Starting phenix.real_space_refine on Sun Jun 30 17:33:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui7_42287/06_2024/8ui7_42287_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui7_42287/06_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_42287/06_2024/8ui7_42287.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui7_42287/06_2024/8ui7_42287.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui7_42287/06_2024/8ui7_42287_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui7_42287/06_2024/8ui7_42287_updated.pdb" } 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 11.42, 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: 8.74 Conformation dependent library (CDL) restraints added in 4.2 seconds 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5252 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 18 sheets defined 44.5% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 891 through 894 No H-bonds generated for 'chain 'A' and resid 891 through 894' Processing helix chain 'A' and resid 941 through 954 Processing helix chain 'A' and resid 960 through 971 Proline residue: A 965 - end of helix Processing helix chain 'A' and resid 1054 through 1057 No H-bonds generated for 'chain 'A' and resid 1054 through 1057' Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1070 through 1097 Processing helix chain 'A' and resid 1138 through 1148 Processing helix chain 'A' and resid 1164 through 1175 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 1317 through 1327 Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.733A pdb=" N MET A1344 " --> pdb=" O PHE A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1372 Processing helix chain 'A' and resid 1379 through 1388 Processing helix chain 'A' and resid 1393 through 1405 Processing helix chain 'A' and resid 1458 through 1462 Processing helix chain 'A' and resid 1465 through 1467 No H-bonds generated for 'chain 'A' and resid 1465 through 1467' Processing helix chain 'A' and resid 1475 through 1480 Processing helix chain 'A' and resid 1486 through 1501 Processing helix chain 'A' and resid 1506 through 1509 No H-bonds generated for 'chain 'A' and resid 1506 through 1509' Processing helix chain 'A' and resid 1511 through 1514 No H-bonds generated for 'chain 'A' and resid 1511 through 1514' Processing helix chain 'A' and resid 1633 through 1661 Processing helix chain 'A' and resid 1700 through 1736 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) removed outlier: 3.961A pdb=" N LEU A1731 " --> pdb=" O ALA A1727 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASN A1732 " --> pdb=" O LEU A1728 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N SER A1733 " --> pdb=" O GLU A1729 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1744 Processing helix chain 'A' and resid 1751 through 1754 No H-bonds generated for 'chain 'A' and resid 1751 through 1754' Processing helix chain 'A' and resid 1765 through 1778 Processing helix chain 'A' and resid 1790 through 1814 Proline residue: A1799 - end of helix Processing helix chain 'A' and resid 1818 through 1821 Processing helix chain 'A' and resid 1825 through 1827 No H-bonds generated for 'chain 'A' and resid 1825 through 1827' Processing helix chain 'A' and resid 1833 through 1839 Processing helix chain 'B' and resid 38 through 41 No H-bonds generated for 'chain 'B' and resid 38 through 41' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 54 through 65 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'B' and resid 96 through 99 removed outlier: 4.270A pdb=" N LYS B 99 " --> pdb=" O PRO B 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 96 through 99' Processing helix chain 'B' and resid 113 through 125 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 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 148 through 160 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) Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 195 through 209 Processing helix chain 'B' and resid 215 through 223 Processing helix chain 'B' and resid 229 through 242 Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 292 through 304 Processing helix chain 'B' and resid 310 through 329 Processing helix chain 'B' and resid 334 through 349 removed outlier: 3.860A 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 4 through 11 Processing helix chain 'C' and resid 22 through 25 No H-bonds generated for 'chain 'C' and resid 22 through 25' Processing helix chain 'C' and resid 38 through 49 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 132 through 145 removed outlier: 4.079A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 145 " --> pdb=" O VAL C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 179 through 193 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 199 through 209 Processing helix chain 'C' and resid 213 through 227 Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 259 through 273 Processing helix chain 'C' and resid 277 through 288 Processing helix chain 'C' and resid 295 through 314 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) Processing helix chain 'C' and resid 318 through 338 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 40 through 43 No H-bonds generated for 'chain 'D' and resid 40 through 43' Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 98 through 104 removed outlier: 4.094A 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 116 through 128 Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 188 through 191 No H-bonds generated for 'chain 'D' and resid 188 through 191' Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 224 through 234 