Starting phenix.real_space_refine on Thu Mar 21 15:08:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/03_2024/7qba_13885_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/03_2024/7qba_13885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/03_2024/7qba_13885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/03_2024/7qba_13885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/03_2024/7qba_13885_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/03_2024/7qba_13885_updated.pdb" } resolution = 3.78 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= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9481 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 6 5.49 5 Mg 2 5.21 5 S 99 5.16 5 C 13351 2.51 5 N 3644 2.21 5 O 3882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "H GLU 443": "OE1" <-> "OE2" Residue "H GLU 480": "OE1" <-> "OE2" Residue "H GLU 628": "OE1" <-> "OE2" Residue "H ARG 632": "NH1" <-> "NH2" Residue "I GLU 443": "OE1" <-> "OE2" Residue "I GLU 559": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20986 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3149 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 16, 'TRANS': 386} Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "C" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "D" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2073 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 8, 'TRANS': 266} Chain: "E" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1966 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 2 Chain: "H" Number of atoms: 4575 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 581, 4567 Classifications: {'peptide': 581} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 25, 'TRANS': 549} Conformer: "B" Number of residues, atoms: 581, 4567 Classifications: {'peptide': 581} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 25, 'TRANS': 549} bond proxies already assigned to first conformer: 4669 Chain: "I" Number of atoms: 4567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4567 Classifications: {'peptide': 581} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 25, 'TRANS': 550} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.01, per 1000 atoms: 0.62 Number of scatterers: 20986 At special positions: 0 Unit cell: (169.65, 162.69, 139.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 99 16.00 P 6 15.00 Mg 2 11.99 O 3882 8.00 N 3644 7.00 C 13351 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: 8.02 Conformation dependent library (CDL) restraints added in 4.2 seconds 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4892 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 33 sheets defined 28.2% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.024A pdb=" N ARG A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'B' and resid 42 through 48 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 161 through 176 Processing helix chain 'B' and resid 191 through 194 No H-bonds generated for 'chain 'B' and resid 191 through 194' Processing helix chain 'B' and resid 212 through 218 Processing helix chain 'B' and resid 235 through 241 Processing helix chain 'B' and resid 263 through 273 removed outlier: 4.338A pdb=" N LEU B 268 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 269 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 272 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 298 Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 70 through 75 removed outlier: 4.211A pdb=" N GLN C 75 " --> pdb=" O GLN C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 106 through 116 removed outlier: 4.533A pdb=" N ASP C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 161 through 176 Processing helix chain 'C' and resid 212 through 219 removed outlier: 3.609A pdb=" N ALA C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 No H-bonds generated for 'chain 'C' and resid 238 through 241' Processing helix chain 'C' and resid 264 through 271 Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'D' and resid 3 through 17 Processing helix chain 'D' and resid 20 through 36 removed outlier: 3.531A pdb=" N ALA D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 74 removed outlier: 3.763A pdb=" N ALA D 59 " --> pdb=" O ILE D 55 " (cutoff:3.500A) Proline residue: D 67 - end of helix Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.655A pdb=" N THR D 92 " --> pdb=" O MET D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 130 Processing helix chain 'D' and resid 136 through 167 Processing helix chain 'D' and resid 171 through 200 removed outlier: 3.544A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP D 190 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 193 " --> pdb=" O PHE D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 214 removed outlier: 3.500A pdb=" N LEU D 212 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 213 " --> pdb=" O PRO D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 227 Processing helix chain 'D' and resid 240 through 243 No H-bonds generated for 'chain 'D' and resid 240 through 243' Processing helix chain 'D' and resid 251 through 272 Processing helix chain 'E' and resid 5 through 17 Processing helix chain 'E' and resid 20 through 37 removed outlier: 4.086A pdb=" N LEU E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 51 through 71 removed outlier: 3.600A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) Proline residue: E 67 - end of helix Processing helix chain 'E' and resid 76 through 84 removed outlier: 4.413A pdb=" N GLU E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 92 Processing helix chain 'E' and resid 97 through 130 removed outlier: 3.597A pdb=" N LEU E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 165 Processing helix chain 'E' and resid 171 through 186 removed outlier: 3.803A pdb=" N GLY E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'E' and resid 206 through 215 Proline residue: E 210 - end of helix Processing