Starting phenix.real_space_refine on Tue Jul 23 07:43:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uii_42295/07_2024/8uii_42295_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uii_42295/07_2024/8uii_42295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uii_42295/07_2024/8uii_42295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uii_42295/07_2024/8uii_42295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uii_42295/07_2024/8uii_42295_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uii_42295/07_2024/8uii_42295_neut.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 4 5.21 5 S 145 5.16 5 C 13664 2.51 5 N 3687 2.21 5 O 4190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1412": "OE1" <-> "OE2" Residue "A GLU 1729": "OE1" <-> "OE2" Residue "A PHE 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 99": "OD1" <-> "OD2" Residue "E ASP 128": "OD1" <-> "OD2" Residue "E TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 191": "OD1" <-> "OD2" Residue "E TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 304": "OD1" <-> "OD2" Residue "E TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F ASP 243": "OD1" <-> "OD2" Residue "F GLU 256": "OE1" <-> "OE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 198": "OE1" <-> "OE2" Residue "G TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 21": "OD1" <-> "OD2" Residue "H ASP 29": "OD1" <-> "OD2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H ASP 113": "OD1" <-> "OD2" Residue "H GLU 132": "OE1" <-> "OE2" Residue "H PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 232": "OD1" <-> "OD2" Residue "H TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 21704 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5117 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 619} 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: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2582 Classifications: {'peptide': 324} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 311} Chain: "D" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2536 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 314} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "F" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "H" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.86, per 1000 atoms: 0.55 Number of scatterers: 21704 At special positions: 0 Unit cell: (127.512, 123.372, 144.9, 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 14 15.00 Mg 4 11.99 O 4190 8.00 N 3687 7.00 C 13664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.70 Conformation dependent library (CDL) restraints added in 4.3 seconds 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5218 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 14 sheets defined 51.1% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 877 through 881 removed outlier: 3.659A pdb=" N CYS A 881 " --> pdb=" O ASP A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 895 Processing helix chain 'A' and resid 940 through 955 Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 1053 through 1058 Processing helix chain 'A' and resid 1069 through 1098 Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1163 through 1177 removed outlier: 6.193A pdb=" N GLU A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ALA A1174 " --> pdb=" O GLN A1170 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A1175 " --> pdb=" O LEU A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1327 Processing helix chain 'A' and resid 1340 through 1345 removed outlier: 3.722A pdb=" N MET A1344 " --> pdb=" O THR A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1373 removed outlier: 3.594A pdb=" N VAL A1362 " --> pdb=" O SER A1358 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A1373 " --> pdb=" O ILE A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1389 removed outlier: 3.715A pdb=" N PHE A1382 " --> pdb=" O ASP A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1406 Processing helix chain 'A' and resid 1457 through 1463 removed outlier: 3.818A pdb=" N THR A1461 " --> pdb=" O GLY A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1474 through 1481 Processing helix chain 'A' and resid 1485 through 1501 Processing helix chain 'A' and resid 1505 through 1510 Processing helix chain 'A' and resid 1510 through 1515 Processing helix chain 'A' and resid 1633 through 1663 removed outlier: 3.805A pdb=" N LEU A1641 " --> pdb=" O LYS A1637 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A1642 " --> pdb=" O CYS A1638 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A1663 " --> pdb=" O LEU A1659 " (cutoff:3.500A) Processing helix chain 'A' and resid 1698 through 1729 removed outlier: 3.580A pdb=" N SER A1702 " --> pdb=" O ASP A1698 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY A1706 " --> pdb=" O SER A1702 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU A1707 " --> pdb=" O GLN A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1737 removed outlier: 3.817A pdb=" N CYS A1734 " --> pdb=" O THR A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1746 Processing helix chain 'A' and resid 1764 through 1779 Processing helix chain 'A' and resid 1783 through 1787 removed outlier: 4.314A pdb=" N TYR A1786 " --> pdb=" O SER A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1814 