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 271 through 283 Processing helix chain 'D' and resid 286 through 298 Processing helix chain 'D' and resid 303 through 316 removed outlier: 3.957A pdb=" N GLU D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 339 Processing helix chain 'D' and resid 344 through 362 removed outlier: 4.144A pdb=" N ASN D 362 " --> pdb=" O GLN D 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 20 through 32 Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 97 through 121 removed outlier: 6.652A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG E 105 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU E 110 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N MET E 111 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 142 through 152 Processing helix chain 'E' and resid 173 through 178 removed outlier: 3.576A pdb=" N ARG E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 202 Processing helix chain 'E' and resid 209 through 219 Processing helix chain 'E' and resid 223 through 236 Processing helix chain 'E' and resid 250 through 264 Processing helix chain 'E' and resid 268 through 283 Processing helix chain 'E' and resid 288 through 301 removed outlier: 4.332A pdb=" N HIS E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 324 removed outlier: 4.004A 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 328 through 347 Processing helix chain 'F' and resid 10 through 18 Processing helix chain 'F' and resid 54 through 56 No H-bonds generated for 'chain 'F' and resid 54 through 56' Processing helix chain 'F' and resid 72 through 81 removed outlier: 3.951A pdb=" N LYS F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N CYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 154 Processing helix chain 'F' and resid 209 through 221 removed outlier: 4.182A pdb=" N ALA F 218 " --> pdb=" O PHE F 214 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR F 219 " --> pdb=" O PHE F 215 " (cutoff:3.500A) Proline residue: F 220 - end of helix Processing helix chain 'G' and resid 9 through 18 Processing helix chain 'G' and resid 54 through 56 No H-bonds generated for 'chain 'G' and resid 54 through 56' Processing helix chain 'G' and resid 72 through 81 removed outlier: 4.340A pdb=" N CYS G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 154 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 221 removed outlier: 4.255A pdb=" N ALA G 218 " --> pdb=" O PHE G 214 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR G 219 " --> pdb=" O PHE G 215 " (cutoff:3.500A) Proline residue: G 220 - end of helix Processing helix chain 'H' and resid 12 through 18 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 81 removed outlier: 4.351A pdb=" N CYS H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 153 removed outlier: 4.028A pdb=" N HIS H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 221 removed outlier: 3.586A pdb=" N LYS H 217 " --> pdb=" O ASN H 213 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA H 218 " --> pdb=" O PHE H 214 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR H 219 " --> pdb=" O PHE H 215 " (cutoff:3.500A) Proline residue: H 220 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 1350 through 1354 removed outlier: 6.804A pdb=" N VAL A1332 " --> pdb=" O VAL A1128 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE A1130 " --> pdb=" O VAL A1332 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A1334 " --> pdb=" O ILE A1130 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N GLY A1132 " --> pdb=" O LEU A1334 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR A1336 " --> pdb=" O GLY A1132 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1519 through 1521 removed outlier: 5.515A pdb=" N PHE A1747 " --> pdb=" O ASP A1520 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 186 through 189 removed outlier: 6.144A 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) Processing sheet with id= D, first strand: chain 'C' and resid 170 through 174 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) Processing sheet with id= E, first strand: chain 'D' and resid 177 through 180 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: 6.283A pdb=" N SER D 195 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR D 77 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N PHE D 197 " --> pdb=" O TYR D 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 105 through 108 removed outlier: 7.104A pdb=" N ILE D 146 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU D 108 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE D 148 " --> pdb=" O LEU D 108 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'E' and resid 180 through 183 removed outlier: 6.255A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 68 through 74 Processing sheet with id= I, 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) Processing sheet with id= J, first strand: chain 'F' and resid 25 through 30 Processing sheet with id= K, first strand: chain 'F' and resid 34 through 40 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= L, first strand: chain 'F' and resid 204 through 208 removed outlier: 6.357A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 60 through 62 Processing sheet with id= N, 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) Processing sheet with id= O, first strand: chain 'G' and resid 203 through 208 removed outlier: 6.359A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 2 through 6 Processing sheet with id= Q, 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= R, first strand: chain 'H' and resid 203 through 208 removed outlier: 3.710A pdb=" N VAL H 167 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA H 171 " --> pdb=" O GLY H 178 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY H 178 " --> pdb=" O ALA H 171 " (cutoff:3.500A) 990 hydrogen bonds defined for protein. 