helix chain 'E' and resid 217 through 224 Processing helix chain 'E' and resid 249 through 273 removed outlier: 4.108A pdb=" N LEU E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG E 273 " --> pdb=" O ALA E 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 117 Processing helix chain 'H' and resid 120 through 122 No H-bonds generated for 'chain 'H' and resid 120 through 122' Processing helix chain 'H' and resid 265 through 268 Processing helix chain 'H' and resid 280 through 289 Processing helix chain 'H' and resid 352 through 360 Proline residue: H 356 - end of helix Processing helix chain 'H' and resid 366 through 369 removed outlier: 3.571A pdb=" N VAL H 369 " --> pdb=" O PRO H 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 366 through 369' Processing helix chain 'H' and resid 406 through 414 Processing helix chain 'H' and resid 515 through 526 removed outlier: 3.518A pdb=" N ALA H 518 " --> pdb=" O PRO H 515 " (cutoff:3.500A) Proline residue: H 519 - end of helix Processing helix chain 'I' and resid 77 through 79 No H-bonds generated for 'chain 'I' and resid 77 through 79' Processing helix chain 'I' and resid 111 through 120 removed outlier: 6.198A pdb=" N ASP I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N SER I 120 " --> pdb=" O ILE I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 268 Processing helix chain 'I' and resid 280 through 289 Processing helix chain 'I' and resid 352 through 359 Proline residue: I 356 - end of helix Processing helix chain 'I' and resid 366 through 369 removed outlier: 3.558A pdb=" N VAL I 369 " --> pdb=" O PRO I 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 366 through 369' Processing helix chain 'I' and resid 406 through 414 Processing helix chain 'I' and resid 515 through 527 Proline residue: I 519 - end of helix Processing helix chain 'I' and resid 626 through 628 No H-bonds generated for 'chain 'I' and resid 626 through 628' Processing sheet with id= A, first strand: chain 'A' and resid 45 through 47 removed outlier: 6.793A pdb=" N GLN A 119 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN A 141 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG A 171 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 51 through 53 removed outlier: 6.114A pdb=" N VAL A 71 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR A 94 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG A 124 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU A 146 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N HIS A 176 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 198 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 220 " --> pdb=" O ILE A 199 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 56 through 58 Processing sheet with id= D, first strand: chain 'A' and resid 109 through 111 removed outlier: 5.816A pdb=" N GLY A 161 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N VAL A 134 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS A 163 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A 185 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N HIS A 163 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASP A 187 " --> pdb=" O HIS A 163 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE A 165 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N HIS A 311 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 265 through 267 removed outlier: 6.601A pdb=" N HIS A 302 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA A 325 " --> pdb=" O PHE A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 24 through 26 removed outlier: 3.648A pdb=" N VAL B 4 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN B 7 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 181 through 183 removed outlier: 7.466A pdb=" N ARG B 197 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N PHE B 35 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA B 199 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.856A pdb=" N LEU B 79 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 224 through 226 Processing sheet with id= J, first strand: chain 'B' and resid 246 through 248 removed outlier: 3.980A pdb=" N SER B 246 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 206 through 211 removed outlier: 6.821A pdb=" N ILE C 200 " --> pdb=" O GLN C 207 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL C 209 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 198 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE C 181 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU C 34 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU C 183 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N GLY C 36 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 279 through 283 removed outlier: 3.721A pdb=" N VAL C 257 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA C 227 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE C 255 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 248 " --> pdb=" O GLU C 256 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 11 through 13 removed outlier: 5.989A pdb=" N TYR C 13 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR C 17 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 498 through 500 removed outlier: 6.764A pdb=" N GLY H 86 " --> pdb=" O GLU H 92 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLU H 92 " --> pdb=" O GLY H 86 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 144 through 149 removed outlier: 5.992A pdb=" N ARG H 159 " --> pdb=" O CYS H 165 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS H 165 " --> pdb=" O ARG H 159 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 180 through 182 removed outlier: 3.868A pdb=" N THR H 217 " --> pdb=" O VAL H 235 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ASP H 223 " --> pdb=" O MET H 229 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N MET H 229 " --> pdb=" O ASP H 223 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE H 234 " --> pdb=" O