removed outlier: 4.727A pdb=" N LEU A1798 " --> pdb=" O ILE A1794 " (cutoff:3.500A) Proline residue: A1799 - end of helix Processing helix chain 'A' and resid 1817 through 1821 Processing helix chain 'A' and resid 1822 through 1827 Processing helix chain 'A' and resid 1832 through 1840 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.833A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 146 Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.901A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.620A pdb=" N ARG B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 208 Processing helix chain 'B' and resid 214 through 225 Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.719A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 Processing helix chain 'B' and resid 333 through 350 Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.919A pdb=" N LEU C 34 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.505A pdb=" N GLU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 78 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 97 through 102 removed outlier: 4.098A pdb=" N ILE C 101 " --> pdb=" O GLY C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 127 through 130 Processing helix chain 'C' and resid 131 through 145 removed outlier: 4.055A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 162 through 169 removed outlier: 3.638A pdb=" N ARG C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 194 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 210 removed outlier: 3.939A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 277 through 291 removed outlier: 3.565A pdb=" N LEU C 286 " --> pdb=" O THR C 282 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 317 through 340 removed outlier: 3.606A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 56 through 68 Processing helix chain 'D' and resid 83 through 96 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 152 through 155 Processing helix chain 'D' and resid 156 through 170 removed outlier: 3.643A pdb=" N ARG D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 187 through 194 removed outlier: 3.732A pdb=" N ARG D 193 " --> pdb=" O PRO D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 219 Processing helix chain 'D' and resid 223 through 235 removed outlier: 3.597A pdb=" N ILE D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.792A pdb=" N GLY D 253 " --> pdb=" O THR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 266 removed outlier: 3.696A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.563A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 315 removed outlier: 3.514A pdb=" N LEU D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 361 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.517A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 30 removed outlier: 3.819A pdb=" N VAL E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 65 removed outlier: 4.095A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 102 removed outlier: 3.500A pdb=" N ALA E 100 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY E 101 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 122 removed outlier: 3.920A pdb=" N MET E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 155 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 188 through 202 removed outlier: 3.667A pdb=" N LYS E 202 " --> pdb=" O THR E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.625A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 Processing helix chain 'E' and resid 287 through 302 Processing helix chain 'E' and resid 306 through 325 removed outlier: 4.183A pdb=" N GLU E 310 " --> pdb=" O GLN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 348 removed outlier: 4.230A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 4.467A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.645A pdb=" N HIS F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 222 Proline residue: F 220 - end of helix No H-bonds generated for 'chain 'F' and resid 217 through 222' Processing helix chain 'G' and resid 9 through 17 removed outlier: 3.815A pdb=" N LEU G 16 " --> pdb=" O LEU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 23 removed outlier: 4.238A pdb=" N LEU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.923A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'G' and resid 218 through 222 removed outlier: 3.646A pdb=" N SER G 222 " --> pdb=" O THR G 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 19 removed outlier: 4.398A pdb=" N LEU H 12 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU H 19 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 72 through 79 Processing helix chain 'H' and resid 141 through 153 Processing helix chain 'H' and resid 209 through 217 Processing helix chain 'H' and resid 218 through 222 removed outlier: 3.681A pdb=" N SER H 222 " --> pdb=" O THR H 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.218A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU D 74 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N CYS D 180 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE D 76 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU D 106 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP D 150 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU D 108 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1151 through 1156 removed outlier: 8.603A pdb=" N ILE A1333 " --> pdb=" O SER A1300 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A1302 " --> pdb=" O ILE A1333 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N THR A1335 " --> pdb=" O ILE A1302 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE A1304 " --> pdb=" O THR A1335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1519 through 1521 Processing sheet with id=AA4, first strand: chain 'A' and resid 1683 through 1685 removed outlier: 4.034A pdb=" N LYS A1683 " --> pdb=" O GLU E 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1683 through 1685 removed outlier: 4.034A pdb=" N LYS A1683 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N CYS E 165 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL E 40 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU E 39 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.390A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N CYS B 171 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE B 74 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 73 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 91 removed outlier: 6.256A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 196 through 197 removed outlier: 6.883A pdb=" N ASP C 196 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 59 through 62 removed outlier: 3.853A pdb=" N THR F 59 " --> pdb=" O ARG F 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.142A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR F 196 " --> pdb=" O LYS F 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 203 through 208 removed outlier: 3.624A pdb=" N LYS F 181 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL H 111 " --> pdb=" O LYS F 181 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE H 87 " --> pdb=" O GLU H 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.920A pdb=" N VAL H 167 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL H 203 " --> pdb=" O CYS H 162 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.150A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY G 245 " --> pdb=" O ILE G 241 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 66 through 71 removed outlier: 5.627A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) 1154 hydrogen bonds defined for protein. 3318 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: 8.14 Time building geometry restraints manager: 8.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7218 1.36 - 1.51: 5553 1.51 - 1.66: 9066 1.66 - 1.80: 120 1.80 - 1.95: 95 Bond restraints: 22052 Sorted by residual: bond pdb=" N LEU B 154 " pdb=" CA LEU B 154 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.35e+00 bond pdb=" N MET H 229 " pdb=" CA MET H 229 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.26e-02 6.30e+03 6.07e+00 bond pdb=" C GLU B 257 " pdb=" N PRO B 258 " ideal model delta sigma weight residual 1.333 1.361 -0.029 1.17e-02 7.31e+03 5.99e+00 bond pdb=" C MET F 139 " pdb=" N PRO F 140 " ideal model delta sigma weight residual 1.330 1.360 -0.030 1.22e-02 6.72e+03 5.97e+00 bond pdb=" N MET F 139 " pdb=" CA MET F 139 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.62e+00 ... (remaining 22047 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.48: 396 105.48 - 113.01: 12199 113.01 - 120.53: 9117 120.53 - 128.06: 7979 128.06 - 135.59: 121 Bond angle restraints: 29812 Sorted by residual: angle pdb=" C MET H 244 " pdb=" N GLY H 245 " pdb=" CA GLY H 245 " ideal model delta sigma weight residual 120.72 114.16 6.56 1.33e+00 5.65e-01 2.43e+01 angle pdb=" N LEU F 90 " pdb=" CA LEU F 90 " pdb=" C LEU F 90 " ideal model delta sigma weight residual 109.59 101.71 7.88 1.61e+00 3.86e-01 2.39e+01 angle pdb=" CB MET G 199 " pdb=" CG MET G 199 " pdb=" SD MET G 199 " ideal model delta sigma weight residual 112.70 125.52 -12.82 3.00e+00 1.11e-01 1.83e+01 angle pdb=" CA GLN F 204 " pdb=" CB GLN F 204 " pdb=" CG GLN F 204 " ideal model delta sigma weight residual 114.10 122.59 -8.49 2.00e+00 2.50e-01 1.80e+01 angle pdb=" CA TYR A1508 " pdb=" CB TYR A1508 " pdb=" CG TYR A1508 " ideal model delta sigma weight residual 113.90 121.44 -7.54 1.80e+00 3.09e-01 1.76e+01 ... (remaining 29807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11732 17.95 - 35.90: 1430 35.90 - 53.85: 347 53.85 - 71.80: 64 71.80 - 89.74: 16 Dihedral angle restraints: 13589 sinusoidal: 5575 harmonic: 8014 Sorted by residual: dihedral pdb=" CA LEU G 247 " pdb=" C LEU G 247 " pdb=" N LYS G 248 " pdb=" CA LYS G 248 " ideal model delta harmonic sigma weight residual -180.00 -155.42 -24.58 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA LEU G 79 " pdb=" C LEU G 79 " pdb=" N LYS G 80 " pdb=" CA LYS G 80 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA PRO G 140 " pdb=" C PRO G 140 " pdb=" N SER G 141 " pdb=" CA SER G 141 " ideal model delta harmonic sigma weight residual -180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 13586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2966 0.064 - 0.129: 443 0.129 - 0.193: 41 0.193 - 0.258: 9 0.258 - 0.322: 2 Chirality restraints: 3461 Sorted by residual: chirality pdb=" CB ILE F 147 " pdb=" CA ILE F 147 " pdb=" CG1 ILE F 147 " pdb=" CG2 