Starting phenix.real_space_refine on Sun Jun 30 16:46:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uii_42295/06_2024/8uii_42295_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uii_42295/06_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_42295/06_2024/8uii_42295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uii_42295/06_2024/8uii_42295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uii_42295/06_2024/8uii_42295_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uii_42295/06_2024/8uii_42295_updated.pdb" } 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-5370/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: 11.52, per 1000 atoms: 0.53 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: 8.03 Conformation dependent library (CDL) restraints added in 3.9 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... running ksdssp... Secondary structure from input PDB file: 111 helices and 18 sheets defined 43.9% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 891 through 894 No H-bonds generated for 'chain 'A' and resid 891 through 894' Processing helix chain 'A' and resid 941 through 954 Processing helix chain 'A' and resid 964 through 971 Processing helix chain 'A' and resid 1054 through 1057 No H-bonds generated for 'chain 'A' and resid 1054 through 1057' Processing helix chain 'A' and resid 1070 through 1097 Processing helix chain 'A' and resid 1138 through 1148 Processing helix chain 'A' and resid 1164 through 1176 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 1317 through 1326 Processing helix chain 'A' and resid 1341 through 1344 No H-bonds generated for 'chain 'A' and resid 1341 through 1344' Processing helix chain 'A' and resid 1359 through 1372 Processing helix chain 'A' and resid 1379 through 1388 Processing helix chain 'A' and resid 1393 through 1405 Processing helix chain 'A' and resid 1458 through 1462 Processing helix chain 'A' and resid 1475 through 1480 Processing helix chain 'A' and resid 1486 through 1500 Processing helix chain 'A' and resid 1506 through 1509 No H-bonds generated for 'chain 'A' and resid 1506 through 1509' Processing helix chain 'A' and resid 1511 through 1514 No H-bonds generated for 'chain 'A' and resid 1511 through 1514' Processing helix chain 'A' and resid 1633 through 1662 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) Processing helix chain 'A' and resid 1699 through 1736 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) removed outlier: 5.327A pdb=" N THR A1730 " --> pdb=" O LYS A1726 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU A1731 " --> pdb=" O ALA A1727 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN A1732 " --> pdb=" O LEU A1728 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N SER A1733 " --> pdb=" O GLU A1729 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS A1734 " --> pdb=" O THR A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1742 through 1745 No H-bonds generated for 'chain 'A' and resid 1742 through 1745' Processing helix chain 'A' and resid 1765 through 1778 Processing helix chain 'A' and resid 1784 through 1786 No H-bonds generated for 'chain 'A' and resid 1784 through 1786' Processing helix chain 'A' and resid 1791 through 1813 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 1818 through 1820 No H-bonds generated for 'chain 'A' and resid 1818 through 1820' Processing helix chain 'A' and resid 1823 through 1826 No H-bonds generated for 'chain 'A' and resid 1823 through 1826' Processing helix chain 'A' and resid 1833 through 1839 Processing helix chain 'B' and resid 38 through 41 No H-bonds generated for 'chain 'B' and resid 38 through 41' Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 82 through 101 Proline residue: B 96 - end of helix removed outlier: 5.712A pdb=" N LYS B 99 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ASP B 100 " --> pdb=" O PRO B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 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 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 157 through 160 No H-bonds generated for 'chain 'B' and resid 157 through 160' Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.620A pdb=" N ARG B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 207 Processing helix chain 'B' and resid 215 through 224 Processing helix chain 'B' and resid 229 through 242 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 292 through 304 Processing helix chain 'B' and resid 310 through 329 Processing helix chain 'B' and resid 334 through 349 Processing helix chain 'C' and resid 22 through 25 No H-bonds generated for 'chain 'C' and resid 22 through 25' Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 83 through 86 No H-bonds generated for 'chain 'C' and resid 83 through 86' Processing helix chain 'C' and resid 98 through 101 No H-bonds generated for 'chain 'C' and resid 98 through 101' Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 132 through 144 removed outlier: 4.055A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 163 through 168 removed outlier: 3.638A pdb=" N ARG C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 199 through 209 Processing helix chain 'C' and resid 213 through 227 Processing helix chain 'C' and resid 232 through 238 Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 259 through 273 Processing helix chain 'C' and resid 278 through 