2826 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: 7.42 Time building geometry restraints manager: 9.54 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: 256 2.57 - 3.16: 17596 3.16 - 3.74: 36955 3.74 - 4.32: 48508 4.32 - 4.90: 77837 Nonbonded interactions: 181152 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 181147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 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: 7.520 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 56.770 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.150 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.730 ------------------------------------------------------------------------------- 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= 0.287 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 : 2.537 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: 0.3428 time to fit residues: 206.2979 Evaluate side-chains 298 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.611 ------------------------------------------------------------------------------- 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: 50.0000 chunk 206 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 70 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 247 optimal weight: 0.0020 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1751 GLN ** B 231 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 126 GLN ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN G 49 GLN ** 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: 0.7875 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22182 Z= 0.255 Angle : 0.638 9.787 29984 Z= 0.329 Chirality : 0.041 0.186 3479 Planarity : 0.004 0.059 3815 Dihedral : 7.684 141.354 3027 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.04 % Allowed : 4.85 % Favored : 95.11 % 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: -0.53 (0.15), residues: 2734 helix: 0.25 (0.14), residues: 1279 sheet: -0.30 (0.23), residues: 499 loop : -1.03 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 22 HIS 0.008 0.001 HIS E 331 PHE 0.027 0.002 PHE F 215 TYR 0.026 0.002 TYR B 322 ARG 0.020 0.001 ARG F 146 *********************** 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 371 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 370 time to evaluate : 2.426 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: 0.8954 (ppp) cc_final: 0.8434 (ppp) REVERT: A 1317 PHE cc_start: 0.7938 (t80) cc_final: 0.7671 (t80) REVERT: A 1708 LEU cc_start: 0.9254 (mt) cc_final: 0.9047 (mt) REVERT: B 100 ASP cc_start: 0.8631 (m-30) cc_final: 0.8370 (m-30) REVERT: B 171 CYS cc_start: 0.6967 (m) cc_final: 0.6562 (m) REVERT: B 223 PHE cc_start: 0.9489 (t80) cc_final: 0.9271 (t80) REVERT: B 293 GLU cc_start: 0.9074 (mp0) cc_final: 0.8848 (mp0) REVERT: C 108 PHE cc_start: 0.9396 (t80) cc_final: 0.8581 (t80) REVERT: C 120 LYS cc_start: 0.9520 (mtmt) cc_final: 0.8984 (mtmt) REVERT: C 135 GLN cc_start: 0.8508 (mt0) cc_final: 0.8064 (mt0) REVERT: C 155 CYS cc_start: 0.8030 (t) cc_final: 0.7638 (t) REVERT: E 37 HIS cc_start: 0.8446 (m-70) cc_final: 0.8236 (m-70) REVERT: E 139 LYS cc_start: 0.9116 (mmtm) cc_final: 0.8827 (mmmt) REVERT: E 335 PHE cc_start: 0.9217 (t80) cc_final: 0.8778 (t80) REVERT: E 339 PHE cc_start: 0.9455 (t80) cc_final: 0.9229 (t80) REVERT: E 340 MET cc_start: 0.9336 (mmp) cc_final: 0.9106 (mmm) REVERT: F 215 PHE cc_start: 0.9092 (m-80) cc_final: 0.8810 (m-80) REVERT: F 229 MET cc_start: 0.7992 (tmm) cc_final: 0.7754 (tmm) REVERT: G 28 TRP cc_start: 0.9082 (m100) cc_final: 0.8819 (m100) REVERT: G 68 MET cc_start: 0.8759 (pmm) cc_final: 0.8516 (pmm) REVERT: G 215 PHE cc_start: 0.9355 (m-80) cc_final: 0.9102 (m-80) REVERT: G 247 LEU cc_start: 0.9297 (tp) cc_final: 0.8729 (tp) REVERT: G 251 LEU cc_start: 0.9676 (tp) cc_final: 0.9470 (tp) outliers start: 1 outliers final: 0 residues processed: 370 average time/residue: 0.3401 time to fit residues: 193.2004 Evaluate side-chains 296 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 2.782 ------------------------------------------------------------------------------- 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: 7.9990 chunk 76 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 267 optimal weight: 30.0000 chunk 220 optimal weight: 30.0000 chunk 245 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 49 GLN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 22182 Z= 0.312 Angle : 0.690 9.462 29984 Z= 0.354 Chirality : 0.042 0.171 3479 Planarity : 0.005 0.058 3815 Dihedral : 7.658 145.091 3027 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 24.