ILE F 147 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA LEU F 90 " pdb=" N LEU F 90 " pdb=" C LEU F 90 " pdb=" CB LEU F 90 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB VAL E 107 " pdb=" CA VAL E 107 " pdb=" CG1 VAL E 107 " pdb=" CG2 VAL E 107 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3458 not shown) Planarity restraints: 3792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 113 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C LYS E 113 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS E 113 " -0.018 2.00e-02 2.50e+03 pdb=" N THR E 114 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 138 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C LYS F 138 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS F 138 " -0.017 2.00e-02 2.50e+03 pdb=" N MET F 139 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 173 " -0.044 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO E 174 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO E 174 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 174 " -0.037 5.00e-02 4.00e+02 ... (remaining 3789 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 240 2.63 - 3.20: 17921 3.20 - 3.76: 34305 3.76 - 4.33: 46471 4.33 - 4.90: 77944 Nonbonded interactions: 176881 Sorted by model distance: nonbonded pdb=" OE2 GLU A1305 " pdb="MG MG A2001 " model vdw 2.061 2.170 nonbonded pdb="MG MG A2001 " pdb=" O1B AGS A2002 " model vdw 2.071 2.170 nonbonded pdb="MG MG A2001 " pdb=" O3G AGS A2002 " model vdw 2.076 2.170 nonbonded pdb=" OG1 THR A1139 " pdb="MG MG A2001 " model vdw 2.102 2.170 nonbonded pdb="MG MG D 401 " pdb=" O3G AGS D 402 " model vdw 2.112 2.170 ... (remaining 176876 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 57.380 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 0.003 0.063 22052 Z= 0.227 Angle : 0.758 12.821 29812 Z= 0.393 Chirality : 0.047 0.322 3461 Planarity : 0.005 0.066 3792 Dihedral : 16.545 89.744 8371 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.70 % Allowed : 23.48 % Favored : 75.82 % 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: -1.06 (0.15), residues: 2717 helix: -0.30 (0.13), residues: 1275 sheet: -0.42 (0.22), residues: 524 loop : -1.22 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 28 HIS 0.006 0.001 HIS A1178 PHE 0.027 0.002 PHE D 96 TYR 0.024 0.002 TYR G 249 ARG 0.013 0.001 ARG E 149 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 328 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1166 GLN cc_start: 0.7145 (mt0) cc_final: 0.6928 (mt0) REVERT: D 93 ARG cc_start: 0.6854 (mtp85) cc_final: 0.6595 (mtp180) REVERT: G 16 LEU cc_start: 0.6994 (pp) cc_final: 0.5862 (mp) REVERT: G 249 TYR cc_start: 0.6687 (m-80) cc_final: 0.6461 (m-80) outliers start: 17 outliers final: 9 residues processed: 337 average time/residue: 0.3552 time to fit residues: 180.4397 Evaluate side-chains 312 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 303 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1346 ASP Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 131 GLN Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 246 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 228 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 109 optimal weight: 0.3980 chunk 212 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 945 ASN A1094 ASN A1789 ASN B 332 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 HIS ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 ASN H 200 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 22052 Z= 0.428 Angle : 0.656 9.171 29812 Z= 0.333 Chirality : 0.045 0.156 3461 Planarity : 0.005 0.053 3792 Dihedral : 8.004 68.544 3040 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.51 % Allowed : 20.79 % Favored : 74.70 % 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: -0.57 (0.15), residues: 2717 helix: 0.30 (0.14), residues: 1259 sheet: -0.47 (0.22), residues: 521 loop : -1.08 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1079 HIS 0.007 0.001 HIS E 92 PHE 0.022 0.002 PHE D 126 TYR 0.033 0.002 TYR G 249 ARG 0.006 0.001 ARG D 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 302 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1157 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7839 (m-40) REVERT: A 1181 ASP cc_start: 0.6969 (t0) cc_final: 0.6713 (t0) REVERT: B 89 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7628 (tp) REVERT: B 98 LEU cc_start: 0.7820 (tt) cc_final: 0.7619 (tp) REVERT: C 182 MET cc_start: 0.7236 (ttt) cc_final: 0.6956 (ttt) REVERT: D 93 ARG cc_start: 0.7000 (mtp85) cc_final: 0.6705 (mtp180) REVERT: D 94 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7248 (mm-30) REVERT: E 105 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7604 (ttp80) REVERT: E 112 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7155 (mt) REVERT: E 340 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7165 (mtt) REVERT: G 131 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7203 (mp10) REVERT: H 209 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.6031 (tm) REVERT: H 251 LEU cc_start: 0.7628 (tt) cc_final: 0.7424 (tp) outliers start: 109 outliers final: 67 residues processed: 378 average time/residue: 0.3436 time to fit residues: 198.3175 Evaluate side-chains 349 