290 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 295 through 311 Processing helix chain 'C' and resid 318 through 339 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 40 through 43 No H-bonds generated for 'chain 'D' and resid 40 through 43' Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 157 through 169 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 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 188 through 193 removed outlier: 3.732A pdb=" N ARG D 193 " --> pdb=" O PRO D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 218 Processing helix chain 'D' and resid 224 through 234 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 259 through 265 Processing helix chain 'D' and resid 271 through 283 Processing helix chain 'D' and resid 286 through 298 Processing helix chain 'D' and resid 303 through 316 removed outlier: 3.763A pdb=" N GLU D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 339 Processing helix chain 'D' and resid 344 through 362 removed outlier: 4.521A pdb=" N ASN D 362 " --> pdb=" O GLN D 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 20 through 29 Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 97 through 121 removed outlier: 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) removed outlier: 3.546A pdb=" N ASP E 104 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG E 105 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU E 110 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET E 111 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 142 through 154 Processing helix chain 'E' and resid 173 through 176 No H-bonds generated for 'chain 'E' and resid 173 through 176' Processing helix chain 'E' and resid 189 through 203 removed outlier: 3.667A pdb=" N LYS E 202 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 218 Processing helix chain 'E' and resid 223 through 236 Processing helix chain 'E' and resid 250 through 264 Processing helix chain 'E' and resid 268 through 284 removed outlier: 3.805A pdb=" N HIS E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 301 Processing helix chain 'E' and resid 307 through 324 Processing helix chain 'E' and resid 328 through 347 Processing helix chain 'F' and resid 9 through 18 Processing helix chain 'F' and resid 72 through 81 removed outlier: 4.354A pdb=" N CYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) 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 221 removed outlier: 3.647A pdb=" N LYS F 217 " --> pdb=" O ASN F 213 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ALA F 218 " --> pdb=" O PHE F 214 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N THR F 219 " --> pdb=" O PHE F 215 " (cutoff:3.500A) Proline residue: F 220 - end of helix Processing helix chain 'G' and resid 10 through 16 removed outlier: 3.815A pdb=" N LEU G 16 " --> pdb=" O LEU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 22 No H-bonds generated for 'chain 'G' and resid 19 through 22' Processing helix chain 'G' and resid 73 through 79 Processing helix chain 'G' and resid 141 through 154 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 221 removed outlier: 4.441A pdb=" N ALA G 218 " --> pdb=" O PHE G 214 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N THR G 219 " --> pdb=" O PHE G 215 " (cutoff:3.500A) Proline residue: G 220 - end of helix Processing helix chain 'H' and resid 9 through 18 Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' Processing helix chain 'H' and resid 72 through 78 Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 210 through 221 removed outlier: 4.435A pdb=" N ALA H 218 " --> pdb=" O PHE H 214 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N THR H 219 " --> pdb=" O PHE H 215 " (cutoff:3.500A) Proline residue: H 220 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 1350 through 1353 removed outlier: 6.339A pdb=" N VAL A1332 " --> pdb=" O VAL A1128 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE A1130 " --> pdb=" O VAL A1332 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A1334 " --> pdb=" O ILE A1130 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1519 through 1521 removed outlier: 5.814A pdb=" N PHE A1747 " --> pdb=" O ASP A1520 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 186 through 189 removed outlier: 6.436A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.256A 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) Processing sheet with id= E, first strand: chain 'D' and resid 195 through 199 removed outlier: 3.509A pdb=" N GLY D 78 " --> pdb=" O CYS D 180 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 180 through 184 removed outlier: 3.725A pdb=" N GLY E 42 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 68 through 75 Processing sheet with id= H, first strand: chain 'F' and resid 59 through 62 removed outlier: 3.853A pdb=" N THR F 59 " --> pdb=" O ARG F 5 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 25 through 30 Processing sheet with id= J, first strand: chain 'F' and resid 34 through 40 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) Processing sheet with id= K, first strand: chain 'F' and resid 203 through 208 Processing sheet with id= L, first strand: chain 'G' and resid 59 through 62 Processing sheet with id= M, first strand: chain 'G' and resid 25 through 30 Processing sheet with id= N, first strand: chain 'G' and resid 34 through 40 