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.16 % Allowed : 5.75 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 2734 helix: 0.35 (0.14), residues: 1286 sheet: -0.27 (0.24), residues: 474 loop : -1.06 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 22 HIS 0.009 0.002 HIS A1644 PHE 0.023 0.002 PHE G 215 TYR 0.023 0.002 TYR B 322 ARG 0.009 0.001 ARG F 61 *********************** 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 362 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 358 time to evaluate : 2.317 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: 0.8470 (ppp) REVERT: A 1506 PHE cc_start: 0.8275 (t80) cc_final: 0.7942 (t80) REVERT: B 71 ASN cc_start: 0.8959 (m-40) cc_final: 0.8733 (m-40) REVERT: B 102 MET cc_start: 0.8995 (tmm) cc_final: 0.7931 (tmm) REVERT: B 171 CYS cc_start: 0.6644 (m) cc_final: 0.6313 (m) REVERT: B 293 GLU cc_start: 0.9096 (mp0) cc_final: 0.8856 (mp0) REVERT: C 108 PHE cc_start: 0.9383 (t80) cc_final: 0.8482 (t80) REVERT: C 120 LYS cc_start: 0.9524 (mtmt) cc_final: 0.8955 (ttmt) REVERT: D 109 ASN cc_start: 0.7442 (p0) cc_final: 0.7205 (p0) REVERT: E 161 LEU cc_start: 0.8928 (pp) cc_final: 0.8529 (pp) REVERT: E 318 TYR cc_start: 0.8823 (m-10) cc_final: 0.8445 (m-10) REVERT: E 335 PHE cc_start: 0.9229 (t80) cc_final: 0.8559 (t80) REVERT: E 339 PHE cc_start: 0.9483 (t80) cc_final: 0.9089 (t80) REVERT: E 340 MET cc_start: 0.9461 (mmp) cc_final: 0.9093 (mmt) REVERT: F 148 CYS cc_start: 0.8856 (m) cc_final: 0.8539 (m) REVERT: F 199 MET cc_start: 0.6151 (ppp) cc_final: 0.5097 (ppp) REVERT: F 215 PHE cc_start: 0.9143 (m-80) cc_final: 0.8788 (m-80) REVERT: F 229 MET cc_start: 0.8102 (tmm) cc_final: 0.7689 (tmm) REVERT: G 68 MET cc_start: 0.8754 (pmm) cc_final: 0.8482 (pmm) REVERT: G 75 MET cc_start: 0.9503 (tpt) cc_final: 0.9300 (tpt) REVERT: G 116 MET cc_start: 0.6715 (tpp) cc_final: 0.5077 (mpp) REVERT: G 215 PHE cc_start: 0.9384 (m-80) cc_final: 0.9059 (m-80) REVERT: G 247 LEU cc_start: 0.9271 (tp) cc_final: 0.8750 (tp) REVERT: H 107 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7678 (t0) REVERT: H 119 MET cc_start: 0.7420 (ppp) cc_final: 0.7201 (ppp) outliers start: 4 outliers final: 2 residues processed: 362 average time/residue: 0.3409 time to fit residues: 188.4912 Evaluate side-chains 288 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 285 time to evaluate : 2.515 ------------------------------------------------------------------------------- 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: 10.0000 chunk 128 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 248 optimal weight: 0.3980 chunk 262 optimal weight: 9.9990 chunk 129 optimal weight: 0.0970 chunk 235 optimal weight: 0.8980 chunk 70 optimal weight: 0.0370 overall best weight: 1.2858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1500 GLN A1644 HIS ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN C 241 HIS C 257 GLN C 265 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** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN E 124 ASN ** E 323 GLN ** 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 49 GLN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS H 107 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2016 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= 0.169 Angle : 0.602 9.007 29984 Z= 0.301 Chirality : 0.041 0.169 3479 Planarity : 0.004 0.050 3815 Dihedral : 7.371 144.858 3027 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 2734 helix: 0.64 (0.14), residues: 1276 sheet: -0.18 (0.24), residues: 478 loop : -0.92 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 28 HIS 0.010 0.001 HIS A1644 PHE 0.031 0.002 PHE C 151 TYR 0.026 0.002 TYR B 322 ARG 0.008 0.000 ARG F 146 *********************** 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 381 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 2.502 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: 0.9192 (ppp) cc_final: 0.8561 (ppp) REVERT: A 1506 PHE cc_start: 0.8253 (t80) cc_final: 0.7931 (t80) REVERT: A 1645 CYS cc_start: 0.9232 (m) cc_final: 0.9022 (p) REVERT: B 71 ASN cc_start: 0.8730 (m-40) cc_final: 0.8511 (m-40) REVERT: B 87 LEU cc_start: 0.9630 (tp) cc_final: 0.9420 (pp) REVERT: B 100 ASP cc_start: 0.8448 (m-30) cc_final: 0.8208 (m-30) REVERT: B 117 ARG cc_start: 0.9285 (tpp-160) cc_final: 0.8548 (mmt90) REVERT: B 171 CYS cc_start: 0.7031 (m) cc_final: 0.6631 (m) REVERT: B 293 GLU cc_start: 0.8998 (mp0) cc_final: 0.8650 (mp0) REVERT: B 308 MET cc_start: 0.8947 (ppp) cc_final: 0.8481 (ppp) REVERT: C 56 LEU cc_start: 0.9323 (mt) cc_final: 0.9023 (pp) REVERT: C 108 PHE cc_start: 0.9354 (t80) cc_final: 0.8684 (t80) REVERT: C 144 LYS cc_start: 0.9513 (tmmt) cc_final: 0.9236 (tppt) REVERT: C 148 ASN cc_start: 0.8856 (t0) cc_final: 0.8510 (t0) REVERT: C 305 MET cc_start: 0.8927 (mtm) cc_final: 0.8671 (mtm) REVERT: D 109 ASN cc_start: 0.7440 (p0) cc_final: 0.7147 (p0) REVERT: E 161 LEU cc_start: 0.8649 (pp) cc_final: 0.8448 (pp) REVERT: E 318 TYR cc_start: 0.8729 (m-10) cc_final: 0.8332 (m-10) REVERT: E 335 PHE cc_start: 0.9166 (t80) cc_final: 0.8606 (t80) REVERT: E 339 PHE cc_start: 0.9435 (t80) cc_final: 0.9065 (t80) REVERT: E 340 MET cc_start: 0.9410 (mmp) cc_final: 0.9140 (mmt) REVERT: F 40 MET cc_start: 0.8518 (ttt) cc_final: 0.7946 (ttt) REVERT: F 148 CYS cc_start: 0.8788 (m) cc_final: 0.8373 (m) REVERT: F 199 MET cc_start: 0.5922 (ppp) cc_final: 0.5063 (ppp) REVERT: F 215 PHE cc_start: 0.9158 (m-80) cc_final: 0.8818 (m-80) REVERT: F 229 MET cc_start: 0.8051 (tmm) cc_final: 0.7603 (tmm) REVERT: G 75 MET cc_start: 0.9454 (tpt) cc_final: 0.9227 (tpt) REVERT: G 116 MET cc_start: 0.6815 (tpp) cc_final: 0.5108 (mpp) REVERT: G 215 PHE cc_start: 0.9393 (m-80) cc_final: 0.9039 (m-80) REVERT: G 247 LEU cc_start: 0.9256 (tp) cc_final: 0.8826 (tp) REVERT: G 251 LEU cc_start: 0.9649 (tp) cc_final: 0.9403 (tp) REVERT: H 119 MET cc_start: 0.7552 (ppp) cc_final: 0.7260 (ppp) outliers start: 0 outliers final: 0 residues processed: 381 average time/residue: 0.3374 time to fit residues: 197.3533 Evaluate side-chains 295 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 2.563 ------------------------------------------------------------------------------- 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: 7.9990 chunk 149 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 195 optimal weight: 0.0020 chunk 108 optimal weight: 0.9990 chunk 224 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 