 harmonic: 8065 Sorted by residual: dihedral pdb=" O2A ADP D2000 " pdb=" O3A ADP D2000 " pdb=" PA ADP D2000 " pdb=" PB ADP D2000 " ideal model delta sinusoidal sigma weight residual -60.00 85.38 -145.38 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O2A ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PA ADP E2000 " pdb=" PB ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 163.45 136.55 1 2.00e+01 2.50e-03 4.14e+01 dihedral pdb=" CA LEU A1662 " pdb=" C LEU A1662 " pdb=" N LEU A1663 " pdb=" CA LEU A1663 " ideal model delta harmonic sigma weight residual 180.00 150.25 29.75 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 13664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2809 0.065 - 0.130: 583 0.130 - 0.195: 73 0.195 - 0.260: 11 0.260 - 0.325: 3 Chirality restraints: 3479 Sorted by residual: chirality pdb=" CG LEU C 255 " pdb=" CB LEU C 255 " pdb=" CD1 LEU C 255 " pdb=" CD2 LEU C 255 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CG LEU G 209 " pdb=" CB LEU G 209 " pdb=" CD1 LEU G 209 " pdb=" CD2 LEU G 209 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL H 123 " pdb=" CA VAL H 123 " pdb=" CG1 VAL H 123 " pdb=" CG2 VAL H 123 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 3476 not shown) Planarity restraints: 3815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 138 " 0.024 2.00e-02 2.50e+03 4.80e-02 2.31e+01 pdb=" C LYS F 138 " -0.083 2.00e-02 2.50e+03 pdb=" O LYS F 138 " 0.032 2.00e-02 2.50e+03 pdb=" N MET F 139 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 215 " -0.017 2.00e-02 2.50e+03 3.24e-02 1.84e+01 pdb=" CG PHE G 215 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE G 215 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 PHE G 215 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE G 215 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE G 215 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE G 215 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 22 " 0.019 2.00e-02 2.50e+03 2.09e-02 1.10e+01 pdb=" CG TRP C 22 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP C 22 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP C 22 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 22 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP C 22 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 22 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 22 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 22 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 22 " 0.006 2.00e-02 2.50e+03 ... (remaining 3812 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 245 2.57 - 3.16: 17518 3.16 - 3.74: 36785 3.74 - 4.32: 48215 4.32 - 4.90: 77757 Nonbonded interactions: 180520 Sorted by model distance: nonbonded pdb="MG MG B 401 " pdb=" O3G AGS B 402 " model vdw 1.992 2.170 nonbonded pdb="MG MG B 401 " pdb=" O1B AGS B 402 " model vdw 2.010 2.170 nonbonded pdb="MG MG C 401 " pdb=" O1B AGS C 402 " model vdw 2.031 2.170 nonbonded pdb="MG MG A2001 " pdb=" O3G AGS A2002 " model vdw 2.040 2.170 nonbonded pdb="MG MG A2001 " pdb=" O1B AGS A2002 " model vdw 2.051 2.170 ... (remaining 180515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 55.800 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.004 0.059 22182 Z= 0.283 Angle : 0.969 13.037 29984 Z= 0.499 Chirality : 0.053 0.325 3479 Planarity : 0.006 0.063 3815 Dihedral : 14.142 145.377 8415 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 0.04 % Allowed : 0.49 % Favored : 99.47 % 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: -1.37 (0.15), residues: 2734 helix: -0.67 (0.13), residues: 1278 sheet: -0.48 (0.22), residues: 495 loop : -1.22 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP C 22 HIS 0.015 0.002 HIS A1644 PHE 0.071 0.003 PHE G 215 TYR 0.030 0.003 TYR G 249 ARG 0.020 0.001 ARG C 333 *********************** 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 395 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 394 time to evaluate : 2.396 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: 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: symmetry clash REVERT: A 1052 MET cc_start: 0.8837 (ppp) cc_final: 0.8605 (ppp) REVERT: A 1317 PHE cc_start: 0.7703 (t80) cc_final: 0.7452 (t80) REVERT: A 1334 LEU cc_start: 0.9428 (mp) cc_final: 0.9194 (mt) REVERT: A 1506 PHE cc_start: 0.8109 (t80) cc_final: 0.7900 (t80) REVERT: A 1707 