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= O, first strand: chain 'G' and resid 203 through 208 Processing sheet with id= P, first strand: chain 'H' and resid 2 through 6 removed outlier: 4.212A pdb=" N ILE H 87 " --> pdb=" O GLU H 104 " (cutoff:3.500A) Processing sheet with id= Q, 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) Processing sheet with id= R, first strand: chain 'H' and resid 203 through 207 removed outlier: 3.641A pdb=" N VAL H 203 " --> pdb=" O CYS H 162 " (cutoff:3.500A) 981 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.63 Time building geometry restraints manager: 8.69 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: 243 2.63 - 3.20: 18028 3.20 - 3.76: 34438 3.76 - 4.33: 46855 4.33 - 4.90: 77997 Nonbonded interactions: 177561 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 177556 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.580 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 57.310 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.660 ------------------------------------------------------------------------------- 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= 0.225 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 : 3.107 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: 0.3629 time to fit residues: 186.9584 Evaluate side-chains 312 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 303 time to evaluate : 2.505 ------------------------------------------------------------------------------- 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: 7.9990 chunk 70 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 109 optimal weight: 0.0470 chunk 212 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 246 optimal weight: 20.0000 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 945 ASN A1094 ASN A1669 GLN 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 22052 Z= 0.481 Angle : 0.682 9.168 29812 Z= 0.345 Chirality : 0.046 0.164 3461 Planarity : 0.005 0.055 3792 Dihedral : 8.070 68.622 3040 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.88 % Allowed : 20.67 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 2717 helix: -0.05 (0.14), residues: 1277 sheet: -0.50 (0.22), residues: 517 loop : -1.11 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1079 HIS 0.008 0.002 HIS E 92 PHE 0.023 0.002 PHE D 126 TYR 0.034 0.002 TYR G 249 ARG 0.007 0.001 ARG B 65 *********************** 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 419 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 301 time to evaluate : 2.267 Fit side-chains revert: symmetry clash REVERT: A 1157 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7982 (m-40) REVERT: A 1181 ASP cc_start: 0.7007 (t0) cc_final: 0.6764 (t0) REVERT: A 1790 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.6269 (mmt180) REVERT: B 54 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: B 89 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7628 (tp) REVERT: C 37 HIS cc_start: 0.8118 (OUTLIER) cc_final: 0.7786 (m90) REVERT: C 182 MET cc_start: 0.7261 (ttt) cc_final: 0.7025 (ttt) REVERT: D 93 ARG cc_start: 0.7077 (mtp85) cc_final: 0.6756 (mtp180) REVERT: D 151 GLU cc_start: 0.7633 (mp0) cc_final: 0.7364 (mp0) REVERT: E 112 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6970 (mt) REVERT: E 340 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7184 (mtt) REVERT: H 251 LEU cc_start: 0.7643 (tt) cc_final: 0.7434 (tp) outliers start: 118 outliers final: 72 residues processed: 385 average time/residue: 0.3383 time to fit residues: 202.0022 Evaluate side-chains 359 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 280 time to evaluate : 2.467 ------------------------------------------------------------------------------- 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 1157 ASN Chi-restraints excluded: chain A residue 1308 ASP Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1346 ASP Chi-restraints excluded: chain A residue 1369 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 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 54 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 89 LEU 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 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 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 86 SER 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 202 LEU 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 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 255 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 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 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 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: 0.3980 chunk 76 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 167 optimal weight: 0.2980 chunk 67 optimal weight: 0.7980 chunk 246 optimal weight: 0.7980 chunk 266 optimal weight: 9.9990 chunk 219 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 G 179 ASN H 200 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22052 Z= 0.146 Angle : 0.507 7.915 29812 Z= 0.256 Chirality : 0.040 0.195 3461 Planarity : 0.003 0.046 3792 Dihedral : 7.482 68.690 3033 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.10 % Allowed : 22.98 % Favored : 73.91 % 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: 0.64 (0.14), residues: 1272 sheet: -0.38 (0.23), residues: 