235 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 135 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 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 49 GLN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22182 Z= 0.253 Angle : 0.644 11.137 29984 Z= 0.329 Chirality : 0.041 0.163 3479 Planarity : 0.004 0.054 3815 Dihedral : 7.282 143.207 3027 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2734 helix: 0.60 (0.14), residues: 1274 sheet: -0.23 (0.23), residues: 489 loop : -0.91 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 22 HIS 0.009 0.001 HIS A1644 PHE 0.018 0.002 PHE A1717 TYR 0.023 0.002 TYR B 322 ARG 0.012 0.001 ARG C 112 *********************** 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 359 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 2.436 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: 0.9024 (ppp) cc_final: 0.8525 (ppp) REVERT: A 1506 PHE cc_start: 0.8293 (t80) cc_final: 0.7921 (t80) REVERT: A 1645 CYS cc_start: 0.9258 (m) cc_final: 0.9058 (p) REVERT: A 1709 LYS cc_start: 0.9090 (ptpp) cc_final: 0.8654 (pttt) REVERT: B 71 ASN cc_start: 0.8932 (m-40) cc_final: 0.8693 (m-40) REVERT: B 102 MET cc_start: 0.8776 (tmm) cc_final: 0.8525 (tmm) REVERT: B 171 CYS cc_start: 0.6797 (m) cc_final: 0.6292 (m) REVERT: B 293 GLU cc_start: 0.9082 (mp0) cc_final: 0.8865 (mp0) REVERT: B 308 MET cc_start: 0.9110 (ppp) cc_final: 0.8877 (ppp) REVERT: C 56 LEU cc_start: 0.9343 (mt) cc_final: 0.8965 (mt) REVERT: C 86 MET cc_start: 0.8485 (mtt) cc_final: 0.8040 (mtt) REVERT: C 121 LEU cc_start: 0.9569 (tp) cc_final: 0.9311 (tp) REVERT: C 136 ASN cc_start: 0.9235 (t0) cc_final: 0.8803 (t0) REVERT: C 148 ASN cc_start: 0.8901 (t0) cc_final: 0.8582 (t0) REVERT: D 109 ASN cc_start: 0.7520 (p0) cc_final: 0.7202 (p0) REVERT: D 327 ILE cc_start: 0.9352 (mt) cc_final: 0.9138 (mt) REVERT: E 248 GLU cc_start: 0.7326 (tp30) cc_final: 0.7056 (tm-30) REVERT: E 318 TYR cc_start: 0.8695 (m-10) cc_final: 0.8454 (m-10) REVERT: E 335 PHE cc_start: 0.9191 (t80) cc_final: 0.8702 (t80) REVERT: E 339 PHE cc_start: 0.9435 (t80) cc_final: 0.8933 (t80) REVERT: E 340 MET cc_start: 0.9460 (mmp) cc_final: 0.9013 (mmt) REVERT: F 148 CYS cc_start: 0.8985 (m) cc_final: 0.8743 (m) REVERT: F 215 PHE cc_start: 0.9243 (m-80) cc_final: 0.8908 (m-80) REVERT: F 229 MET cc_start: 0.8232 (tmm) cc_final: 0.7784 (tmm) REVERT: G 75 MET cc_start: 0.9480 (tpt) cc_final: 0.9262 (tpt) REVERT: G 116 MET cc_start: 0.6880 (tpp) cc_final: 0.5186 (mpp) REVERT: G 215 PHE cc_start: 0.9394 (m-80) cc_final: 0.9060 (m-80) REVERT: G 247 LEU cc_start: 0.9232 (tp) cc_final: 0.8721 (tp) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.3373 time to fit residues: 185.7601 Evaluate side-chains 284 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 2.568 ------------------------------------------------------------------------------- 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: 2.9990 chunk 236 optimal weight: 0.0570 chunk 51 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 263 optimal weight: 40.0000 chunk 218 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1644 HIS B 231 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 265 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** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN E 124 ASN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS H 107 ASN H 213 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22182 Z= 0.167 Angle : 0.624 11.684 29984 Z= 0.310 Chirality : 0.042 0.167 3479 Planarity : 0.004 0.051 3815 Dihedral : 7.105 143.731 3027 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % 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: -0.01 (0.16), residues: 2734 helix: 0.77 (0.15), residues: 1270 sheet: -0.14 (0.23), residues: 479 loop : -0.84 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP G 28 HIS 0.009 0.001 HIS A1644 PHE 0.031 0.002 PHE C 151 TYR 0.022 0.001 TYR B 322 ARG 0.007 0.000 ARG C 333 *********************** 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 385 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.536 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: 0.9037 (ppp) cc_final: 0.8493 (ppp) REVERT: A 1709 LYS cc_start: 0.9020 (ptpp) cc_final: 0.8754 (mtmt) REVERT: A 1790 ARG cc_start: 0.9067 (mtm-85) cc_final: 0.8865 (ptp90) REVERT: A 1797 TYR cc_start: 0.8803 (m-10) cc_final: 0.8410 (m-80) REVERT: B 117 ARG cc_start: 0.9267 (tpp-160) cc_final: 0.8696 (mmt90) REVERT: B 171 CYS cc_start: 0.6990 (m) cc_final: 0.6506 (m) REVERT: B 293 GLU cc_start: 0.9044 (mp0) cc_final: 0.8720 (mp0) REVERT: B 308 MET cc_start: 0.9021 (ppp) cc_final: 0.8800 (ppp) REVERT: C 56 LEU cc_start: 0.9286 (mt) cc_final: 0.8923 (mt) REVERT: C 86 MET cc_start: 0.8514 (mtt) cc_final: 0.8186 (mtt) REVERT: C 121 LEU cc_start: 0.9563 (tp) cc_final: 0.9325 (tp) REVERT: C 123 ILE cc_start: 0.9580 (pt) cc_final: 0.9094 (tp) REVERT: C 136 ASN cc_start: 0.9129 (t0) cc_final: 0.8785 (t0) REVERT: C 148 ASN cc_start: 0.8830 (t0) cc_final: 0.8552 (t0) REVERT: D 109 ASN cc_start: 0.7696 (p0) cc_final: 0.7363 (p0) REVERT: E 99 ASP cc_start: 0.8372 (p0) cc_final: 0.8165 (p0) REVERT: E 134 LEU cc_start: 0.9556 (mt) cc_final: 0.9276 (pp) REVERT: E 161 LEU cc_start: 0.8823 (pp) cc_final: 0.8491 (pp) REVERT: E 162 ILE cc_start: 0.9285 (mm) cc_final: 0.8754 (tp) REVERT: E 314 MET cc_start: 0.9132 (ptt) cc_final: 0.8621 (ptp) REVERT: E 335 PHE cc_start: 0.9112 (t80) cc_final: 0.8705 (t80) REVERT: E 339 PHE cc_start: 0.9412 (t80) cc_final: 0.8905 (t80) REVERT: E 340 MET cc_start: 0.9419 (mmp) cc_final: 0.9062 (mmt) REVERT: F 148 CYS cc_start: 0.8960 (m) cc_final: 0.8672 (m) REVERT: F 