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8856 (mt-10) REVERT: A 1709 LYS cc_start: 0.9074 (ptpp) cc_final: 0.8823 (mtmm) REVERT: B 100 ASP cc_start: 0.8531 (m-30) cc_final: 0.8071 (m-30) REVERT: B 121 LYS cc_start: 0.9361 (ttmt) cc_final: 0.9078 (mttp) REVERT: B 123 PHE cc_start: 0.9406 (t80) cc_final: 0.9118 (t80) REVERT: B 293 GLU cc_start: 0.8916 (mp0) cc_final: 0.8589 (mp0) REVERT: B 308 MET cc_start: 0.9053 (ppp) cc_final: 0.8769 (ppp) REVERT: B 316 PHE cc_start: 0.9257 (m-10) cc_final: 0.9049 (m-80) REVERT: C 120 LYS cc_start: 0.9398 (mtmt) cc_final: 0.9013 (ttmt) REVERT: C 121 LEU cc_start: 0.9471 (tp) cc_final: 0.9265 (tp) REVERT: C 133 ASP cc_start: 0.9090 (m-30) cc_final: 0.8817 (m-30) REVERT: C 155 CYS cc_start: 0.7954 (t) cc_final: 0.7683 (t) REVERT: C 168 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.7628 (tpp80) REVERT: E 139 LYS cc_start: 0.9169 (mmtm) cc_final: 0.8876 (mmmt) REVERT: E 313 GLN cc_start: 0.9090 (pm20) cc_final: 0.8500 (mp10) REVERT: E 314 MET cc_start: 0.9081 (ptp) cc_final: 0.8711 (ptt) REVERT: G 116 MET cc_start: 0.6136 (tpt) cc_final: 0.4942 (mpp) REVERT: G 215 PHE cc_start: 0.9293 (m-80) cc_final: 0.9001 (m-80) REVERT: G 247 LEU cc_start: 0.9324 (tp) cc_final: 0.8846 (tp) REVERT: G 249 TYR cc_start: 0.8883 (m-80) cc_final: 0.8674 (m-80) REVERT: G 251 LEU cc_start: 0.9647 (tp) cc_final: 0.9366 (tp) outliers start: 1 outliers final: 0 residues processed: 394 average time/residue: 0.3433 time to fit residues: 207.0661 Evaluate side-chains 298 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 40.0000 chunk 206 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 247 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1751 GLN B 237 GLN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 HIS ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN D 309 GLN ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 22182 Z= 0.420 Angle : 0.810 10.862 29984 Z= 0.420 Chirality : 0.045 0.178 3479 Planarity : 0.006 0.085 3815 Dihedral : 7.839 150.253 3027 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.12 % Allowed : 6.04 % Favored : 93.84 % 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: -0.75 (0.15), residues: 2734 helix: -0.00 (0.14), residues: 1286 sheet: -0.38 (0.23), residues: 483 loop : -1.05 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 22 HIS 0.010 0.002 HIS C 289 PHE 0.029 0.003 PHE F 215 TYR 0.028 0.002 TYR B 322 ARG 0.025 0.001 ARG F 61 *********************** 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 345 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 342 time to evaluate : 2.439 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: 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: symmetry clash REVERT: A 1052 MET cc_start: 0.8974 (ppp) cc_final: 0.8364 (ppp) REVERT: A 1664 THR cc_start: 0.7787 (p) cc_final: 0.7274 (t) REVERT: A 1708 LEU cc_start: 0.9287 (mt) cc_final: 0.9077 (mt) REVERT: A 1709 LYS cc_start: 0.9065 (ptpp) cc_final: 0.8757 (pttt) REVERT: A 1790 ARG cc_start: 0.9045 (ptp90) cc_final: 0.8687 (ptp90) REVERT: B 171 CYS cc_start: 0.6623 (m) cc_final: 0.6242 (m) REVERT: C 108 PHE cc_start: 0.9459 (t80) cc_final: 0.8811 (t80) REVERT: C 120 LYS cc_start: 0.9557 (mtmt) cc_final: 0.9343 (mtmt) REVERT: C 155 CYS cc_start: 0.8199 (t) cc_final: 0.7849 (t) REVERT: E 126 GLN cc_start: 0.1962 (OUTLIER) cc_final: 0.1049 (tm-30) REVERT: E 139 LYS cc_start: 0.9143 (mmtm) cc_final: 0.8832 (mmmt) REVERT: E 248 GLU cc_start: 0.7516 (tp30) cc_final: 0.7286 (tp30) REVERT: E 335 PHE cc_start: 0.9297 (t80) cc_final: 0.8742 (t80) REVERT: E 339 PHE cc_start: 0.9481 (t80) cc_final: 0.9161 (t80) REVERT: E 340 MET cc_start: 0.9474 (mmp) cc_final: 0.9067 (mmt) REVERT: F 75 MET cc_start: 0.9243 (mtm) cc_final: 0.9021 (mtm) REVERT: F 139 MET cc_start: 0.9252 (ptt) cc_final: 0.9015 (ptm) REVERT: F 215 PHE cc_start: 0.9284 (m-80) cc_final: 0.9004 (m-80) REVERT: F 229 MET cc_start: 0.8037 (tmm) cc_final: 0.7605 (tmm) REVERT: F 248 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8278 (mmtm) REVERT: G 68 MET cc_start: 0.8810 (pmm) cc_final: 0.8518 (pmm) REVERT: G 116 MET cc_start: 0.6256 (tpt) cc_final: 0.5897 (tpp) REVERT: G 215 PHE cc_start: 0.9393 (m-80) cc_final: 0.9135 (m-80) REVERT: G 247 LEU cc_start: 0.9321 (tp) cc_final: 0.8805 (tp) REVERT: H 119 MET cc_start: 0.7170 (ppp) cc_final: 0.6855 (ppp) outliers start: 3 outliers