521 loop : -0.84 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1403 HIS 0.003 0.001 HIS C 37 PHE 0.021 0.001 PHE D 126 TYR 0.027 0.001 TYR G 249 ARG 0.004 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 386 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 311 time to evaluate : 2.664 Fit side-chains REVERT: A 1181 ASP cc_start: 0.6973 (t0) cc_final: 0.6678 (t0) REVERT: B 89 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7316 (tp) REVERT: D 151 GLU cc_start: 0.7672 (mp0) cc_final: 0.7374 (mp0) REVERT: D 317 ASN cc_start: 0.7926 (m-40) cc_final: 0.7624 (m-40) REVERT: E 105 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7251 (ttp80) REVERT: E 112 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6850 (mt) REVERT: F 25 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: F 89 THR cc_start: 0.7741 (m) cc_final: 0.7506 (m) REVERT: H 162 CYS cc_start: 0.4322 (m) cc_final: 0.3809 (p) outliers start: 75 outliers final: 41 residues processed: 368 average time/residue: 0.3294 time to fit residues: 187.7675 Evaluate side-chains 332 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 287 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1346 ASP Chi-restraints excluded: chain A residue 1359 LEU 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 1728 LEU Chi-restraints excluded: chain A residue 1777 SER 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 41 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 197 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 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 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 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 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain G residue 72 LEU 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 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: 3.9990 chunk 185 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 27 optimal weight: 0.4980 chunk 117 optimal weight: 1.9990 chunk 165 optimal weight: 0.0670 chunk 247 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.7779 moved from start: 0.1055 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= 0.154 Angle : 0.491 9.226 29812 Z= 0.246 Chirality : 0.040 0.161 3461 Planarity : 0.003 0.042 3792 Dihedral : 7.168 66.219 3029 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.18 % Allowed : 23.60 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2717 helix: 1.00 (0.15), residues: 1260 sheet: -0.32 (0.23), residues: 521 loop : -0.73 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1403 HIS 0.003 0.001 HIS E 301 PHE 0.013 0.001 PHE H 169 TYR 0.011 0.001 TYR D 77 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 395 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 318 time to evaluate : 2.512 Fit side-chains revert: symmetry clash REVERT: A 1166 GLN cc_start: 0.7247 (mt0) cc_final: 0.7007 (mt0) REVERT: A 1181 ASP cc_start: 0.6887 (t0) cc_final: 0.6613 (t0) REVERT: B 54 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: B 89 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7346 (tp) REVERT: D 151 GLU cc_start: 0.7685 (mp0) cc_final: 0.7387 (mp0) REVERT: D 317 ASN cc_start: 0.7919 (m-40) cc_final: 0.7565 (m-40) REVERT: E 105 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7205 (ttp80) REVERT: E 112 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6829 (mt) REVERT: F 25 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: F 89 THR cc_start: 0.7778 (m) cc_final: 0.7554 (m) REVERT: H 162 CYS cc_start: 0.4354 (m) cc_final: 0.3876 (p) outliers start: 77 outliers final: 53 residues processed: 370 average time/residue: 0.3384 time to fit residues: 191.6820 Evaluate side-chains 354 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 296 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1346 ASP 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 1495 LEU 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 160 ILE Chi-restraints excluded: chain B residue 164 THR 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 41 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 197 ILE 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 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 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 79 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 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 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 81 CYS 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: 0.9980 chunk 148 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 195 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 133 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 G 179 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22052 Z= 0.374 Angle : 0.602 10.733 29812 Z= 0.302 Chirality : 0.044 0.165 3461 Planarity : 0.004 0.046 3792 Dihedral : 7.467 67.933 3025 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.84 % Allowed : 22.28 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2717 helix: 0.65 (0.15), residues: 1267 sheet: -0.45 (0.22), residues: 521 loop : -0.76 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1079 HIS 0.006 0.001 HIS E 92 PHE 0.017 0.002 PHE A1154 TYR 0.018 0.002 TYR A1823 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: 117 poor density : 309 time to evaluate : 2.640 Fit side-chains revert: symmetry