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 275 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1157 ASN Chi-restraints excluded: chain A residue 1308 ASP Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 340 MET Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 131 GLN Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 136 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 204 optimal weight: 0.9990 chunk 167 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 246 optimal weight: 0.8980 chunk 266 optimal weight: 0.9980 chunk 219 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 HIS B 332 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 HIS F 95 ASN G 131 GLN G 179 ASN H 200 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22052 Z= 0.166 Angle : 0.517 8.260 29812 Z= 0.262 Chirality : 0.040 0.243 3461 Planarity : 0.003 0.046 3792 Dihedral : 7.530 69.033 3032 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.56 % Allowed : 22.49 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2717 helix: 0.87 (0.14), residues: 1271 sheet: -0.40 (0.23), residues: 519 loop : -0.91 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1403 HIS 0.004 0.001 HIS C 37 PHE 0.021 0.001 PHE D 126 TYR 0.014 0.001 TYR G 250 ARG 0.005 0.000 ARG A1414 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 309 time to evaluate : 2.412 Fit side-chains revert: symmetry clash REVERT: A 1181 ASP cc_start: 0.6965 (t0) cc_final: 0.6678 (t0) REVERT: B 54 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: B 89 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7354 (tp) REVERT: B 158 MET cc_start: 0.8010 (mtt) cc_final: 0.7741 (mtt) REVERT: C 37 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.7617 (m90) REVERT: C 182 MET cc_start: 0.6931 (ttt) cc_final: 0.6706 (ttt) REVERT: D 93 ARG cc_start: 0.6828 (mtp85) cc_final: 0.6560 (mtp180) REVERT: D 94 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7229 (mm-30) REVERT: D 151 GLU cc_start: 0.7792 (mp0) cc_final: 0.7407 (mp0) REVERT: D 317 ASN cc_start: 0.7957 (m-40) cc_final: 0.7659 (m-40) REVERT: E 105 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7385 (ttp80) REVERT: E 112 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7066 (mt) REVERT: F 89 THR cc_start: 0.7792 (m) cc_final: 0.7558 (m) REVERT: H 162 CYS cc_start: 0.4414 (m) cc_final: 0.3798 (p) REVERT: H 209 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.6029 (tm) outliers start: 86 outliers final: 46 residues processed: 373 average time/residue: 0.3435 time to fit residues: 196.7060 Evaluate side-chains 335 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 283 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1346 ASP Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 243 optimal weight: 8.9990 chunk 185 optimal weight: 0.0270 chunk 127 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 165 optimal weight: 0.0070 chunk 247 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 129 optimal weight: 0.9990 chunk 234 optimal weight: 4.9990 chunk 70 optimal weight: 0.1980 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 ASN B 332 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 HIS G 84 ASN G 179 ASN H 200 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22052 Z= 0.157 Angle : 0.492 9.190 29812 Z= 0.248 Chirality : 0.040 0.155 3461 Planarity : 0.003 0.042 3792 Dihedral : 7.125 66.762 3027 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.18 % Allowed : 22.78 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.16), residues: 2717 helix: 1.26 (0.15), residues: 1264 sheet: -0.35 (0.23), residues: 520 loop : -0.76 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1403 HIS 0.004 0.001 HIS E 301 PHE 0.016 0.001 PHE D 126 TYR 0.012 0.001 TYR G 249 ARG 0.006 0.000 ARG A1414 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 321 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1181 ASP cc_start: 0.6959 (t0) cc_final: 0.6661 (t0) REVERT: A 1501 MET cc_start: 0.7022 (mmp) cc_final: 0.6712 (mmm) REVERT: B 89 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7339 (tp) REVERT: D 93 ARG cc_start: 0.6840 (mtp85) cc_final: 0.6572 (mtp180) REVERT: D 151 GLU cc_start: 0.7767 (mp0) cc_final: 0.7402 (mp0) REVERT: D 317 ASN cc_start: 0.7914 (m-40) cc_final: 0.7561 (m-40) REVERT: E 105 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7360 (ttp80) REVERT: E 112 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7036 (mt) REVERT: F 25 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7750 (pm20) REVERT: F 89 THR cc_start: 0.7784 (m) cc_final: 0.7573 (m) REVERT: G 75 MET cc_start: 0.8229 (ttt) cc_final: 0.7492 (tpt) REVERT: H 162 CYS cc_start: 0.4332 (m) cc_final: 0.3806 (p) REVERT: H 209 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.6027 (tm) outliers start: 77 outliers final: 50 residues processed: 373 average time/residue: 0.3522 time to fit residues: 201.2911 Evaluate side-chains 342 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 287 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 218 optimal weight: 0.1980 chunk 148 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 235 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 ASN B 332 ASN C 148 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 HIS F 95 ASN G 84 ASN