PRO H 301 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU H 303 " --> pdb=" O ILE H 234 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 242 through 244 Processing sheet with id= R, first strand: chain 'H' and resid 328 through 330 removed outlier: 6.385A pdb=" N ALA H 351 " --> pdb=" O ILE H 370 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE H 370 " --> pdb=" O ALA H 351 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 383 through 385 removed outlier: 4.036A pdb=" N GLN H 423 " --> pdb=" O LYS H 403 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASN H 405 " --> pdb=" O ILE H 421 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE H 421 " --> pdb=" O ASN H 405 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 434 through 436 removed outlier: 3.550A pdb=" N HIS H 485 " --> pdb=" O LEU H 473 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASP H 475 " --> pdb=" O LEU H 483 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU H 483 " --> pdb=" O ASP H 475 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 536 through 540 removed outlier: 6.032A pdb=" N GLU H 567 " --> pdb=" O VAL H 544 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL H 546 " --> pdb=" O GLU H 567 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR H 569 " --> pdb=" O VAL H 546 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N MET H 548 " --> pdb=" O THR H 569 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR H 571 " --> pdb=" O MET H 548 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N SER H 550 " --> pdb=" O THR H 571 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR H 573 " --> pdb=" O SER H 550 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP H 566 " --> pdb=" O ALA H 608 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 559 through 563 removed outlier: 9.690A pdb=" N PHE H 560 " --> pdb=" O VAL H 630 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG H 632 " --> pdb=" O PHE H 560 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL H 562 " --> pdb=" O ARG H 632 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N MET H 634 " --> pdb=" O VAL H 562 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 583 through 587 removed outlier: 4.129A pdb=" N VAL H 592 " --> pdb=" O VAL H 587 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 498 through 500 removed outlier: 6.753A pdb=" N GLY I 86 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU I 92 " --> pdb=" O GLY I 86 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 144 through 149 removed outlier: 3.704A pdb=" N LYS I 167 " --> pdb=" O ARG I 157 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG I 159 " --> pdb=" O CYS I 165 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N CYS I 165 " --> pdb=" O ARG I 159 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 177 through 182 removed outlier: 6.228A pdb=" N ASN I 194 " --> pdb=" O HIS I 178 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU I 180 " --> pdb=" O PHE I 192 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE I 192 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU I 182 " --> pdb=" O TYR I 190 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N TYR I 190 " --> pdb=" O LEU I 182 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA I 195 " --> pdb=" O MET I 218 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N MET I 218 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR I 217 " --> pdb=" O VAL I 235 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL I 235 " --> pdb=" O THR I 217 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASP I 223 " --> pdb=" O MET I 229 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N MET I 229 " --> pdb=" O ASP I 223 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 316 through 320 removed outlier: 4.217A pdb=" N TRP I 274 " --> pdb=" O CYS I 255 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN I 241 " --> pdb=" O THR I 254 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 336 through 339 removed outlier: 3.593A pdb=" N ALA I 339 " --> pdb=" O SER I 348 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 391 through 395 Processing sheet with id= AD, first strand: chain 'I' and resid 434 through 436 removed outlier: 6.415A pdb=" N ASP I 475 " --> pdb=" O LEU I 483 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU I 483 " --> pdb=" O ASP I 475 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 536 through 540 removed outlier: 6.000A pdb=" N GLU I 567 " --> pdb=" O VAL I 544 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL I 546 " --> pdb=" O GLU I 567 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR I 569 " --> pdb=" O VAL I 546 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N MET I 548 " --> pdb=" O THR I 569 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR I 571 " --> pdb=" O MET I 548 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N SER I 550 " --> pdb=" O THR I 571 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR I 573 " --> pdb=" O SER I 550 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 559 through 563 removed outlier: 7.367A pdb=" N ARG I 632 " --> pdb=" O PHE I 560 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL I 562 " --> pdb=" O ARG I 632 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N MET I 634 " --> pdb=" O VAL I 562 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 583 through 587 removed outlier: 4.186A pdb=" N VAL I 592 " --> pdb=" O VAL I 587 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 1904 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: 6.74 Time building geometry restraints manager: 8.