final: 0 residues processed: 345 average time/residue: 0.3452 time to fit residues: 182.0022 Evaluate side-chains 271 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 247 optimal weight: 30.0000 chunk 267 optimal weight: 30.0000 chunk 220 optimal weight: 30.0000 chunk 245 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1644 HIS ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN E 323 GLN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22182 Z= 0.221 Angle : 0.644 8.545 29984 Z= 0.328 Chirality : 0.042 0.170 3479 Planarity : 0.004 0.062 3815 Dihedral : 7.621 149.873 3027 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % 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: -0.42 (0.15), residues: 2734 helix: 0.37 (0.14), residues: 1306 sheet: -0.31 (0.23), residues: 478 loop : -1.01 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 28 HIS 0.010 0.001 HIS A1644 PHE 0.028 0.002 PHE G 215 TYR 0.025 0.002 TYR B 322 ARG 0.010 0.001 ARG F 149 *********************** 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 370 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 368 time to evaluate : 2.483 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: 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: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.9076 (ppp) cc_final: 0.8496 (ppp) REVERT: A 1506 PHE cc_start: 0.8505 (t80) cc_final: 0.8195 (t80) REVERT: A 1644 HIS cc_start: 0.8626 (m90) cc_final: 0.8215 (m90) REVERT: B 100 ASP cc_start: 0.8584 (m-30) cc_final: 0.8332 (m-30) REVERT: B 171 CYS cc_start: 0.7063 (m) cc_final: 0.6649 (m) REVERT: B 295 ILE cc_start: 0.9062 (mt) cc_final: 0.8855 (mt) REVERT: C 56 LEU cc_start: 0.9302 (mt) cc_final: 0.9075 (mt) REVERT: C 108 PHE cc_start: 0.9401 (t80) cc_final: 0.8335 (t80) REVERT: C 120 LYS cc_start: 0.9491 (mtmt) cc_final: 0.9110 (ttmt) REVERT: C 148 ASN cc_start: 0.8908 (t0) cc_final: 0.8514 (t0) REVERT: C 307 ASP cc_start: 0.9547 (m-30) cc_final: 0.9342 (m-30) REVERT: D 109 ASN cc_start: 0.7620 (p0) cc_final: 0.7344 (p0) REVERT: E 139 LYS cc_start: 0.9121 (mmtm) cc_final: 0.8813 (mmmt) REVERT: E 161 LEU cc_start: 0.8643 (pp) cc_final: 0.8410 (pp) REVERT: E 314 MET cc_start: 0.9145 (ptt) cc_final: 0.8753 (ptt) REVERT: E 318 TYR cc_start: 0.8741 (m-10) cc_final: 0.8390 (m-10) REVERT: E 335 PHE cc_start: 0.9176 (t80) cc_final: 0.8602 (t80) REVERT: E 339 PHE cc_start: 0.9472 (t80) cc_final: 0.9070 (t80) REVERT: E 340 MET cc_start: 0.9422 (mmp) cc_final: 0.9139 (mmt) REVERT: F 144 PHE cc_start: 0.8935 (t80) cc_final: 0.8718 (t80) REVERT: F 215 PHE cc_start: 0.9145 (m-80) cc_final: 0.8808 (m-80) REVERT: G 68 MET cc_start: 0.8744 (pmm) cc_final: 0.8502 (pmm) REVERT: G 116 MET cc_start: 0.6323 (tpt) cc_final: 0.5918 (tpp) REVERT: G 139 MET cc_start: 0.8369 (tmm) cc_final: 0.8156 (tmm) REVERT: G 215 PHE cc_start: 0.9376 (m-80) cc_final: 0.9033 (m-80) REVERT: G 247 LEU cc_start: 0.9266 (tp) cc_final: 0.8691 (tp) outliers start: 2 outliers final: 0 residues processed: 370 average time/residue: 0.3454 time to fit residues: 195.1713 Evaluate side-chains 292 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 166 optimal weight: 20.0000 chunk 248 optimal weight: 0.1980 chunk 262 optimal weight: 8.9990 chunk 129 optimal weight: 0.0170 chunk 235 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 overall best weight: 3.2424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1500 GLN B 237 GLN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 GLN E 323 GLN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22182 Z= 0.234 Angle : 0.645 9.431 29984 Z= 0.328 Chirality : 0.042 0.173 3479 Planarity : 0.004 0.063 3815 Dihedral : 7.530 148.283 3027 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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: -0.34 (0.16), residues: 2734 helix: 0.45 (0.14), residues: 1316 sheet: -0.30 (0.23), residues: 477 loop : -0.98 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1083 HIS 0.007 0.001 HIS B 287 PHE 0.033 0.002 PHE C 151 TYR 0.022 0.002 TYR B 322 ARG 0.010 0.001 ARG G 210 *********************** 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 368 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 2.539 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: 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: 0.9143 (ppp) cc_final: 0.8499 (ppp) REVERT: A 1506 PHE cc_start: 0.8548 (t80) cc_final: 0.8214 (t80) REVERT: A 1644 HIS cc_start: 0.8700 (m90) cc_final: 0.8350 (m90) REVERT: A 1645 CYS cc_start: 0.9236 (m) cc_final: 0.9013 (p) REVERT: B 87 LEU cc_start: 0.9612 (tp) cc_final: 0.9348 (tt) REVERT: B 102 MET cc_start: 0.8970 (tmm) cc_final: 0.8728 (tmm) REVERT: B 171 CYS cc_start: 0.7061 (m) cc_final: 0.6668 (m) REVERT: B 203 MET cc_start: 0.9180 (ptp) cc_final: 0.8953 (ptt) REVERT: B 295 ILE cc_start: 0.9044 (mt) cc_final: 0.8829 (mt) REVERT: B 308 MET cc_start: 0.8984 (ppp) cc_final: 0.8773 (ppp) REVERT: C 56 LEU cc_start: 0.9290 (mt) cc_final: 0.8871 (pp) REVERT: C 58 LEU cc_start: 0.8936 (mp) cc_final: 0.8707 (mp) REVERT: C 86 MET cc_start: 0.7876 (mtt) cc_final: 0.7665 (mtt) REVERT: C 108 PHE cc_start: 0.9374 (t80) cc_final: 0.8689 (t80) REVERT: C 148 ASN cc_start: 0.8864 (t0) cc_final: 0.8614 (t0) REVERT: C 160 LYS cc_start: 0.8781 (tmtt) cc_final: 0.8246 (tmtt) REVERT: C 305 MET cc_start: 0.9030 (mtm) cc_final: 0.8826 (mtm) REVERT: D 109 ASN cc_start: 0.7589 (p0) cc_final: 0.7275 (p0) REVERT: D 356 MET cc_start: 0.8356 (tpt) cc_final: 0.8105 (tpt) REVERT: E 139 LYS cc_start: 0.9134 (mmtm) cc_final: 0.8839 (mmmt) REVERT: E 314 MET cc_start: 0.9211 (ptt) cc_final: 0.8781 (ptt) REVERT: E 318 TYR cc_start: 0.8647 (m-10) cc_final: 0.8397 (m-10) REVERT: E 335 PHE cc_start: 0.9181 (t80) cc_final: 0.8667 (t80) REVERT: E 339 PHE cc_start: 0.9435 (t80) cc_final: 0.8998 (t80) REVERT: E 340 MET cc_start: 0.9434 (mmp) cc_final: 0.9049 (mmt) REVERT: F 214 PHE cc_start: 0.9210 (m-80) cc_final: 0.8937 (m-80) REVERT: F 215 PHE cc_start: 0.9197 (m-80) cc_final: 0.8852 (m-80) REVERT: F 229 MET cc_start: 0.7960 (tmm) cc_final: 0.7513 (tmm) REVERT: G 68 MET cc_start: 0.8749 (pmm) cc_final: 0.8473 (pmm) REVERT: G 116 MET cc_start: 0.6376 (tpt) cc_final: 0.5940 (tpp) REVERT: G 215 PHE cc_start: 0.9347 (m-80) cc_final: 0.9047 (m-80) REVERT: G 247 LEU cc_start: 0.9270 (tp) cc_final: 0.8774 (tp) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.3489 time to fit residues: 196.3220 Evaluate side-chains 283 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 195 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 134 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1094 ASN ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 HIS ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 22182 Z= 0.350 Angle : 0.732 11.052 29984 Z= 0.376 Chirality : 0.044 0.161 3479 Planarity : 0.005 0.057 3815 Dihedral : 7.712 149.664 3027 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2734 helix: 0.22 (0.14), residues: 1319 sheet: -0.39 (0.23), residues: 484 loop : -1.00 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP G 28 HIS 0.009 0.002 HIS E 37 PHE 0.021 0.002 PHE C 108 TYR 0.035 0.002 TYR G 211 ARG 0.007 0.001 ARG C 333 *********************** 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 350 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 2.490 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.8915 (ppp) cc_final: 0.8389 (ppp) REVERT: A 1506 PHE cc_start: 0.8594 (t80) cc_final: 0.8255 (t80) REVERT: A 1644 HIS cc_start: 0.8789 (m90) cc_final: 0.8355 (m90) REVERT: B 121 LYS cc_start: 0.9421 (ttmt) cc_final: 0.8979 (mttt) REVERT: B 171 CYS cc_start: 0.6381 (m) cc_final: 0.6089 (m) REVERT: B 203 MET cc_start: 0.9212 (ptp) cc_final: 0.8981 (ptt) REVERT: B 295 ILE cc_start: 0.9101 (mt) cc_final: 0.8854 (mt) REVERT: C 56 LEU cc_start: 0.9291 (mt) cc_final: 0.8838 (pp) REVERT: C 58 LEU cc_start: 0.8940 (mp) cc_final: 0.8657 (mp) REVERT: C 108 PHE cc_start: 0.9303 (t80) cc_final: 0.8880 (t80) REVERT: C 148 ASN cc_start: 0.8941 (t0) cc_final: 0.8592 (t0) REVERT: C 305 MET cc_start: 0.9095 (mtm) cc_final: 0.8882 (mtm) REVERT: D 109 ASN cc_start: 0.7575 (p0) cc_final: 0.7295 (p0) REVERT: E 139 LYS cc_start: 0.9125 (mmtm) cc_final: 0.8802 (mmmt) REVERT: E 161 LEU cc_start: 0.8834 (pp) cc_final: 0.8617 (pp) REVERT: E 339 PHE cc_start: 0.9436 (t80) cc_final: 0.8862 (t80) REVERT: E 340 MET cc_start: 0.9463 (mmp) cc_final: 0.9015 (mmt) REVERT: F 215 PHE cc_start: 0.9321 (m-80) cc_final: 0.8950 (m-80) REVERT: F 229 MET cc_start: 0.8018 (tmm) cc_final: 0.7524 (tmm) REVERT: G 68 MET cc_start: 0.8735 (pmm) cc_final: 0.8327 (pmm) REVERT: G 116 MET cc_start: 0.6351 (tpt) cc_final: 0.5711 (tpp) REVERT: G 215 PHE cc_start: 0.9385 (m-80) cc_final: 0.9154 (m-80) REVERT: G 247 LEU cc_start: 0.9234 (tp) cc_final: 0.8737 (tp) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.3476 time to fit residues: 185.5076 Evaluate side-chains 267 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 8.9990 chunk 236 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 263 optimal weight: 30.0000 chunk 218 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 138 optimal weight: 0.0870 overall best weight: 2.