H 177 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 22052 Z= 0.430 Angle : 0.643 10.155 29812 Z= 0.323 Chirality : 0.045 0.173 3461 Planarity : 0.004 0.044 3792 Dihedral : 7.534 69.131 3023 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.33 % Allowed : 21.62 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2717 helix: 0.77 (0.14), residues: 1257 sheet: -0.50 (0.22), residues: 521 loop : -0.94 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1079 HIS 0.007 0.001 HIS E 92 PHE 0.019 0.002 PHE A1154 TYR 0.016 0.002 TYR B 279 ARG 0.006 0.001 ARG E 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 297 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1181 ASP cc_start: 0.6933 (t0) cc_final: 0.6620 (t0) REVERT: B 54 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: B 89 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7493 (tp) REVERT: C 37 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7664 (m90) REVERT: D 93 ARG cc_start: 0.6951 (mtp85) cc_final: 0.6591 (mtp180) REVERT: D 151 GLU cc_start: 0.7774 (mp0) cc_final: 0.7448 (mp0) REVERT: D 232 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8520 (tttp) REVERT: D 317 ASN cc_start: 0.8070 (m-40) cc_final: 0.7772 (m-40) REVERT: E 105 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7435 (ttp80) REVERT: E 112 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7069 (mt) REVERT: F 25 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7940 (pp20) REVERT: F 28 TRP cc_start: 0.8095 (m100) cc_final: 0.7628 (m100) REVERT: H 162 CYS cc_start: 0.4530 (m) cc_final: 0.3887 (p) REVERT: H 251 LEU cc_start: 0.7747 (tt) cc_final: 0.7546 (tp) outliers start: 129 outliers final: 90 residues processed: 391 average time/residue: 0.3492 time to fit residues: 212.0854 Evaluate side-chains 368 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 271 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1308 ASP Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 177 ASN Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 88 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 153 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 262 optimal weight: 30.0000 chunk 217 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 137 optimal weight: 0.0170 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 HIS F 95 ASN G 153 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22052 Z= 0.154 Angle : 0.517 8.440 29812 Z= 0.259 Chirality : 0.040 0.171 3461 Planarity : 0.003 0.041 3792 Dihedral : 7.098 68.892 3023 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.02 % Allowed : 24.22 % Favored : 72.76 % 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: 0.26 (0.16), residues: 2717 helix: 1.20 (0.15), residues: 1263 sheet: -0.45 (0.23), residues: 521 loop : -0.75 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1403 HIS 0.004 0.001 HIS F 246 PHE 0.014 0.001 PHE A1717 TYR 0.013 0.001 TYR G 249 ARG 0.007 0.000 ARG E 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 307 time to evaluate : 2.328 Fit side-chains revert: symmetry clash REVERT: A 1181 ASP cc_start: 0.6900 (t0) cc_final: 0.6567 (t0) REVERT: A 1490 HIS cc_start: 0.7701 (t-170) cc_final: 0.7484 (t-170) REVERT: A 1501 MET cc_start: 0.7034 (mmp) cc_final: 0.6701 (mmm) REVERT: B 54 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: B 89 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7303 (tp) REVERT: C 37 HIS cc_start: 0.7821 (OUTLIER) cc_final: 0.7507 (m90) REVERT: D 151 GLU cc_start: 0.7735 (mp0) cc_final: 0.7411 (mp0) REVERT: D 317 ASN cc_start: 0.7919 (m-40) cc_final: 0.7603 (m-40) REVERT: E 105 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7182 (ttp80) REVERT: E 112 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7099 (mt) REVERT: F 25 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7759 (pm20) REVERT: F 28 TRP cc_start: 0.8030 (m100) cc_final: 0.7573 (m100) REVERT: G 40 MET cc_start: 0.8296 (tpt) cc_final: 0.7868 (tpp) REVERT: G 75 MET cc_start: 0.7993 (ttt) cc_final: 0.7504 (tpt) REVERT: H 162 CYS cc_start: 0.4543 (m) cc_final: 0.3913 (p) REVERT: H 175 LEU cc_start: 0.4858 (tt) cc_final: 0.4355 (tt) outliers start: 73 outliers final: 51 residues processed: 359 average time/residue: 0.3378 time to fit residues: 186.1757 Evaluate side-chains 340 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 283 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 252 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 149 optimal weight: 0.2980 chunk 191 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 261 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 ASN B 332 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 HIS F 95 ASN G 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22052 Z= 0.200 Angle : 0.530 10.058 29812 Z= 0.263 Chirality : 0.041 0.198 3461 Planarity : 0.003 0.042 3792 Dihedral : 7.031 67.168 3023 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.64 % Allowed : 23.77 % Favored : 72.59 % 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: 2717 helix: 1.27 (0.15), residues: 1268 sheet: -0.43 (0.23), residues: 523 loop : -0.70 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1403 HIS 0.003 0.001 HIS E 301 PHE 0.012 0.001 PHE A1717 TYR 0.014 0.001 TYR G 249 ARG 0.007 0.000 ARG