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3502 1.28 - 1.42: 5400 1.42 - 1.55: 12347 1.55 - 1.68: 19 1.68 - 1.81: 170 Bond restraints: 21438 Sorted by residual: bond pdb=" C LEU D 196 " pdb=" O LEU D 196 " ideal model delta sigma weight residual 1.236 1.151 0.086 1.15e-02 7.56e+03 5.55e+01 bond pdb=" CA SER H 456 " pdb=" CB SER H 456 " ideal model delta sigma weight residual 1.534 1.439 0.095 1.45e-02 4.76e+03 4.28e+01 bond pdb=" CA SER C 130 " pdb=" CB SER C 130 " ideal model delta sigma weight residual 1.530 1.448 0.082 1.49e-02 4.50e+03 3.04e+01 bond pdb=" CG PRO I 380 " pdb=" CD PRO I 380 " ideal model delta sigma weight residual 1.503 1.317 0.186 3.40e-02 8.65e+02 2.99e+01 bond pdb=" C LEU D 197 " pdb=" O LEU D 197 " ideal model delta sigma weight residual 1.236 1.294 -0.057 1.15e-02 7.56e+03 2.48e+01 ... (remaining 21433 not shown) Histogram of bond angle deviations from ideal: 90.16 - 99.00: 9 99.00 - 107.83: 1107 107.83 - 116.66: 13880 116.66 - 125.50: 13693 125.50 - 134.33: 404 Bond angle restraints: 29093 Sorted by residual: angle pdb=" PB ATP B 402 " pdb=" O3B ATP B 402 " pdb=" PG ATP B 402 " ideal model delta sigma weight residual 139.87 117.39 22.48 1.00e+00 1.00e+00 5.05e+02 angle pdb=" PB ATP C 402 " pdb=" O3B ATP C 402 " pdb=" PG ATP C 402 " ideal model delta sigma weight residual 139.87 122.38 17.49 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PA ATP B 402 " pdb=" O3A ATP B 402 " pdb=" PB ATP B 402 " ideal model delta sigma weight residual 136.83 121.93 14.90 1.00e+00 1.00e+00 2.22e+02 angle pdb=" N PRO A 411 " pdb=" CA PRO A 411 " pdb=" C PRO A 411 " ideal model delta sigma weight residual 110.80 90.30 20.50 1.51e+00 4.39e-01 1.84e+02 angle pdb=" PA ATP C 402 " pdb=" O3A ATP C 402 " pdb=" PB ATP C 402 " ideal model delta sigma weight residual 136.83 123.42 13.41 1.00e+00 1.00e+00 1.80e+02 ... (remaining 29088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11506 17.94 - 35.88: 996 35.88 - 53.81: 187 53.81 - 71.75: 35 71.75 - 89.69: 23 Dihedral angle restraints: 12747 sinusoidal: 5089 harmonic: 7658 Sorted by residual: dihedral pdb=" C ASP C 160 " pdb=" N ASP C 160 " pdb=" CA ASP C 160 " pdb=" CB ASP C 160 " ideal model delta harmonic sigma weight residual -122.60 -106.43 -16.17 0 2.50e+00 1.60e-01 4.18e+01 dihedral pdb=" C TYR B 13 " pdb=" N TYR B 13 " pdb=" CA TYR B 13 " pdb=" CB TYR B 13 " ideal model delta harmonic sigma weight residual -122.60 -137.43 14.83 0 2.50e+00 1.60e-01 3.52e+01 dihedral pdb=" C THR D 54 " pdb=" N THR D 54 " pdb=" CA THR D 54 " pdb=" CB THR D 54 " ideal model delta harmonic sigma weight residual -122.00 -134.87 12.87 0 2.50e+00 1.60e-01 2.65e+01 ... (remaining 12744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2887 0.092 - 0.185: 296 0.185 - 0.277: 45 0.277 - 0.369: 17 0.369 - 0.462: 8 Chirality restraints: 3253 Sorted by residual: chirality pdb=" CA TRP A 358 " pdb=" N TRP A 358 " pdb=" C TRP A 358 " pdb=" CB TRP A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" CA PRO E 52 " pdb=" N PRO E 52 " pdb=" C PRO E 52 " pdb=" CB PRO E 52 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA TYR B 13 " pdb=" N TYR B 13 " pdb=" C TYR B 13 " pdb=" CB TYR B 13 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 3250 not shown) Planarity restraints: 3755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 197 " -0.039 2.00e-02 2.50e+03 7.77e-02 6.03e+01 pdb=" C LEU D 197 " 0.134 2.00e-02 2.50e+03 pdb=" O LEU D 197 " -0.049 2.00e-02 2.50e+03 pdb=" N VAL D 198 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 196 " 0.033 2.00e-02 2.50e+03 6.88e-02 4.73e+01 pdb=" C LEU D 196 " -0.119 2.00e-02 2.50e+03 pdb=" O LEU D 196 " 0.045 2.00e-02 2.50e+03 pdb=" N LEU D 197 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 50 " -0.032 2.00e-02 2.50e+03 6.47e-02 4.19e+01 pdb=" C SER E 50 " 0.112 2.00e-02 2.50e+03 pdb=" O SER E 50 " -0.043 2.00e-02 2.50e+03 pdb=" N ILE E 51 " -0.037 2.00e-02 2.50e+03 ... (remaining 3752 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 5 2.07 - 2.78: 4374 2.78 - 3.49: 30002 3.49 - 4.19: 51299 4.19 - 4.90: 90943 Nonbonded interactions: 176623 Sorted by model distance: nonbonded pdb=" O GLN E 45 " pdb=" CD1 LEU E 46 " model vdw 1.363 3.460 nonbonded pdb=" OD2 ASP H 273 " pdb="CA CA H 701 " model vdw 1.515 2.510 nonbonded pdb=" C GLN E 45 " pdb=" CD1 LEU E 46 " model vdw 1.940 3.690 nonbonded pdb=" OE2 GLU H 259 " pdb="CA CA H 701 " model vdw 1.962 2.510 nonbonded pdb="MG MG B 401 " pdb=" O2B ATP B 402 " model vdw 2.057 2.170 ... (remaining 176618 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 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 137 or resid 139 through 229 or resid 245 throug \ h 275)) selection = chain 'E' } ncs_group { reference = (chain 'H' and (resid 58 through 136 or resid 138 through 601 or resid 603 throu \ gh 638 or resid 701)) selection = (chain 'I' and (resid 58 through 136 or resid 138 through 601 or resid 603 throu \ gh 638 or resid 701)) } 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=0.28 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 4.080 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 57.570 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.006 0.186 21438 Z= 0.387 Angle : 1.074 22.483 29093 Z= 0.684 Chirality : 0.065 0.462 3253 Planarity : 0.007 0.132 3755 Dihedral : 14.321 89.692 7855 Min Nonbonded Distance : 1.363 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.57 % Favored : 94.06 % Rotamer: Outliers : 0.72 % Allowed : 1.70 % Favored : 97.58 % Cbeta Deviations : 0.74 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % 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: -1.57 (0.16), residues: 2678 helix: 0.38 (0.19), residues: 755 sheet: -0.94 (0.22), residues: 583 loop : -1.96 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP H 74 HIS 0.013 0.002 HIS H 494 PHE 0.044 0.002 PHE H 385 TYR 0.045 0.002 TYR H 256 ARG 0.008 0.001 ARG H 459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 760 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.8493 (p) cc_final: 0.8099 (p) REVERT: A 126 ARG cc_start: 0.7299 (ttp-170) cc_final: 0.7072 (ttp80) REVERT: A 150 ASP cc_start: 0.7703 (m-30) cc_final: 0.7278 (m-30) REVERT: A 219 ASN cc_start: 0.8729 (m-40) cc_final: 0.8016 (m-40) REVERT: B 16 MET cc_start: 0.6712 (ttt) cc_final: 