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN E 28 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 GLN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22182 Z= 0.210 Angle : 0.654 8.851 29984 Z= 0.332 Chirality : 0.043 0.176 3479 Planarity : 0.004 0.055 3815 Dihedral : 7.591 149.221 3027 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.04 % Allowed : 2.10 % Favored : 97.86 % 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: -0.30 (0.16), residues: 2734 helix: 0.47 (0.14), residues: 1315 sheet: -0.29 (0.23), residues: 471 loop : -0.94 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 28 HIS 0.008 0.001 HIS B 287 PHE 0.030 0.002 PHE C 151 TYR 0.021 0.002 TYR B 322 ARG 0.008 0.001 ARG F 149 *********************** 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 361 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 2.573 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: 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: 0.9024 (ppp) cc_final: 0.8461 (ppp) REVERT: A 1365 TYR cc_start: 0.9595 (t80) cc_final: 0.9337 (t80) REVERT: A 1506 PHE cc_start: 0.8567 (t80) cc_final: 0.8226 (t80) REVERT: A 1644 HIS cc_start: 0.8747 (m90) cc_final: 0.8304 (m90) REVERT: A 1709 LYS cc_start: 0.9233 (ptpp) cc_final: 0.8854 (pttt) REVERT: A 1790 ARG cc_start: 0.8572 (ptp90) cc_final: 0.8331 (mtm-85) REVERT: B 87 LEU cc_start: 0.9641 (tp) cc_final: 0.9437 (pp) REVERT: B 102 MET cc_start: 0.8756 (tmm) cc_final: 0.8473 (tmm) REVERT: B 121 LYS cc_start: 0.9503 (ttmt) cc_final: 0.9265 (mttp) REVERT: B 156 ARG cc_start: 0.9055 (tpt170) cc_final: 0.8436 (tpm170) REVERT: B 171 CYS cc_start: 0.6803 (m) cc_final: 0.6451 (m) REVERT: B 203 MET cc_start: 0.9156 (ptp) cc_final: 0.8910 (ptt) REVERT: C 56 LEU cc_start: 0.9303 (mt) cc_final: 0.8898 (pp) REVERT: C 58 LEU cc_start: 0.8934 (mp) cc_final: 0.8631 (mp) REVERT: C 88 LEU cc_start: 0.9140 (tp) cc_final: 0.8887 (tp) REVERT: C 148 ASN cc_start: 0.8872 (t0) cc_final: 0.8533 (t0) REVERT: D 109 ASN cc_start: 0.7761 (p0) cc_final: 0.7421 (p0) REVERT: E 139 LYS cc_start: 0.9140 (mmtm) cc_final: 0.8823 (mmmt) REVERT: E 156 MET cc_start: 0.8656 (pmm) cc_final: 0.8454 (pmm) REVERT: E 161 LEU cc_start: 0.8788 (pp) cc_final: 0.8456 (pp) REVERT: E 339 PHE cc_start: 0.9364 (t80) cc_final: 0.8839 (t80) REVERT: E 340 MET cc_start: 0.9440 (mmp) cc_final: 0.8995 (mmt) REVERT: F 150 ASP cc_start: 0.9329 (m-30) cc_final: 0.9055 (m-30) REVERT: F 199 MET cc_start: 0.6401 (ppp) cc_final: 0.5632 (ppp) REVERT: F 214 PHE cc_start: 0.9219 (m-80) cc_final: 0.8956 (m-80) REVERT: F 215 PHE cc_start: 0.9345 (m-80) cc_final: 0.9036 (m-80) REVERT: F 229 MET cc_start: 0.8017 (tmm) cc_final: 0.7526 (tmm) REVERT: G 68 MET cc_start: 0.8692 (pmm) cc_final: 0.8331 (pmm) REVERT: G 116 MET cc_start: 0.6306 (tpt) cc_final: 0.5803 (tpp) REVERT: G 215 PHE cc_start: 0.9383 (m-80) cc_final: 0.9148 (m-80) REVERT: G 247 LEU cc_start: 0.9240 (tp) cc_final: 0.8775 (tp) REVERT: H 119 MET cc_start: 0.7391 (ppp) cc_final: 0.7022 (ppp) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.3387 time to fit residues: 187.9953 Evaluate side-chains 283 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 30.0000 chunk 29 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 22182 Z= 0.382 Angle : 0.788 11.946 29984 Z= 0.403 Chirality : 0.045 0.202 3479 Planarity : 0.005 0.096 3815 Dihedral : 7.764 150.406 3027 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: -0.71 (0.15), residues: 2734 helix: 0.07 (0.14), residues: 1319 sheet: -0.47 (0.23), residues: 481 loop : -1.06 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP G 28 HIS 0.008 0.002 HIS E 331 PHE 0.043 0.003 PHE C 151 TYR 0.025 0.002 TYR E 330 ARG 0.007 0.001 ARG B 43 *********************** 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 335 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 2.863 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: 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: 0.9077 (ppp) cc_final: 