clash REVERT: A 1181 ASP cc_start: 0.6967 (t0) cc_final: 0.6622 (t0) REVERT: B 54 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: B 89 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7475 (tp) REVERT: C 37 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.7763 (m90) REVERT: D 151 GLU cc_start: 0.7728 (mp0) cc_final: 0.7476 (mp0) REVERT: D 232 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8497 (tttp) REVERT: D 317 ASN cc_start: 0.8014 (m-40) cc_final: 0.7690 (m-40) REVERT: E 112 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6926 (mt) REVERT: F 25 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7326 (pp20) REVERT: H 162 CYS cc_start: 0.4458 (m) cc_final: 0.3831 (p) REVERT: H 175 LEU cc_start: 0.4911 (tt) cc_final: 0.4436 (tt) outliers start: 117 outliers final: 82 residues processed: 393 average time/residue: 0.3289 time to fit residues: 199.6667 Evaluate side-chains 364 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 276 time to evaluate : 2.433 ------------------------------------------------------------------------------- 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 1308 ASP Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1346 ASP 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 1648 SER Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1789 ASN 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 129 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 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 98 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 38 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 263 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 354 THR 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 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 253 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 345 LYS 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 87 ILE Chi-restraints excluded: chain F residue 94 ASP 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 167 VAL 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 257 ASP Chi-restraints excluded: chain G residue 27 CYS 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 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 79 LEU Chi-restraints excluded: chain H residue 81 CYS 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: 2.9990 chunk 235 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 64 optimal weight: 0.0370 chunk 262 optimal weight: 40.0000 chunk 217 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.8660 ------------------------------------------------------------------------------- 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 118 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 G 84 ASN G 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22052 Z= 0.156 Angle : 0.501 9.534 29812 Z= 0.252 Chirality : 0.040 0.164 3461 Planarity : 0.003 0.042 3792 Dihedral : 7.099 67.748 3025 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.35 % Allowed : 23.77 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 2717 helix: 0.99 (0.15), residues: 1262 sheet: -0.36 (0.23), residues: 521 loop : -0.65 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1403 HIS 0.005 0.001 HIS F 246 PHE 0.014 0.001 PHE H 169 TYR 0.011 0.001 TYR D 77 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 392 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 311 time to evaluate : 2.504 Fit side-chains revert: symmetry clash REVERT: A 1181 ASP cc_start: 0.6893 (t0) cc_final: 0.6568 (t0) REVERT: A 1790 ARG cc_start: 0.6121 (OUTLIER) cc_final: 0.5857 (mpt180) REVERT: B 54 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: B 89 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7327 (tp) REVERT: D 151 GLU cc_start: 0.7677 (mp0) cc_final: 0.7420 (mp0) REVERT: D 317 ASN cc_start: 0.7944 (m-40) cc_final: 0.7620 (m-40) REVERT: E 105 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7311 (ttp80) REVERT: E 112 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6875 (mt) REVERT: F 25 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7757 (pm20) REVERT: F 28 TRP cc_start: 0.8062 (m100) cc_final: 0.7615 (m100) REVERT: G 40 MET cc_start: 0.8452 (tpt) cc_final: 0.8127 (tpp) REVERT: G 179 ASN cc_start: 0.7069 (m-40) cc_final: 0.6806 (m-40) REVERT: H 162 CYS cc_start: 0.4499 (m) cc_final: 0.3872 (p) REVERT: H 175 LEU cc_start: 0.4936 (tt) cc_final: 0.4470 (tt) outliers start: 81 outliers final: 55 residues processed: 374 average time/residue: 0.3385 time to fit residues: 194.5336 Evaluate side-chains 355 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 294 time to evaluate : 2.389 ------------------------------------------------------------------------------- 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 1346 ASP 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 1728 LEU Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1794 ILE 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 C residue 24 GLU 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 191 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 295 ASP 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 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 163 LEU 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 250 ASP 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 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain G residue 45 VAL 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 246 HIS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 CYS 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: 10.0000 chunk 29 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 148 optimal weight: 0.3980 chunk 220 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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 118 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 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22052 Z= 0.292 Angle : 0.565 10.307 29812 Z= 0.282 Chirality : 0.042 0.167 3461 Planarity : 0.004 0.043 3792 Dihedral : 7.240 67.394 3025 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.42 % Allowed : 23.27 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2717 helix: 0.83 (0.15), residues: 1266 sheet: -0.42 (0.23), residues: 519 loop : -0.64 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1489 HIS 0.004 0.001 HIS E 92 PHE 0.015 0.001 PHE A1154 TYR 0.015 0.002 TYR A1823 ARG 0.006 0.000 ARG E 149 *********************** 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 401 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 294 time to evaluate : 2.301 Fit side-chains revert: symmetry clash REVERT: A 1089 LEU cc_start: 0.6129 (OUTLIER) cc_final: 0.5829 (mp) REVERT: A 1181 ASP cc_start: 0.6903 (t0) cc_final: 0.6611 (t0) REVERT: B 54 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: B 89 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7396 (tp) REVERT: C 37 HIS cc_start: 0.7953 (OUTLIER) cc_final: 0.7646 (m90) REVERT: D 101 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6010 (t80) REVERT: D 151 GLU cc_start: 0.7690 (mp0) cc_final: 0.7447 (mp0) REVERT: D 232 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8497 (tttp) REVERT: D 317 ASN cc_start: 0.7979 (m-40) cc_final: 0.7631 (m-40) REVERT: E 15 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6622 (mtt-85) REVERT: E 105 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6731 (ttp80) REVERT: E 112 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6910 (mt) REVERT: F 25 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7927 (pp20) REVERT: F 28 TRP cc_start: 0.8068 (m100) cc_final: 0.7613 (m100) REVERT: F 109 GLU cc_start: 0.5268 (OUTLIER) cc_final: 0.4998 (tt0) REVERT: F 216 THR cc_start: 0.7664 (t) cc_final: 0.7334 (t) REVERT: G 40 MET cc_start: 0.8477 (tpt) cc_final: 0.8152 (tpp) REVERT: H 162 CYS cc_start: 0.4660 (m) cc_final: 0.3934 (p) REVERT: H 175 LEU cc_start: 0.5008 (tt) cc_final: 0.4561 (tt) REVERT: H 251 LEU cc_start: 0.7701 (tt) cc_final: 0.7450 (tp) outliers start: 107 outliers final: 75 residues processed: 369 average time/residue: 0.3401 time to fit residues: 192.2688 Evaluate side-chains 370 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 284 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 870 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 1308 ASP Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1346 ASP Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1794 ILE 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 129 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 17 ILE 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 41 LEU 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 197 ILE 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 232 LYS 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 105 ARG 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 163 LEU 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 250 ASP Chi-restraints excluded: chain E residue 253 VAL 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 109 GLU 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 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 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 90 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 79 LEU Chi-restraints excluded: chain H residue 81 CYS 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: 8.9990 chunk 104 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 177 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 205 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 HIS F 95 ASN G 84 ASN G 179 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1412 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= 0.156 Angle : 0.507 9.308 29812 Z= 0.252 Chirality : 0.040 0.188 3461 Planarity : 0.003 0.041 3792 Dihedral : 6.911 66.144 3025 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.51 % Allowed : 24.14 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.16), residues: 2717 helix: 1.14 (0.15), residues: 1258 sheet: -0.44 (0.23), residues: 533 loop : -0.56 (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 0.013 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 394 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 309 time to evaluate : 2.294 Fit side-chains revert: symmetry clash REVERT: A 1089 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5768 (mp) REVERT: A 1181 ASP cc_start: 0.6854 (t0) cc_final: 0.6545 (t0) REVERT: A 1318 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7886 (mm) REVERT: B 54 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: B 89 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7298 (tp) REVERT: D 151 GLU cc_start: 0.7681 (mp0) cc_final: 0.7429 (mp0) REVERT: D 317 ASN cc_start: 0.7932 (m-40) cc_final: 0.7587 (m-40) REVERT: E 15 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6572 (mtt-85) REVERT: E 105 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6666 (ttp80) REVERT: E 112 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6835 (mt) REVERT: F 25 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: F 28 TRP cc_start: 0.8027 (m100) cc_final: 0.7578 (m100) REVERT: F 109 GLU cc_start: 0.5086 (OUTLIER) cc_final: 0.4849 (tt0) REVERT: H 162 CYS cc_start: 0.4595 (m) cc_final: 0.3928 (p) REVERT: H 175 LEU cc_start: 0.4996 (tt) cc_final: 0.4555 (tt) REVERT: H 251 LEU cc_start: 0.7665 (tt) cc_final: 0.7430 (tp) outliers start: 85 outliers final: 61 residues processed: 368 average time/residue: 0.3345 time to fit residues: 190.7617 Evaluate side-chains 367 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 297 time to evaluate : 2.466 ------------------------------------------------------------------------------- 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 1327 THR Chi-restraints excluded: chain A residue 1346 ASP 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 1510 ASN Chi-restraints excluded: chain A residue 1664 THR 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 A residue 1781 SER Chi-restraints excluded: chain A residue 1794 ILE 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 254 VAL Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 30 THR 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 98 ILE 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 295 ASP Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 105 ARG 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 163 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 253 VAL 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 97 ASP Chi-restraints excluded: chain F residue 109 GLU 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 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 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 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: 0.9990 chunk 250 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 243 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 242 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** A1166 GLN A1789 ASN ** B 118 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22052 Z= 0.307 Angle : 0.580 11.479 29812 Z= 0.287 Chirality : 0.042 0.179 3461 Planarity : 0.004 0.043 3792 Dihedral : 7.179 66.519 3025 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.93 % Allowed : 23.56 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 2717 helix: 0.88 (0.15), residues: 1266 sheet: -0.41 (0.23), residues: 521 loop : -0.58 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1489 HIS 0.004 0.001 HIS E 92 PHE 0.031 0.002 PHE D 126 TYR 0.015 0.002 TYR A1823 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 391 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 296 time to evaluate : 2.473 Fit side-chains revert: symmetry clash REVERT: A 1089 LEU cc_start: 0.6111 (OUTLIER) cc_final: 0.5789 (mp) REVERT: A 1318 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7976 (mm) REVERT: B 54 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: B 89 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7379 (tp) REVERT: C 37 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7655 (m90) REVERT: D 151 GLU cc_start: 0.7703 (mp0) cc_final: 0.7446 (mp0) REVERT: D 317 ASN cc_start: 0.7992 (m-40) cc_final: 0.7654 (m-40) REVERT: E 15 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6609 (mtt-85) REVERT: E 105 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6725 (ttp80) REVERT: E 112 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6838 (mt) REVERT: E 279 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: F 25 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7856 (pm20) REVERT: F 28 TRP cc_start: 0.8081 (m100) cc_final: 0.7631 (m100) REVERT: F 109 GLU cc_start: 0.5307 (OUTLIER) cc_final: 0.5072 (tt0) REVERT: H 162 CYS cc_start: 0.4638 (m) cc_final: 0.3889 (p) REVERT: H 175 LEU cc_start: 0.5009 (tt) cc_final: 0.4574 (tt) REVERT: H 251 LEU cc_start: 0.7687 (tt) cc_final: 0.7455 (tp) outliers start: 95 outliers final: 81 residues processed: 368 average time/residue: 0.3334 time to fit residues: 189.2216 Evaluate side-chains 375 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 283 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 870 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 1346 ASP 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 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 1765 LEU Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1794 ILE 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 254 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain C residue 17 ILE 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 41 LEU 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 114 ILE Chi-restraints excluded: chain C residue 197 ILE 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 118 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 256 GLU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 105 ARG 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 163 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 279 TYR 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 109 GLU 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 