0.6503 (mmt) REVERT: B 111 GLU cc_start: 0.6311 (mt-10) cc_final: 0.6078 (tt0) REVERT: B 115 GLN cc_start: 0.8040 (tt0) cc_final: 0.7097 (mt0) REVERT: C 127 LYS cc_start: 0.8687 (tttt) cc_final: 0.8410 (tptm) REVERT: C 216 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7372 (ttm-80) REVERT: D 211 TRP cc_start: 0.7838 (OUTLIER) cc_final: 0.7082 (m100) REVERT: H 144 TYR cc_start: 0.8449 (m-80) cc_final: 0.7989 (m-80) REVERT: H 234 ILE cc_start: 0.8734 (mt) cc_final: 0.8506 (mt) REVERT: H 267 MET cc_start: 0.8465 (mtt) cc_final: 0.8227 (mtt) REVERT: H 298 SER cc_start: 0.8893 (t) cc_final: 0.8460 (m) REVERT: H 307 LYS cc_start: 0.7331 (mttm) cc_final: 0.6838 (mtmt) REVERT: H 308 LYS cc_start: 0.7473 (tppt) cc_final: 0.6531 (ttmm) REVERT: H 419 ASN cc_start: 0.7045 (m-40) cc_final: 0.6834 (m-40) REVERT: H 512 ARG cc_start: 0.8262 (mmm160) cc_final: 0.7943 (tpp80) REVERT: H 526 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8031 (mmmt) REVERT: H 551 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7823 (ttt) REVERT: H 567 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7883 (mt-10) REVERT: I 68 ASP cc_start: 0.7457 (m-30) cc_final: 0.7252 (m-30) REVERT: I 119 ASP cc_start: 0.8200 (p0) cc_final: 0.7884 (p0) REVERT: I 257 ASN cc_start: 0.8901 (t0) cc_final: 0.8377 (t0) REVERT: I 272 ARG cc_start: 0.7385 (mtp85) cc_final: 0.6957 (mtt180) REVERT: I 300 THR cc_start: 0.9050 (m) cc_final: 0.8741 (p) REVERT: I 354 LYS cc_start: 0.7523 (mttt) cc_final: 0.7316 (mttm) REVERT: I 440 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8331 (mm-30) REVERT: I 498 MET cc_start: 0.8246 (mtt) cc_final: 0.8044 (mtt) REVERT: I 564 GLN cc_start: 0.8648 (tt0) cc_final: 0.8394 (tt0) REVERT: I 601 THR cc_start: 0.9410 (m) cc_final: 0.9011 (m) outliers start: 16 outliers final: 3 residues processed: 767 average time/residue: 0.3298 time to fit residues: 392.2648 Evaluate side-chains 649 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 644 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 551 MET Chi-restraints excluded: chain H residue 557 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 68 optimal weight: 0.0570 chunk 135 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 208 optimal weight: 0.0270 chunk 80 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 overall best weight: 0.9958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN B 108 GLN B 154 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** H 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 626 HIS ** I 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN I 187 HIS ** I 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21438 Z= 0.210 Angle : 0.661 12.538 29093 Z= 0.333 Chirality : 0.045 0.188 3253 Planarity : 0.005 0.080 3755 Dihedral : 6.928 68.948 2983 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.16 % Favored : 94.77 % Rotamer: Outliers : 2.60 % Allowed : 12.60 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % 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: -1.12 (0.16), residues: 2678 helix: 0.71 (0.19), residues: 771 sheet: -0.61 (0.23), residues: 528 loop : -1.68 (0.15), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 98 HIS 0.006 0.001 HIS B 97 PHE 0.032 0.002 PHE H 385 TYR 0.019 0.002 TYR B 13 ARG 0.005 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 645 time to evaluate : 2.446 Fit side-chains revert: symmetry clash REVERT: A 200 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7407 (mt-10) REVERT: A 219 ASN cc_start: 0.8862 (m-40) cc_final: 0.8538 (m-40) REVERT: A 403 ARG cc_start: 0.6895 (ptp-170) cc_final: 0.6525 (mtm110) REVERT: B 16 MET cc_start: 0.6724 (ttt) cc_final: 0.6301 (mmt) REVERT: B 73 ARG cc_start: 0.9000 (mtm180) cc_final: 0.8119 (mtm110) REVERT: B 218 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6648 (tm-30) REVERT: B 295 MET cc_start: 0.7690 (tpp) cc_final: 0.7247 (tpp) REVERT: C 11 GLN cc_start: 0.7719 (tp40) cc_final: 0.7386 (tp40) REVERT: C 16 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7512 (ttm) REVERT: C 127 LYS cc_start: 0.8634 (tttt) cc_final: 0.8345 (tptm) REVERT: C 211 SER cc_start: 0.7939 (p) cc_final: 0.7630 (p) REVERT: C 216 ARG cc_start: 0.7691 (mtp85) cc_final: 0.7417 (ttm-80) REVERT: D 102 LEU cc_start: 0.8648 (mt) cc_final: 0.8380 (mp) REVERT: D 211 TRP cc_start: 0.7738 (OUTLIER) cc_final: 0.6953 (m100) REVERT: E 272 ARG cc_start: 0.7364 (mtm180) cc_final: 0.6810 (mtt180) REVERT: H 61 HIS cc_start: 0.7238 (m-70) cc_final: 0.6946 (m-70) REVERT: H 94 MET cc_start: 0.8535 (tpt) cc_final: 0.8282 (tpt) REVERT: H 144 TYR cc_start: 0.8594 (m-80) cc_final: 0.8108 (m-80) REVERT: H 257 ASN cc_start: 0.9168 (t0) cc_final: 0.8936 (t0) REVERT: H 308 LYS cc_start: 0.7577 (tppt) cc_final: 0.6522 (ttmm) REVERT: H 419 ASN cc_start: 0.7038 (m-40) cc_final: 0.6508 (m-40) REVERT: H 492 GLU cc_start: 0.7969 (tt0) cc_final: 0.7620 (tt0) REVERT: H 512 ARG cc_start: 0.8407 (mmm160) cc_final: 0.7842 (tpp80) REVERT: H 526 LYS cc_start: 0.8264 (mmtt) cc_final: 0.7974 (mmmt) REVERT: H 567 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7927 (mt-10) REVERT: H 621 PHE cc_start: 0.8169 (t80) cc_final: 0.7852 (t80) REVERT: H 629 MET cc_start: 0.7578 (mtp) cc_final: 0.7377 (mtp) REVERT: I 68 ASP cc_start: 0.7460 (m-30) cc_final: 0.7201 (m-30) REVERT: I 135 MET cc_start: 0.7837 (ptp) cc_final: 0.7635 (ptp) REVERT: I 152 ASN cc_start: 0.9240 (m-40) cc_final: 0.9021 (m-40) REVERT: I 272 ARG cc_start: 0.7386 (mtp85) cc_final: 0.7024 (mtt180) REVERT: I 475 ASP cc_start: 0.8208 (t0) cc_final: 0.7872 (t70) REVERT: I 532 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: I 558 GLN cc_start: 0.7886 (mt0) cc_final: 0.7613 (mt0) REVERT: I 636 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7652 (mt-10) outliers start: 58 outliers final: 40 residues processed: 657 average time/residue: 0.3096 time to fit residues: 321.5604 Evaluate side-chains 655 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 612 