0.8452 (ppp) REVERT: A 1506 PHE cc_start: 0.8597 (t80) cc_final: 0.8192 (t80) REVERT: A 1644 HIS cc_start: 0.8761 (m90) cc_final: 0.8313 (m90) REVERT: A 1709 LYS cc_start: 0.9156 (ptpp) cc_final: 0.8797 (pttp) REVERT: B 171 CYS cc_start: 0.6278 (m) cc_final: 0.6010 (m) REVERT: B 203 MET cc_start: 0.9224 (ptp) cc_final: 0.9002 (ptt) REVERT: C 56 LEU cc_start: 0.9269 (mt) cc_final: 0.8876 (pp) REVERT: C 58 LEU cc_start: 0.8963 (mp) cc_final: 0.8664 (mp) REVERT: C 88 LEU cc_start: 0.9298 (tp) cc_final: 0.9096 (tp) REVERT: C 121 LEU cc_start: 0.9488 (tp) cc_final: 0.9272 (tp) REVERT: C 152 CYS cc_start: 0.8505 (m) cc_final: 0.8075 (m) REVERT: C 166 GLN cc_start: 0.9462 (mt0) cc_final: 0.9190 (mt0) REVERT: C 305 MET cc_start: 0.9152 (mtp) cc_final: 0.8824 (mtm) REVERT: C 307 ASP cc_start: 0.9497 (m-30) cc_final: 0.9288 (m-30) REVERT: D 109 ASN cc_start: 0.7676 (p0) cc_final: 0.7162 (p0) REVERT: E 99 ASP cc_start: 0.8626 (p0) cc_final: 0.8381 (p0) REVERT: E 139 LYS cc_start: 0.9102 (mmtm) cc_final: 0.8773 (mmmt) REVERT: E 179 CYS cc_start: 0.9576 (m) cc_final: 0.8640 (t) REVERT: E 339 PHE cc_start: 0.9420 (t80) cc_final: 0.9109 (t80) REVERT: E 340 MET cc_start: 0.9445 (mmp) cc_final: 0.9186 (mmt) REVERT: F 75 MET cc_start: 0.9216 (mtm) cc_final: 0.8980 (mtm) REVERT: F 77 LYS cc_start: 0.9001 (tttt) cc_final: 0.8718 (tttt) REVERT: F 199 MET cc_start: 0.6464 (ppp) cc_final: 0.6199 (ppp) REVERT: F 215 PHE cc_start: 0.9431 (m-80) cc_final: 0.9135 (m-80) REVERT: F 229 MET cc_start: 0.8068 (tmm) cc_final: 0.7552 (tmm) REVERT: G 68 MET cc_start: 0.8652 (pmm) cc_final: 0.8092 (pmm) REVERT: G 116 MET cc_start: 0.6369 (tpt) cc_final: 0.5687 (tpp) REVERT: G 119 MET cc_start: 0.4834 (tmm) cc_final: 0.4462 (tmm) REVERT: G 215 PHE cc_start: 0.9436 (m-80) cc_final: 0.9177 (m-80) REVERT: G 247 LEU cc_start: 0.9248 (tp) cc_final: 0.8695 (tp) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.3410 time to fit residues: 177.4347 Evaluate side-chains 266 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 178 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 148 ASN ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN F 107 ASN ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22182 Z= 0.198 Angle : 0.674 9.910 29984 Z= 0.340 Chirality : 0.044 0.171 3479 Planarity : 0.004 0.058 3815 Dihedral : 7.634 149.722 3027 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: -0.33 (0.16), residues: 2734 helix: 0.43 (0.14), residues: 1313 sheet: -0.30 (0.23), residues: 477 loop : -0.94 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 22 HIS 0.008 0.001 HIS E 331 PHE 0.036 0.002 PHE A1324 TYR 0.022 0.002 TYR B 322 ARG 0.011 0.001 ARG C 112 *********************** 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 346 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 2.492 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.9050 (ppp) cc_final: 0.8697 (ppp) REVERT: A 1365 TYR cc_start: 0.9581 (t80) cc_final: 0.9337 (t80) REVERT: A 1506 PHE cc_start: 0.8573 (t80) cc_final: 0.8210 (t80) REVERT: A 1644 HIS cc_start: 0.8734 (m90) cc_final: 0.8279 (m90) REVERT: A 1709 LYS cc_start: 0.9202 (ptpp) cc_final: 0.8817 (pttt) REVERT: A 1790 ARG cc_start: 0.9089 (mtm-85) cc_final: 0.8888 (mtm-85) REVERT: A 1797 TYR cc_start: 0.8828 (m-10) cc_final: 0.8478 (m-80) REVERT: B 142 GLU cc_start: 0.8898 (tp30) cc_final: 0.8680 (tp30) REVERT: B 156 ARG cc_start: 0.9069 (tpt170) cc_final: 0.8486 (tpm170) REVERT: B 171 CYS cc_start: 0.6739 (m) cc_final: 0.6377 (m) REVERT: B 203 MET cc_start: 0.9186 (ptp) cc_final: 0.8972 (ptt) REVERT: C 56 LEU cc_start: 0.9323 (mt) cc_final: 0.8892 (pp) REVERT: C 58 LEU cc_start: 0.8938 (mp) cc_final: 0.8585 (mp) REVERT: C 121 LEU cc_start: 0.9315 (tp) cc_final: 0.9088 (tp) REVERT: C 152 CYS cc_start: 0.8408 (m) cc_final: 0.8025 (m) REVERT: C 166 GLN cc_start: 0.9349 (mt0) cc_final: 0.9036 (mt0) REVERT: C 307 ASP cc_start: 0.9455 (m-30) cc_final: 0.9250 (m-30) REVERT: D 109 ASN cc_start: 0.7796 (p0) cc_final: 0.7254 (p0) REVERT: E 99 ASP cc_start: 0.8564 (p0) cc_final: 0.8352 (p0) REVERT: E 139 LYS cc_start: 0.9129 (mmtm) cc_final: 0.8799 (mmmt) REVERT: E 156 MET cc_start: 0.8696 (pmm) cc_final: 0.8470 (pmm) REVERT: E 179 CYS cc_start: 0.9562 (m) cc_final: 0.8671 (t) REVERT: E 180 LEU cc_start: 0.8559 (tt) cc_final: 0.7535 (mp) REVERT: F 77 LYS cc_start: 0.8975 (tttt) cc_final: 0.8685 (tttt) REVERT: F 199 