A1414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 297 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1181 ASP cc_start: 0.6853 (t0) cc_final: 0.6551 (t0) REVERT: A 1501 MET cc_start: 0.7055 (mmp) cc_final: 0.6734 (mmm) REVERT: B 54 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: B 89 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7354 (tp) REVERT: C 37 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7585 (m90) REVERT: D 151 GLU cc_start: 0.7733 (mp0) cc_final: 0.7400 (mp0) REVERT: D 317 ASN cc_start: 0.7950 (m-40) cc_final: 0.7599 (m-40) REVERT: E 105 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7203 (ttp80) REVERT: E 112 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7103 (mt) REVERT: F 25 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7786 (pm20) REVERT: F 28 TRP cc_start: 0.8027 (m100) cc_final: 0.7581 (m100) REVERT: G 40 MET cc_start: 0.8349 (tpt) cc_final: 0.7924 (tpp) REVERT: G 75 MET cc_start: 0.8076 (ttt) cc_final: 0.7615 (tpt) REVERT: H 162 CYS cc_start: 0.4569 (m) cc_final: 0.3934 (p) REVERT: H 175 LEU cc_start: 0.4854 (tt) cc_final: 0.4373 (tt) REVERT: H 251 LEU cc_start: 0.7694 (tt) cc_final: 0.7442 (tp) outliers start: 88 outliers final: 67 residues processed: 360 average time/residue: 0.3473 time to fit residues: 192.8682 Evaluate side-chains 354 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 281 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 161 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 78 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 ASN B 332 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 HIS F 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22052 Z= 0.160 Angle : 0.513 9.878 29812 Z= 0.254 Chirality : 0.040 0.211 3461 Planarity : 0.003 0.041 3792 Dihedral : 6.913 66.339 3023 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.64 % Allowed : 23.89 % Favored : 72.47 % 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: 0.47 (0.16), residues: 2717 helix: 1.39 (0.15), residues: 1267 sheet: -0.39 (0.23), residues: 524 loop : -0.67 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1403 HIS 0.003 0.001 HIS E 301 PHE 0.012 0.001 PHE A1717 TYR 0.012 0.001 TYR G 249 ARG 0.008 0.000 ARG A1414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 307 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1089 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5794 (mp) REVERT: A 1181 ASP cc_start: 0.6861 (t0) cc_final: 0.6553 (t0) REVERT: A 1318 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7862 (mm) REVERT: A 1344 MET cc_start: 0.8488 (mmt) cc_final: 0.6646 (ptp) REVERT: A 1490 HIS cc_start: 0.7701 (t-170) cc_final: 0.7482 (t-170) REVERT: A 1501 MET cc_start: 0.7028 (mmp) cc_final: 0.6726 (mmm) REVERT: A 1729 GLU cc_start: 0.7878 (pm20) cc_final: 0.7385 (pm20) REVERT: B 54 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: B 89 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7354 (tp) REVERT: C 37 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7562 (m90) REVERT: D 151 GLU cc_start: 0.7717 (mp0) cc_final: 0.7383 (mp0) REVERT: D 317 ASN cc_start: 0.7935 (m-40) cc_final: 0.7559 (m-40) REVERT: E 15 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6616 (mtt-85) REVERT: E 105 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7160 (ttp80) REVERT: E 112 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7074 (mt) REVERT: F 25 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: F 28 TRP cc_start: 0.8016 (m100) cc_final: 0.7568 (m100) REVERT: G 40 MET cc_start: 0.8324 (tpt) cc_final: 0.7812 (tpp) REVERT: H 162 CYS cc_start: 0.4564 (m) cc_final: 0.3943 (p) REVERT: H 175 LEU cc_start: 0.4782 (tt) cc_final: 0.4302 (tt) REVERT: H 251 LEU cc_start: 0.7681 (tt) cc_final: 0.7440 (tp) outliers start: 88 outliers final: 68 residues processed: 369 average time/residue: 0.3558 time to fit residues: 205.3348 Evaluate side-chains 370 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 293 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1842 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 237 optimal weight: 0.8980 chunk 250 optimal weight: 6.9990 chunk 228 optimal weight: 20.0000 chunk 243 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 106 optimal weight: 0.0980 chunk 191 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 ASN B 332 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 HIS F 95 ASN H 177 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22052 Z= 0.337 Angle : 0.606 12.862 29812 Z= 0.299 Chirality : 0.043 0.234 3461 Planarity : 0.004 0.042 3792 Dihedral : 7.212 67.511 3023 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.26 % Allowed : 23.52 % Favored : 72.22 % 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: 0.17 (0.16), residues: 2717 helix: 1.09 (0.15), residues: 1256 sheet: -0.39 (0.23), residues: 513 loop : -0.80 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1489 HIS 0.004 0.001 HIS E 92 PHE 0.017 0.002 PHE A1154 TYR 0.014 0.002 TYR B 279 ARG 0.008 0.000 ARG A1414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 299 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1089 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5816 (mp) REVERT: A 1318 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7902 (mm) REVERT: A 1490 HIS