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 353 ASP Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 316 THR Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 563 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 241 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 135 GLN B 194 HIS B 196 ASN B 214 GLN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** H 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 589 ASN ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 21438 Z= 0.423 Angle : 0.725 12.159 29093 Z= 0.371 Chirality : 0.048 0.204 3253 Planarity : 0.005 0.053 3755 Dihedral : 7.006 63.955 2979 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.61 % Favored : 93.31 % Rotamer: Outliers : 4.75 % Allowed : 15.87 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % 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: -1.42 (0.16), residues: 2678 helix: 0.24 (0.18), residues: 779 sheet: -0.86 (0.22), residues: 563 loop : -1.69 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 74 HIS 0.006 0.001 HIS H 201 PHE 0.043 0.002 PHE H 385 TYR 0.021 0.002 TYR H 256 ARG 0.005 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 608 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8638 (tt) REVERT: A 200 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7657 (mt-10) REVERT: A 219 ASN cc_start: 0.9001 (m-40) cc_final: 0.8713 (m-40) REVERT: A 241 ASN cc_start: 0.8465 (m-40) cc_final: 0.8011 (t0) REVERT: B 16 MET cc_start: 0.6764 (ttt) cc_final: 0.6420 (mmt) REVERT: B 125 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6272 (mtt-85) REVERT: B 295 MET cc_start: 0.7928 (tpp) cc_final: 0.7586 (tpp) REVERT: C 50 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8891 (mm) REVERT: C 127 LYS cc_start: 0.8691 (tttt) cc_final: 0.8374 (tptm) REVERT: C 216 ARG cc_start: 0.7753 (mtp85) cc_final: 0.7357 (mtp-110) REVERT: D 211 TRP cc_start: 0.7870 (OUTLIER) cc_final: 0.7387 (m100) REVERT: D 236 MET cc_start: 0.6117 (mmp) cc_final: 0.4854 (mmm) REVERT: E 45 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: H 144 TYR cc_start: 0.8699 (m-80) cc_final: 0.8215 (m-80) REVERT: H 333 ASP cc_start: 0.8176 (p0) cc_final: 0.7835 (p0) REVERT: H 419 ASN cc_start: 0.6970 (m-40) cc_final: 0.6603 (m-40) REVERT: H 526 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8359 (mmmt) REVERT: H 580 ASP cc_start: 0.8174 (t0) cc_final: 0.7810 (t0) REVERT: I 148 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8962 (p0) REVERT: I 300 THR cc_start: 0.9247 (m) cc_final: 0.8930 (p) REVERT: I 382 HIS cc_start: 0.7079 (t-90) cc_final: 0.6843 (t-90) REVERT: I 511 ASP cc_start: 0.8050 (m-30) cc_final: 0.7536 (t0) REVERT: I 529 ILE cc_start: 0.8509 (mm) cc_final: 0.8171 (tp) REVERT: I 532 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8062 (t0) outliers start: 106 outliers final: 73 residues processed: 648 average time/residue: 0.2816 time to fit residues: 292.0533 Evaluate side-chains 658 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 578 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 215 SER Chi-restraints excluded: chain H residue 352 ILE Chi-restraints excluded: chain H residue 353 ASP Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 593 SER Chi-restraints excluded: chain H residue 601 THR Chi-restraints excluded: chain H residue 605 THR Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 316 THR Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 561 THR Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** H 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21438 Z= 0.196 Angle : 0.609 11.560 29093 Z= 0.308 Chirality : 0.044 0.173 3253 Planarity : 0.004 0.102 3755 Dihedral : 6.606 67.792 2979 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.04 % Favored : 94.88 % Rotamer: Outliers : 4.08 % Allowed : 18.74 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % 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: -1.15 (0.16), residues: 2678 helix: 0.55 (0.19), residues: 786 sheet: -0.79 (0.22), residues: 586 loop : -1.56 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 141 HIS 0.008 0.001 HIS B 97 PHE 0.031 0.002 PHE H 262 TYR 0.026 0.002 TYR C 78 ARG 0.005 0.000 ARG H 512 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 591 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8617 (tt) REVERT: A 174 HIS cc_start: 0.7892 (m-70) cc_final: 0.7505 (m90) REVERT: A 200 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7536 (mt-10) REVERT: A 219 ASN cc_start: 0.8986 (m-40) cc_final: 0.8704 (m-40) REVERT: B 16 MET cc_start: 0.6777 (ttt) cc_final: 0.6431 (mmt) REVERT: B 291 TYR cc_start: 0.8230 (t80) cc_final: 0.8001 (t80) REVERT: B 295 MET cc_start: 0.7877 (tpp) cc_final: 0.7653 (tpp) REVERT: C 16 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7475 (ttm) REVERT: C 127 LYS cc_start: 0.8676 (tttt) cc_final: 0.8361 (tptm) REVERT: C 216 ARG cc_start: 0.7694 (mtp85) cc_final: 0.7277 (mtp85) REVERT: D 211 TRP cc_start: 0.7784 (OUTLIER) cc_final: 0.7326 (m100) REVERT: E 272 ARG cc_start: 0.7463 (mtm180) cc_final: 0.6875 (mtt180) REVERT: H 144 TYR cc_start: 0.8614 (m-80) cc_final: 0.8117 (m-80) REVERT: H 419 ASN cc_start: 0.6889 (m-40) cc_final: 0.6533 (m-40) REVERT: H 501 ARG cc_start: 0.8289 (ttt180) cc_final: 0.7870 (ttt-90) REVERT: H 512 ARG cc_start: 0.8614 (mmm160) cc_final: 0.8054 (tpp80) REVERT: H 526 LYS cc_start: 0.8613 (mmtt) cc_final: 0.8383 (mmmt) REVERT: I 68 ASP cc_start: 0.7469 (m-30) cc_final: 0.7261 (m-30) REVERT: I 94 MET cc_start: 0.8410 (tpt) cc_final: 0.8113 (tpt) REVERT: I 95 ARG cc_start: 0.7819 (mtp-110) cc_final: 0.7453 (mtp-110) REVERT: I 300 THR cc_start: 0.9150 (m) cc_final: 0.8847 (p) REVERT: I 355 LEU cc_start: 0.8558 (mt) cc_final: 0.8071 (mt) REVERT: I 440 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8429 (mm-30) REVERT: I 532 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8294 (m-30) outliers start: 91 outliers final: 57 residues processed: 634 average time/residue: 0.3009 time to fit