MET cc_start: 0.6283 (ppp) cc_final: 0.5986 (ppp) REVERT: F 214 PHE cc_start: 0.9210 (m-80) cc_final: 0.8989 (m-80) REVERT: F 215 PHE cc_start: 0.9411 (m-80) cc_final: 0.9113 (m-80) REVERT: F 229 MET cc_start: 0.8055 (tmm) cc_final: 0.7582 (tmm) REVERT: G 116 MET cc_start: 0.6256 (tpt) cc_final: 0.5757 (tpp) REVERT: G 215 PHE cc_start: 0.9404 (m-80) cc_final: 0.9041 (m-80) REVERT: G 247 LEU cc_start: 0.9240 (tp) cc_final: 0.8738 (tp) REVERT: G 251 LEU cc_start: 0.9648 (tp) cc_final: 0.9394 (tp) REVERT: H 119 MET cc_start: 0.7597 (ppp) cc_final: 0.7342 (ppp) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.3344 time to fit residues: 181.0820 Evaluate side-chains 291 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 8.9990 chunk 251 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN C 136 ASN ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 22182 Z= 0.375 Angle : 0.797 12.087 29984 Z= 0.408 Chirality : 0.046 0.202 3479 Planarity : 0.005 0.061 3815 Dihedral : 7.764 150.744 3027 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.04 % Allowed : 0.94 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2734 helix: 0.16 (0.14), residues: 1300 sheet: -0.51 (0.23), residues: 501 loop : -0.94 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP G 28 HIS 0.008 0.002 HIS E 331 PHE 0.039 0.003 PHE B 123 TYR 0.029 0.002 TYR E 330 ARG 0.012 0.001 ARG C 112 *********************** 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 327 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 326 time to evaluate : 2.494 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: 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: 0.9108 (ppp) cc_final: 0.8670 (ppp) REVERT: A 1506 PHE cc_start: 0.8592 (t80) cc_final: 0.8309 (t80) REVERT: A 1644 HIS cc_start: 0.8708 (m90) cc_final: 0.8255 (m90) REVERT: A 1709 LYS cc_start: 0.9127 (ptpp) cc_final: 0.8751 (pttp) REVERT: A 1790 ARG cc_start: 0.9166 (mtm-85) cc_final: 0.8566 (mtm-85) REVERT: A 1797 TYR cc_start: 0.8815 (m-10) cc_final: 0.8459 (m-80) REVERT: B 102 MET cc_start: 0.9107 (tmm) cc_final: 0.8213 (tmm) REVERT: B 142 GLU cc_start: 0.8930 (tp30) cc_final: 0.8696 (tp30) REVERT: B 171 CYS cc_start: 0.6270 (m) cc_final: 0.5944 (m) REVERT: B 203 MET cc_start: 0.9233 (ptp) cc_final: 0.9021 (ptt) REVERT: C 56 LEU cc_start: 0.9279 (mt) cc_final: 0.9050 (pp) REVERT: C 58 LEU cc_start: 0.8962 (mp) cc_final: 0.8757 (mp) REVERT: C 88 LEU cc_start: 0.9238 (tp) cc_final: 0.9021 (tp) REVERT: C 121 LEU cc_start: 0.9492 (tp) cc_final: 0.9238 (tp) REVERT: C 166 GLN cc_start: 0.9426 (mt0) cc_final: 0.9135 (mt0) REVERT: C 307 ASP cc_start: 0.9478 (m-30) cc_final: 0.9262 (m-30) REVERT: D 109 ASN cc_start: 0.7794 (p0) cc_final: 0.7280 (p0) REVERT: E 53 MET cc_start: 0.9360 (mtm) cc_final: 0.9157 (mtm) REVERT: E 99 ASP cc_start: 0.8714 (p0) cc_final: 0.8508 (p0) REVERT: E 139 LYS cc_start: 0.9091 (mmtm) cc_final: 0.8761 (mmmt) REVERT: E 179 CYS cc_start: 0.9555 (m) cc_final: 0.8645 (t) REVERT: E 180 LEU cc_start: 0.8587 (tt) cc_final: 0.7559 (mm) REVERT: E 339 PHE cc_start: 0.9509 (t80) cc_final: 0.9046 (t80) REVERT: E 340 MET cc_start: 0.9509 (mmt) cc_final: 0.9236 (mmm) REVERT: F 75 MET cc_start: 0.9207 (mtm) cc_final: 0.8980 (mtm) REVERT: F 77 LYS cc_start: 0.8988 (tttt) cc_final: 0.8681 (tttt) REVERT: F 139 MET cc_start: 0.9202 (ptt) cc_final: 0.8939 (ptt) REVERT: F 199 MET cc_start: 0.6433 (ppp) cc_final: 0.6091 (ppp) REVERT: F 215 PHE cc_start: 0.9464 (m-80) cc_final: 0.9236 (m-80) REVERT: F 229 MET cc_start: 0.8044 (tmm) cc_final: 0.7552 (tmm) REVERT: G 116 MET cc_start: 0.6095 (tpt) cc_final: 0.5411 (tpp) REVERT: G 119 MET cc_start: 0.5868 (tmm) cc_final: 0.5273 (tmm) REVERT: G 215 PHE cc_start: 0.9462 (m-80) cc_final: 0.9172 (m-80) REVERT: G 247 LEU cc_start: 0.9245 (tp) cc_final: 0.8677 (tp) outliers start: 1 outliers final: 0 residues processed: 327 average time/residue: 0.3320 time to fit residues: 169.9054 Evaluate side-chains 272 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 9.9990 chunk 258 optimal weight: 0.0030 chunk 157 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 270 optimal weight: 7.9990 chunk 249 optimal weight: 30.0000 chunk 215 optimal weight: 0.8980 chunk 22 optimal weight: 20.0000 chunk 166 optimal weight: 0.0030 chunk 132 optimal weight: 4.9990 overall best weight: 0.