257 ASP Chi-restraints excluded: chain G residue 27 CYS 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 90 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 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 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: 20.0000 chunk 157 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 178 optimal weight: 7.9990 chunk 269 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 214 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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** A1822 HIS ** B 118 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 F 187 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 22052 Z= 0.292 Angle : 0.846 59.200 29812 Z= 0.485 Chirality : 0.043 0.658 3461 Planarity : 0.004 0.059 3792 Dihedral : 7.196 66.561 3025 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.97 % Allowed : 23.65 % Favored : 72.39 % 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: 0.11 (0.16), residues: 2717 helix: 0.88 (0.15), residues: 1266 sheet: -0.41 (0.23), residues: 521 loop : -0.58 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1489 HIS 0.004 0.001 HIS E 37 PHE 0.028 0.002 PHE D 126 TYR 0.040 0.002 TYR G 249 ARG 0.010 0.000 ARG F 5 ********************** 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 379 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 283 time to evaluate : 2.538 Fit side-chains revert: symmetry clash REVERT: A 1089 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.5786 (mp) REVERT: A 1318 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7972 (mm) REVERT: B 54 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: B 89 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7372 (tp) REVERT: C 37 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.7650 (m90) REVERT: D 101 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.6027 (t80) REVERT: D 151 GLU cc_start: 0.7703 (mp0) cc_final: 0.7446 (mp0) REVERT: D 317 ASN cc_start: 0.7987 (m-40) cc_final: 0.7649 (m-40) REVERT: E 15 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6607 (mtt-85) REVERT: E 105 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.6720 (ttp80) REVERT: E 112 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6836 (mt) REVERT: E 279 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: F 25 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7849 (pm20) REVERT: F 28 TRP cc_start: 0.8077 (m100) cc_final: 0.7634 (m100) REVERT: F 109 GLU cc_start: 0.5279 (OUTLIER) cc_final: 0.5045 (tt0) REVERT: H 162 CYS cc_start: 0.4635 (m) cc_final: 0.3886 (p) REVERT: H 175 LEU cc_start: 0.5009 (tt) cc_final: 0.4577 (tt) REVERT: H 251 LEU cc_start: 0.7686 (tt) cc_final: 0.7454 (tp) outliers start: 96 outliers final: 79 residues processed: 355 average time/residue: 0.3472 time to fit residues: 190.8137 Evaluate side-chains 371 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 280 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 870 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 1346 ASP 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 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 1765 LEU Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1794 ILE 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 160 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 17 ILE 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 41 LEU 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 114 ILE Chi-restraints excluded: chain C residue 197 ILE 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 118 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 256 GLU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 105 ARG 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 163 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 279 TYR 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 84 ASN Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 109 GLU 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 224 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 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 90 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 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 79 LEU Chi-restraints excluded: chain H residue 81 CYS 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: 20.0000 chunk 65 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 221 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.192269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.148162 restraints weight = 27623.292| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.44 r_work: 0.3556 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 22052 Z= 0.292 Angle : 0.846 59.200 29812 Z= 0.485 Chirality : 0.043 0.658 3461 Planarity : 0.004 0.059 3792 Dihedral : 7.196 66.561 3025 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.76 % Allowed : 23.77 % Favored : 72.47 % 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: 0.11 (0.16), residues: 2717 helix: 0.88 (0.15), residues: 1266 sheet: -0.41 (0.23), residues: 521 loop : -0.58 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1489 HIS 0.004 0.001 HIS E 37 PHE 0.028 0.002 PHE D 126 TYR 0.040 0.002 TYR G 249 ARG 0.010 0.000 ARG F 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4837.59 seconds wall clock time: 86 minutes 58.22 seconds (5218.22 seconds total)