cc_start: 0.7798 (t-170) cc_final: 0.7571 (t-170) REVERT: B 54 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: B 89 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7408 (tp) REVERT: C 37 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7545 (m90) REVERT: D 151 GLU cc_start: 0.7733 (mp0) cc_final: 0.7413 (mp0) REVERT: D 317 ASN cc_start: 0.8003 (m-40) cc_final: 0.7671 (m-40) REVERT: E 15 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6574 (mtt-85) REVERT: E 105 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6715 (ttp80) REVERT: E 112 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7021 (mt) REVERT: F 25 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7940 (pp20) REVERT: F 28 TRP cc_start: 0.8065 (m100) cc_final: 0.7610 (m100) REVERT: H 162 CYS cc_start: 0.4687 (m) cc_final: 0.3978 (p) REVERT: H 175 LEU cc_start: 0.4823 (tt) cc_final: 0.4354 (tt) REVERT: H 251 LEU cc_start: 0.7702 (tt) cc_final: 0.7467 (tp) outliers start: 103 outliers final: 79 residues processed: 370 average time/residue: 0.3298 time to fit residues: 188.5044 Evaluate side-chains 369 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 281 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain A residue 1842 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 177 ASN Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 159 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 157 optimal weight: 0.0770 chunk 122 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 269 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 ASN B 332 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 HIS F 95 ASN H 177 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 22052 Z= 0.301 Angle : 0.778 59.200 29812 Z= 0.435 Chirality : 0.045 0.883 3461 Planarity : 0.005 0.188 3792 Dihedral : 7.234 67.673 3023 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.84 % Allowed : 24.18 % Favored : 71.97 % Cbeta Deviations : 0.04 % 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: 2717 helix: 1.08 (0.15), residues: 1262 sheet: -0.43 (0.23), residues: 513 loop : -0.81 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1489 HIS 0.004 0.001 HIS E 92 PHE 0.019 0.001 PHE G 215 TYR 0.040 0.002 TYR G 249 ARG 0.007 0.000 ARG A1414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 283 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1089 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5813 (mp) REVERT: A 1318 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7894 (mm) REVERT: A 1490 HIS cc_start: 0.7789 (t-170) cc_final: 0.7564 (t-170) REVERT: B 54 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: B 89 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7396 (tp) REVERT: C 37 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7538 (m90) REVERT: D 101 PHE cc_start: 0.6786 (OUTLIER) cc_final: 0.5979 (t80) REVERT: D 151 GLU cc_start: 0.7733 (mp0) cc_final: 0.7411 (mp0) REVERT: D 317 ASN cc_start: 0.7998 (m-40) cc_final: 0.7664 (m-40) REVERT: E 15 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6568 (mtt-85) REVERT: E 105 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.6738 (ttp80) REVERT: E 112 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7012 (mt) REVERT: F 25 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7940 (pp20) REVERT: F 28 TRP cc_start: 0.8059 (m100) cc_final: 0.7610 (m100) REVERT: H 162 CYS cc_start: 0.4683 (m) cc_final: 0.3977 (p) REVERT: H 175 LEU cc_start: 0.4830 (tt) cc_final: 0.4361 (tt) REVERT: H 251 LEU cc_start: 0.7699 (tt) cc_final: 0.7469 (tp) outliers start: 93 outliers final: 79 residues processed: 346 average time/residue: 0.3389 time to fit residues: 180.6482 Evaluate side-chains 370 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 281 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1648 SER Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1838 THR Chi-restraints excluded: chain A residue 1842 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 81 CYS Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 170 optimal weight: 0.9980 chunk 229 optimal weight: 0.4980 chunk 65 optimal weight: 0.0010 chunk 198 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 221 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 ASN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 HIS F 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.192344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.148039 restraints weight = 27542.181| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.47 r_work: 0.3555 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 22052 Z= 0.301 Angle : 0.778 59.200 29812 Z= 0.435 Chirality : 0.045 0.883 3461 Planarity : 0.005 0.188 3792 Dihedral : 7.234 67.673 3023 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.76 % Allowed : 24.22 % Favored : 72.01 % Cbeta Deviations : 0.04 % 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: 2717 helix: 1.08 (0.15), residues: 1262 sheet: -0.43 (0.23), residues: 513 loop : -0.81 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1489 HIS 0.004 0.001 HIS E 92 PHE 0.019 0.001 PHE G 215 TYR 0.040 0.002 TYR G 249 ARG 0.007 0.000 ARG A1414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4962.80 seconds wall clock time: 89 minutes 31.46 seconds (5371.46 seconds total)