199 MET cc_start: 0.6040 (ppp) cc_final: 0.5710 (ppp) REVERT: F 214 PHE cc_start: 0.9310 (m-80) cc_final: 0.9107 (m-80) REVERT: F 215 PHE cc_start: 0.9207 (m-80) cc_final: 0.8892 (m-80) REVERT: F 229 MET cc_start: 0.8123 (tmm) cc_final: 0.7678 (tmm) REVERT: G 1 MET cc_start: 0.8473 (mmm) cc_final: 0.8213 (tpt) REVERT: G 28 TRP cc_start: 0.9140 (m100) cc_final: 0.8352 (m100) REVERT: G 75 MET cc_start: 0.9453 (tpt) cc_final: 0.9194 (tpt) REVERT: G 116 MET cc_start: 0.6908 (tpp) cc_final: 0.5208 (mpp) REVERT: G 215 PHE cc_start: 0.9358 (m-80) cc_final: 0.9039 (m-80) REVERT: G 247 LEU cc_start: 0.9258 (tp) cc_final: 0.8827 (tp) REVERT: G 251 LEU cc_start: 0.9653 (tp) cc_final: 0.9374 (tp) REVERT: H 119 MET cc_start: 0.7443 (ppp) cc_final: 0.7113 (ppp) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.3319 time to fit residues: 196.4404 Evaluate side-chains 288 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 2.440 ------------------------------------------------------------------------------- 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: 0.8980 chunk 149 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1374 ASN A1644 HIS ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 265 ASN ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 GLN ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 22182 Z= 0.334 Angle : 0.733 10.116 29984 Z= 0.374 Chirality : 0.043 0.176 3479 Planarity : 0.005 0.058 3815 Dihedral : 7.283 145.180 3027 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 26.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: -0.35 (0.16), residues: 2734 helix: 0.46 (0.14), residues: 1279 sheet: -0.23 (0.23), residues: 483 loop : -1.01 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP G 28 HIS 0.012 0.002 HIS C 289 PHE 0.023 0.002 PHE C 151 TYR 0.020 0.002 TYR E 343 ARG 0.011 0.001 ARG F 61 *********************** 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 345 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 2.614 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: A 1052 MET cc_start: 0.9084 (ppp) cc_final: 0.8483 (ppp) REVERT: A 1506 PHE cc_start: 0.8356 (t80) cc_final: 0.7999 (t80) REVERT: A 1709 LYS cc_start: 0.8974 (ptpp) cc_final: 0.8634 (mtmt) REVERT: B 71 ASN cc_start: 0.9066 (m-40) cc_final: 0.8726 (m-40) REVERT: B 102 MET cc_start: 0.8791 (tmm) cc_final: 0.8589 (tmm) REVERT: B 142 GLU cc_start: 0.8831 (tp30) cc_final: 0.8630 (tp30) REVERT: B 231 GLN cc_start: 0.9188 (mm110) cc_final: 0.8950 (mm-40) REVERT: C 56 LEU cc_start: 0.9319 (mt) cc_final: 0.8926 (mt) REVERT: C 86 MET cc_start: 0.8612 (mtt) cc_final: 0.8077 (mtt) REVERT: C 136 ASN cc_start: 0.9223 (t0) cc_final: 0.8882 (t0) REVERT: C 148 ASN cc_start: 0.8986 (t0) cc_final: 0.8697 (t0) REVERT: D 109 ASN cc_start: 0.7757 (p0) cc_final: 0.7491 (p0) REVERT: D 327 ILE cc_start: 0.9385 (mt) cc_final: 0.9181 (mt) REVERT: E 99 ASP cc_start: 0.8405 (p0) cc_final: 0.8174 (p0) REVERT: E 134 LEU cc_start: 0.9587 (mt) cc_final: 0.9193 (pp) REVERT: E 139 LYS cc_start: 0.8987 (mmpt) cc_final: 0.8676 (mmmt) REVERT: E 248 GLU cc_start: 0.7406 (tp30) cc_final: 0.7126 (tm-30) REVERT: E 314 MET cc_start: 0.9145 (ptt) cc_final: 0.8682 (ptt) REVERT: E 318 TYR cc_start: 0.8736 (m-10) cc_final: 0.8518 (m-10) REVERT: E 335 PHE cc_start: 0.9174 (t80) cc_final: 0.8546 (t80) REVERT: E 339 PHE cc_start: 0.9416 (t80) cc_final: 0.8854 (t80) REVERT: E 340 MET cc_start: 0.9440 (mmp) cc_final: 0.8951 (mmt) REVERT: F 144 PHE cc_start: 0.8809 (t80) cc_final: 0.8491 (t80) REVERT: F 148 CYS cc_start: 0.9211 (m) cc_final: 0.8982 (m) REVERT: F 199 MET cc_start: 0.6257 (ppp) cc_final: 0.5981 (ppp) REVERT: F 215 PHE cc_start: 0.9365 (m-80) cc_final: 0.9069 (m-80) REVERT: F 229 MET cc_start: 0.8255 (tmm) cc_final: 0.7721 (tmm) REVERT: G 68 MET cc_start: 0.8626 (pmm) cc_final: 0.8368 (pmm) REVERT: G 215 PHE cc_start: 0.9392 (m-80) cc_final: 0.9068 (m-80) REVERT: G 247 LEU cc_start: 0.9224 (tp) cc_final: 0.8749 (tp) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.3328 time to fit residues: 179.3281 Evaluate side-chains 267 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 2.419 ------------------------------------------------------------------------------- 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: 9.9990 chunk 104 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 24 optimal weight: 0.2980 chunk 206 optimal weight: 6.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** 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 246 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 302 ASN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 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: 0.7902 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 22182 Z= 0.184 Angle : 0.643 9.820 29984 Z= 0.322 Chirality : 0.042 0.168 3479 Planarity : 0.004 0.050 3815 Dihedral : 7.086 146.275 3027 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.04 % Allowed : 1.44 % Favored : 98.52 % 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: -0.07 (0.16), residues: 2734 helix: 0.70 (0.15), residues: 1268 sheet: -0.14 (0.23), residues: 485 loop : -0.85 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 28 HIS 0.010 0.001 HIS A1644 PHE 0.029 0.002 PHE C 151 TYR 0.021 0.002 TYR B 322 ARG 0.007 0.000 ARG C 333 *********************** 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 361 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 2.544 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: A 1052 MET cc_start: 0.9135 (ppp) cc_final: 0.8565 (ppp) REVERT: A 1325 MET cc_start: 0.9132 (ptp) cc_final: 0.8915 (ptp) REVERT: A 1506 PHE cc_start: 0.8358 (t80) cc_final: 0.7982 (t80) REVERT: A 1644 HIS cc_start: 0.8729 (m90) cc_final: 0.8287 (m90) REVERT: A 1709 LYS cc_start: 0.9042 (ptpp) cc_final: 0.8792 (mtmt) REVERT: A 1797 TYR cc_start: 0.8799 (m-10) cc_final: 0.8474 (m-80) REVERT: B 117 ARG cc_start: 0.9277 (tpp-160) cc_final: 0.8720 (mmt90) REVERT: B 171 CYS cc_start: 0.7025 (m) cc_final: 0.6517 (m) REVERT: B 231 GLN cc_start: 0.9227 (mm110) cc_final: 0.8803 (mm-40) REVERT: C 56 LEU cc_start: 0.9307 (mt) cc_final: 0.8936 (mt) REVERT: C 86 MET cc_start: 0.8315 (mtt) cc_final: 0.8100 (mtt) REVERT: C 88 LEU cc_start: 0.9255 (tp) cc_final: 0.9033 (tp) REVERT: C 121 LEU cc_start: 0.9548 (tp) cc_final: 0.9277 (tp) REVERT: C 123 ILE cc_start: 0.9561 (pt) cc_final: 0.9124 (tp) REVERT: C 136 ASN cc_start: 0.9132 (t0) cc_final: 0.8822 (t0) REVERT: C 148 ASN cc_start: 0.8966 (t0) cc_final: 0.8634 (t0) REVERT: D 109 ASN cc_start: 0.7807 (p0) cc_final: 0.7526 (p0) REVERT: D 327 ILE cc_start: 0.9305 (mt) cc_final: 0.9096 (mt) REVERT: E 99 ASP cc_start: 0.8380 (p0) cc_final: 0.8149 (p0) REVERT: E 134 LEU cc_start: 0.9556 (mt) cc_final: 0.9058 (pp) REVERT: E 139 LYS cc_start: 0.9038 (mmpt) cc_final: 0.8709 (mmmt) REVERT: E 162 ILE cc_start: 0.9317 (mm) cc_final: 0.8613 (tp) REVERT: E 164 CYS cc_start: 0.8551 (t) cc_final: 0.8103 (p) REVERT: E 248 GLU cc_start: 0.7364 (tp30) cc_final: 0.7047 (tm-30) REVERT: E 339 PHE cc_start: 0.9411 (t80) cc_final: 0.8852 (t80) REVERT: E 340 MET cc_start: 0.9418 (mmp) cc_final: 0.9041 (mmt) REVERT: F 144 PHE cc_start: 0.8623 (t80) cc_final: 0.8295 (t80) REVERT: F 199 MET cc_start: 0.5973 (ppp) cc_final: 0.5480 (ppp) REVERT: F 215 PHE cc_start: 0.9332 (m-80) cc_final: 0.9003 (m-80) REVERT: F 229 MET cc_start: 0.8220 (tmm) cc_final: 0.7813 (tmm) REVERT: G 68 MET cc_start: 0.8500 (pmm) cc_final: 0.8233 (pmm) REVERT: G 116 MET cc_start: 0.6588 (tpp) cc_final: 0.4473 (mpp) REVERT: G 215 PHE cc_start: 0.9353 (m-80) cc_final: 0.9026 (m-80) REVERT: G 247 LEU cc_start: 0.9252 (tp) cc_final: 0.8853 (tp) REVERT: H 119 MET cc_start: 0.7545 (ppp) cc_final: 0.7297 (ppp) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.3326 time to fit residues: 185.7400 Evaluate side-chains 284 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 2.422 ------------------------------------------------------------------------------- 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: 0.9990 chunk 251 optimal weight: 0.0470 chunk 229 optimal weight: 40.0000 chunk 244 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 191 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 220 optimal weight: 20.0000 chunk 231 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 overall best weight: 1.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1069 ASN ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 284 HIS ** 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22182 Z= 0.172 Angle : 0.631 9.854 29984 Z= 0.313 Chirality : 0.042 0.172 3479 Planarity : 0.004 0.050 3815 Dihedral : 6.874 142.300 3027 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 0.06 (0.16), residues: 2734 helix: 0.79 (0.15), residues: 1281 sheet: -0.11 (0.23), residues: 500 loop : -0.79 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 22 HIS 0.007 0.001 HIS B 287 PHE 0.038 0.002 PHE F 214 TYR 0.018 0.002 TYR B 322 ARG 0.006 0.000 ARG C 264 *********************** 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 364 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 2.514 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: A 1052 MET cc_start: 0.9106 (ppp) cc_final: 0.8511 (ppp) REVERT: A 1325 MET cc_start: 0.9147 (ptp) cc_final: 0.8902 (ptp) REVERT: A 1365 TYR cc_start: 0.9509 (t80) cc_final: 0.9241 (t80) REVERT: A 1506 PHE cc_start: 0.8318 (t80) cc_final: 0.7959 (t80) REVERT: A 1644 HIS cc_start: 0.8690 (m90) cc_final: 0.8287 (m90) REVERT: A 1709 LYS cc_start: 0.9024 (ptpp) cc_final: 0.8781 (mtmt) REVERT: A 1797 TYR cc_start: 0.8800 (m-10) cc_final: 0.8482 (m-80) REVERT: B 71 ASN cc_start: 0.8841 (m-40) cc_final: 0.8637 (m-40) REVERT: B 89 LEU cc_start: 0.9553 (tp) cc_final: 0.9318 (pp) REVERT: B 117 ARG cc_start: 0.9280 (tpp-160) cc_final: 0.8748 (mmt90) REVERT: B 171 CYS cc_start: 0.7059 (m) cc_final: 0.6519 (m) REVERT: B 231 GLN cc_start: 0.9119 (mm110) cc_final: 0.8802 (mm-40) REVERT: C 56 LEU cc_start: 0.9336 (mt) cc_final: 0.9010 (mt) REVERT: C 88 LEU cc_start: 0.9139 (tp) cc_final: 0.8921 (tp) REVERT: C 121 LEU cc_start: 0.9464 (tp) cc_final: 0.9216 (tp) REVERT: C 136 ASN cc_start: 0.9113 (t0) cc_final: 0.8824 (t0) REVERT: C 148 ASN cc_start: 0.8962 (t0) cc_final: 0.8642 (t0) REVERT: D 109 ASN cc_start: 0.7722 (p0) cc_final: 0.7431 (p0) REVERT: E 99 ASP cc_start: 0.8409 (p0) cc_final: 0.8070 (p0) REVERT: E 134 LEU cc_start: 0.9567 (mt) cc_final: 0.9209 (pp) REVERT: E 139 LYS cc_start: 0.9072 (mmpt) cc_final: 0.8733 (mmmt) REVERT: E 161 LEU cc_start: 0.8879 (pp) cc_final: 0.8567 (pp) REVERT: E 248 GLU cc_start: 0.7327 (tp30) cc_final: 0.6999 (tm-30) REVERT: E 335 PHE cc_start: 0.9207 (t80) cc_final: 0.8911 (t80) REVERT: E 339 PHE cc_start: 0.9366 (t80) cc_final: 0.8818 (t80) REVERT: E 340 MET cc_start: 0.9395 (mmp) cc_final: 0.9016 (mmt) REVERT: F 77 LYS cc_start: 0.8965 (tttt) cc_final: 0.8699 (tttt) REVERT: F 199 MET cc_start: 0.5973 (ppp) cc_final: 0.5268 (ppp) REVERT: F 215 PHE cc_start: 0.9285 (m-80) cc_final: 0.8977 (m-80) REVERT: F 229 MET cc_start: 0.8162 (tmm) cc_final: 0.7759 (tmm) REVERT: G 1 MET cc_start: 0.8532 (mmm) cc_final: 0.8268 (tpt) REVERT: G 68 MET cc_start: 0.8413 (pmm) cc_final: 0.8182 (pmm) REVERT: G 116 MET cc_start: 0.6600 (tpp) cc_final: 0.4498 (mpp) REVERT: G 215 PHE cc_start: 0.9378 (m-80) cc_final: 0.9115 (m-80) REVERT: G 247 LEU cc_start: 0.9242 (tp) cc_final: 0.8826 (tp) REVERT: G 251 LEU cc_start: 0.9646 (tp) cc_final: 0.9380 (tp) REVERT: H 119 MET cc_start: 0.7569 (ppp) cc_final: 0.7284 (ppp) REVERT: H 249 TYR cc_start: 0.9010 (m-10) cc_final: 0.8740 (m-10) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.3397 time to fit residues: 193.4512 Evaluate side-chains 289 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 2.499 ------------------------------------------------------------------------------- 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: 0.0970 chunk 258 optimal weight: 0.6980 chunk 157 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 270 optimal weight: 30.0000 chunk 249 optimal weight: 0.5980 chunk 215 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 166 optimal weight: 10.0000 chunk 132 optimal weight: 0.0270 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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** ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 265 ASN ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN E 124 ASN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 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: 0.7854 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 22182 Z= 0.161 Angle : 0.641 12.230 29984 Z= 0.317 Chirality : 0.042 0.166 3479 Planarity : 0.004 0.049 3815 Dihedral : 6.747 138.848 3027 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 0.13 (0.16), residues: 2734 helix: 0.82 (0.15), residues: 1283 sheet: -0.03 (0.23), residues: 511 loop : -0.74 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 22 HIS 0.008 0.001 HIS B 287 PHE 0.021 0.001 PHE F 144 TYR 0.018 0.001 TYR B 322 ARG 0.010 0.000 ARG F 149 ********************** 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 374 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 2.565 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: 0.9083 (ppp) cc_final: 0.8498 (ppp) REVERT: A 1325 MET cc_start: 0.9162 (ptp) cc_final: 0.8882 (ptp) REVERT: A 1365 TYR cc_start: 0.9488 (t80) cc_final: 0.9241 (t80) REVERT: A 1644 HIS cc_start: 0.8695 (m90) cc_final: 0.8294 (m90) REVERT: A 1709 LYS cc_start: 0.9031 (ptpp) cc_final: 0.8798 (mtmt) REVERT: A 1797 TYR cc_start: 0.8787 (m-10) cc_final: 0.8471 (m-80) REVERT: B 71 ASN cc_start: 0.8762 (m-40) cc_final: 0.8540 (m-40) REVERT: B 89 LEU cc_start: 0.9556 (tp) cc_final: 0.9319 (pp) REVERT: B 117 ARG cc_start: 0.9250 (tpp-160) cc_final: 0.8743 (mmt90) REVERT: B 171 CYS cc_start: 0.7203 (m) cc_final: 0.6678 (m) REVERT: B 231 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8598 (mm-40) REVERT: C 56 LEU cc_start: 0.9303 (mt) cc_final: 0.9088 (pp) REVERT: C 86 MET cc_start: 0.8109 (mtt) cc_final: 0.7877 (mtt) REVERT: C 88 LEU cc_start: 0.9196 (tp) cc_final: 0.8867 (tp) REVERT: C 121 LEU cc_start: 0.9476 (tp) cc_final: 0.9201 (tp) REVERT: C 123 ILE cc_start: 0.9556 (pt) cc_final: 0.9042 (tp) REVERT: C 136 ASN cc_start: 0.9071 (t0) cc_final: 0.8799 (t0) REVERT: C 148 ASN cc_start: 0.8961 (t0) cc_final: 0.8621 (t0) REVERT: C 217 LEU cc_start: 0.9305 (mt) cc_final: 0.9093 (mt) REVERT: D 109 ASN cc_start: 0.7731 (p0) cc_final: 0.7433 (p0) REVERT: E 139 LYS cc_start: 0.9104 (mmpt) cc_final: 0.8744 (mmmt) REVERT: E 339 PHE cc_start: 0.9359 (t80) cc_final: 0.8859 (t80) REVERT: E 340 MET cc_start: 0.9380 (mmp) cc_final: 0.9054 (mmt) REVERT: F 139 MET cc_start: 0.8841 (ppp) cc_final: 0.8497 (ppp) REVERT: F 150 ASP cc_start: 0.9335 (m-30) cc_final: 0.9078 (m-30) REVERT: F 199 MET cc_start: 0.5906 (ppp) cc_final: 0.4952 (ppp) REVERT: F 214 PHE cc_start: 0.9423 (m-80) cc_final: 0.9104 (m-80) REVERT: F 215 PHE cc_start: 0.9243 (m-80) cc_final: 0.8896 (m-80) REVERT: G 1 MET cc_start: 0.8491 (mmm) cc_final: 0.8215 (tpt) REVERT: G 116 MET cc_start: 0.6579 (tpp) cc_final: 0.4524 (mpp) REVERT: G 185 THR cc_start: 0.9133 (p) cc_final: 0.8781 (t) REVERT: G 247 LEU cc_start: 0.9254 (tp) cc_final: 0.8863 (tp) REVERT: H 119 MET cc_start: 0.7511 (ppp) cc_final: 0.7213 (ppp) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.3257 time to fit residues: 189.9307 Evaluate side-chains 293 residues out of total 2434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 2.379 ------------------------------------------------------------------------------- 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: 0.9980 chunk 229 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 216 optimal weight: 8.9990 chunk 90 optimal weight: 0.4980 chunk 221 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- 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** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN C 265 ASN ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.107580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.077127 restraints weight = 93007.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.077981 restraints weight = 79355.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.078392 restraints weight = 72161.962| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22182 Z= 0.245 Angle : 0.672 11.592 29984 Z= 0.340 Chirality : 0.042 0.171 3479 Planarity : 0.004 0.051 3815 Dihedral : 6.772 138.814 3027 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 0.01 (0.16), residues: 2734 helix: 0.76 (0.15), residues: 1292 sheet: -0.18 (0.23), residues: 505 loop : -0.80 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 22 HIS 0.007 0.001 HIS B 287 PHE 0.046 0.002 PHE G 215 TYR 0.017 0.002 TYR E 343 ARG 0.008 0.001 ARG F 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4537.24 seconds wall clock time: 82 minutes 31.89 seconds (4951.89 seconds total)