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN C 136 ASN C 148 ASN ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN F 107 ASN ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 22182 Z= 0.189 Angle : 0.717 12.309 29984 Z= 0.360 Chirality : 0.045 0.175 3479 Planarity : 0.004 0.060 3815 Dihedral : 7.589 148.667 3027 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.30 (0.16), residues: 2734 helix: 0.46 (0.14), residues: 1310 sheet: -0.35 (0.23), residues: 484 loop : -0.88 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP G 28 HIS 0.008 0.001 HIS B 287 PHE 0.027 0.002 PHE C 151 TYR 0.030 0.002 TYR E 318 ARG 0.009 0.001 ARG C 112 ********************** 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 347 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 2.693 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.9062 (ppp) cc_final: 0.8645 (ppp) REVERT: A 1365 TYR cc_start: 0.9571 (t80) cc_final: 0.9297 (t80) REVERT: A 1506 PHE cc_start: 0.8526 (t80) cc_final: 0.8322 (t80) REVERT: A 1644 HIS cc_start: 0.8702 (m90) cc_final: 0.8332 (m90) REVERT: A 1709 LYS cc_start: 0.9158 (ptpp) cc_final: 0.8776 (pttt) REVERT: A 1790 ARG cc_start: 0.9053 (mtm-85) cc_final: 0.8552 (mtm-85) REVERT: A 1797 TYR cc_start: 0.8827 (m-10) cc_final: 0.8499 (m-80) REVERT: B 102 MET cc_start: 0.8772 (tmm) cc_final: 0.8403 (tmm) REVERT: B 155 ARG cc_start: 0.8737 (ptm160) cc_final: 0.7673 (ptm160) REVERT: B 156 ARG cc_start: 0.9073 (tpt170) cc_final: 0.8503 (tpm170) REVERT: B 171 CYS cc_start: 0.6896 (m) cc_final: 0.6514 (m) REVERT: B 308 MET cc_start: 0.8976 (ppp) cc_final: 0.8614 (ppp) REVERT: C 56 LEU cc_start: 0.9260 (mt) cc_final: 0.8816 (pp) REVERT: C 58 LEU cc_start: 0.8956 (mp) cc_final: 0.8570 (mp) REVERT: C 121 LEU cc_start: 0.9350 (tp) cc_final: 0.9139 (tp) REVERT: C 136 ASN cc_start: 0.9060 (t160) cc_final: 0.8632 (t0) REVERT: C 152 CYS cc_start: 0.8351 (m) cc_final: 0.7828 (m) REVERT: C 166 GLN cc_start: 0.9322 (mt0) cc_final: 0.8982 (mt0) REVERT: C 305 MET cc_start: 0.9133 (mtm) cc_final: 0.8540 (mtm) REVERT: D 109 ASN cc_start: 0.7898 (p0) cc_final: 0.7382 (p0) REVERT: E 139 LYS cc_start: 0.9110 (mmtm) cc_final: 0.8749 (mmmt) REVERT: E 179 CYS cc_start: 0.9533 (m) cc_final: 0.8733 (t) REVERT: E 180 LEU cc_start: 0.8540 (tt) cc_final: 0.7509 (mp) REVERT: E 339 PHE cc_start: 0.9446 (t80) cc_final: 0.9224 (t80) REVERT: E 340 MET cc_start: 0.9458 (mmt) cc_final: 0.9155 (mmm) REVERT: F 40 MET cc_start: 0.7844 (ttt) cc_final: 0.7258 (tmm) REVERT: F 77 LYS cc_start: 0.8939 (tttt) cc_final: 0.8679 (tttt) REVERT: F 150 ASP cc_start: 0.9466 (m-30) cc_final: 0.8955 (m-30) REVERT: F 199 MET cc_start: 0.6261 (ppp) cc_final: 0.5925 (ppp) REVERT: F 215 PHE cc_start: 0.9417 (m-80) cc_final: 0.9151 (m-80) REVERT: G 68 MET cc_start: 0.8345 (pmm) cc_final: 0.7911 (pmm) REVERT: G 116 MET cc_start: 0.6037 (tpt) cc_final: 0.5510 (tpp) REVERT: G 119 MET cc_start: 0.5872 (tmm) cc_final: 0.5331 (tmm) REVERT: G 215 PHE cc_start: 0.9383 (m-80) cc_final: 0.9147 (m-80) REVERT: G 247 LEU cc_start: 0.9226 (tp) cc_final: 0.8637 (tp) REVERT: G 251 LEU cc_start: 0.9641 (tp) cc_final: 0.9439 (tp) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.3410 time to fit residues: 181.9392 Evaluate side-chains 275 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 198 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 216 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 221 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 323 GLN ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.107078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.079262 restraints weight = 109968.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.080919 restraints weight = 81672.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.082058 restraints weight = 66987.113| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22182 Z= 0.177 Angle : 0.677 11.221 29984 Z= 0.341 Chirality : 0.044 0.174 3479 Planarity : 0.004 0.062 3815 Dihedral : 7.325 143.113 3027 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.14 (0.16), residues: 2734 helix: 0.60 (0.14), residues: 1309 sheet: -0.28 (0.23), residues: 502 loop : -0.81 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 28 HIS 0.009 0.001 HIS B 287 PHE 0.037 0.002 PHE F 214 TYR 0.020 0.002 TYR B 322 ARG 0.008 0.001 ARG C 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4435.87 seconds wall clock time: 81 minutes 6.51 seconds (4866.51 seconds total)