residues: 299.6952 Evaluate side-chains 634 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 573 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 215 SER Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 353 ASP Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 601 THR Chi-restraints excluded: chain H residue 626 HIS Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 471 ASP Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 7.9990 chunk 145 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 chunk 64 optimal weight: 50.0000 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 154 GLN C 38 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 589 ASN ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 211 GLN I 326 HIS I 382 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 21438 Z= 0.524 Angle : 0.772 12.991 29093 Z= 0.395 Chirality : 0.050 0.210 3253 Planarity : 0.005 0.100 3755 Dihedral : 7.054 66.438 2979 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.47 % Favored : 92.45 % Rotamer: Outliers : 5.83 % Allowed : 18.83 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % 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: -1.63 (0.16), residues: 2678 helix: -0.04 (0.18), residues: 781 sheet: -1.06 (0.21), residues: 605 loop : -1.72 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 141 HIS 0.008 0.001 HIS H 435 PHE 0.042 0.003 PHE H 385 TYR 0.027 0.003 TYR C 78 ARG 0.005 0.001 ARG I 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 591 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8666 (tt) REVERT: A 157 ASP cc_start: 0.8396 (t0) cc_final: 0.8021 (t0) REVERT: A 200 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7747 (mt-10) REVERT: A 219 ASN cc_start: 0.9041 (m-40) cc_final: 0.8835 (m-40) REVERT: A 241 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8039 (t0) REVERT: A 244 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7527 (mt-10) REVERT: B 16 MET cc_start: 0.6741 (ttt) cc_final: 0.6358 (mmt) REVERT: B 125 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6296 (mtt-85) REVERT: B 150 LEU cc_start: 0.8207 (tp) cc_final: 0.7908 (tp) REVERT: B 291 TYR cc_start: 0.8229 (t80) cc_final: 0.7983 (t80) REVERT: B 295 MET cc_start: 0.8073 (tpp) cc_final: 0.7839 (tpp) REVERT: C 127 LYS cc_start: 0.8637 (tttt) cc_final: 0.8309 (tptm) REVERT: D 211 TRP cc_start: 0.7935 (OUTLIER) cc_final: 0.7490 (m100) REVERT: D 236 MET cc_start: 0.6313 (mmp) cc_final: 0.4907 (mmm) REVERT: H 228 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7624 (mm-30) REVERT: H 239 LEU cc_start: 0.8758 (mt) cc_final: 0.8349 (mp) REVERT: H 250 PHE cc_start: 0.8944 (m-80) cc_final: 0.8697 (m-10) REVERT: H 419 ASN cc_start: 0.7033 (m-40) cc_final: 0.6691 (m-40) REVERT: H 454 LYS cc_start: 0.8638 (mmmm) cc_final: 0.8027 (mmtp) REVERT: H 501 ARG cc_start: 0.8254 (ttt180) cc_final: 0.7911 (ttt-90) REVERT: I 94 MET cc_start: 0.8500 (tpt) cc_final: 0.8109 (tpt) REVERT: I 137 ASP cc_start: 0.8143 (t0) cc_final: 0.7877 (t0) REVERT: I 300 THR cc_start: 0.9290 (m) cc_final: 0.9040 (p) REVERT: I 440 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8360 (mm-30) REVERT: I 517 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.9109 (p90) outliers start: 130 outliers final: 95 residues processed: 652 average time/residue: 0.3029 time to fit residues: 307.5472 Evaluate side-chains 670 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 570 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 215 SER Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 352 ILE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 582 SER Chi-restraints excluded: chain H residue 593 SER Chi-restraints excluded: chain H residue 601 THR Chi-restraints excluded: chain H residue 626 HIS Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 274 TRP Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 316 THR Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 437 SER Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 471 ASP Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 517 PHE Chi-restraints excluded: chain I residue 561 THR Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 8.9990 chunk 231 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 63 optimal weight: 0.0470 chunk 257 optimal weight: 0.7980 chunk 213 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN C 23 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 589 ASN ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 HIS ** I 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21438 Z= 0.179 Angle : 0.621 11.861 29093 Z= 0.311 Chirality : 0.044 0.172 3253 Planarity : 0.004 0.083 3755 Dihedral : 6.522 72.043 2979 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 3.63 % Allowed : 22.01 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % 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: -1.20 (0.16), residues: 2678 helix: 0.51 (0.19), residues: 785 sheet: -0.77 (0.22), residues: 574 loop : -1.62 (0.16), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 352 HIS 0.006 0.001 HIS B 97 PHE 0.031 0.002 PHE H 262 TYR 0.017 0.002 TYR C 78 ARG 0.007 0.000 ARG H 512 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 579 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8649 (tt) REVERT: A 157 ASP cc_start: 0.8208 (t0) cc_final: 0.7749 (t0) REVERT: A 174 HIS cc_start: 0.7875 (m-70) cc_final: 0.7490 (m90) REVERT: A 200 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7402 (mt-10) REVERT: A 219 ASN cc_start: 0.9006 (m-40) cc_final: 0.8783 (m-40) REVERT: A 244 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7385 (mt-10) REVERT: B 16 MET cc_start: 0.6740 (ttt) cc_final: 0.6402 (mmt) REVERT: B 73 ARG cc_start: 0.9006 (mtm180) cc_final: 0.8742 (mtm-85) REVERT: B 291 TYR cc_start: 0.8239 (t80) cc_final: 0.7746 (t80) REVERT: C 46 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8630 (mtm) REVERT: C 127 LYS cc_start: 0.8618 (tttt) cc_final: 0.8259 (tptm) REVERT: C 183 LEU cc_start: 0.8255 (tt) cc_final: 0.8036 (tt) REVERT: C 216 ARG cc_start: 0.7623 (mtp85) cc_final: 0.7152 (mtp-110) REVERT: C 221 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7627 (tt) REVERT: D 211 TRP cc_start: 0.7813 (OUTLIER) cc_final: 0.7416 (m100) REVERT: H 228 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7463 (mm-30) REVERT: H 419 ASN cc_start: 0.6879 (m-40) cc_final: 0.6577 (m-40) REVERT: H 492 GLU cc_start: 0.8024 (tt0) cc_final: 0.7679 (tp30) REVERT: H 501 ARG cc_start: 0.8291 (ttt180) cc_final: 0.7944 (ttt-90) REVERT: H 512 ARG cc_start: 0.8650 (mmm160) cc_final: 0.8048 (tpp80) REVERT: H 525 LYS cc_start: 0.7895 (mptt) cc_final: 0.7681 (mptt) REVERT: I 94 MET cc_start: 0.8391 (tpt) cc_final: 0.8122 (tpt) REVERT: I 123 PHE cc_start: 0.9273 (m-10) cc_final: 0.9022 (m-10) REVERT: I 137 ASP cc_start: 0.7976 (t0) cc_final: 0.7717 (t0) REVERT: I 300 THR cc_start: 0.9313 (m) cc_final: 0.9038 (p) REVERT: I 335 LYS cc_start: 0.8840 (ptmm) cc_final: 0.8437 (ptmm) REVERT: I 355 LEU cc_start: 0.8568 (mt) cc_final: 0.8038 (mt) REVERT: I 382 HIS cc_start: 0.7167 (t70) cc_final: 0.6866 (t70) REVERT: I 440 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8259 (mm-30) REVERT: I 532 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8202 (t0) REVERT: I 627 MET cc_start: 0.7521 (mmp) cc_final: 0.7271 (mmm) outliers start: 81 outliers final: 55 residues processed: 618 average time/residue: 0.3025 time to fit residues: 294.3054 Evaluate side-chains 616 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 556 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 215 SER Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 353 ASP Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 601 THR Chi-restraints excluded: chain H residue 626 HIS Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 471 ASP Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 156 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 283 HIS ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 HIS ** I 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21438 Z= 0.285 Angle : 0.639 12.315 29093 Z= 0.322 Chirality : 0.045 0.173 3253 Planarity : 0.004 0.093 3755 Dihedral : 6.558 71.747 2978 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.35 % Favored : 93.57 % Rotamer: Outliers : 3.81 % Allowed : 22.01 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.16), residues: 2678 helix: 0.52 (0.18), residues: 772 sheet: -0.84 (0.22), residues: 591 loop : -1.59 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 141 HIS 0.006 0.001 HIS B 97 PHE 0.031 0.002 PHE H 262 TYR 0.018 0.002 TYR I 216 ARG 0.004 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 571 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8632 (tt) REVERT: A 157 ASP cc_start: 0.8307 (t0) cc_final: 0.7852 (t0) REVERT: A 187 ASP cc_start: 0.7269 (t0) cc_final: 0.7052 (t0) REVERT: A 200 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7564 (mt-10) REVERT: A 219 ASN cc_start: 0.8999 (m-40) cc_final: 0.8796 (m-40) REVERT: A 244 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7510 (mt-10) REVERT: B 16 MET cc_start: 0.6696 (ttt) cc_final: 0.6361 (mmt) REVERT: B 73 ARG cc_start: 0.9049 (mtm180) cc_final: 0.8747 (mtm-85) REVERT: B 113 LEU cc_start: 0.8274 (tp) cc_final: 0.7759 (mp) REVERT: C 127 LYS cc_start: 0.8612 (tttt) cc_final: 0.8297 (tptm) REVERT: C 183 LEU cc_start: 0.8232 (tt) cc_final: 0.8031 (tt) REVERT: C 221 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7682 (tt) REVERT: D 211 TRP cc_start: 0.7862 (OUTLIER) cc_final: 0.7560 (m100) REVERT: D 230 GLU cc_start: 0.5891 (mt-10) cc_final: 0.5687 (mt-10) REVERT: H 228 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7460 (mm-30) REVERT: H 419 ASN cc_start: 0.6864 (m-40) cc_final: 0.6581 (m-40) REVERT: H 454 LYS cc_start: 0.8634 (mmmm) cc_final: 0.8084 (mmtp) REVERT: H 501 ARG cc_start: 0.8298 (ttt180) cc_final: 0.7938 (ttt-90) REVERT: H 512 ARG cc_start: 0.8705 (mmm160) cc_final: 0.8161 (tpp80) REVERT: I 94 MET cc_start: 0.8419 (tpt) cc_final: 0.8147 (tpt) REVERT: I 137 ASP cc_start: 0.8003 (t0) cc_final: 0.7690 (t0) REVERT: I 300 THR cc_start: 0.9420 (m) cc_final: 0.9123 (p) REVERT: I 405 ASN cc_start: 0.7565 (m110) cc_final: 0.7149 (m-40) REVERT: I 523 MET cc_start: 0.7859 (ttm) cc_final: 0.7600 (ttm) REVERT: I 532 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8384 (m-30) outliers start: 85 outliers final: 67 residues processed: 619 average time/residue: 0.3019 time to fit residues: 295.8331 Evaluate side-chains 637 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 566 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 215 SER Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 298 SER Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 601 THR Chi-restraints excluded: chain H residue 626 HIS Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 274 TRP Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 471 ASP Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN C 38 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21438 Z= 0.335 Angle : 0.664 12.434 29093 Z= 0.335 Chirality : 0.046 0.174 3253 Planarity : 0.004 0.091 3755 Dihedral : 6.697 77.613 2978 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.91 % Favored : 93.01 % Rotamer: Outliers : 4.39 % Allowed : 21.92 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % 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: -1.29 (0.16), residues: 2678 helix: 0.42 (0.18), residues: 775 sheet: -0.82 (0.22), residues: 587 loop : -1.66 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 141 HIS 0.006 0.001 HIS H 626 PHE 0.045 0.002 PHE H 250 TYR 0.017 0.002 TYR B 78 ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 577 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8602 (tt) REVERT: A 157 ASP cc_start: 0.8331 (t0) cc_final: 0.7878 (t0) REVERT: A 200 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7605 (mt-10) REVERT: A 244 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7530 (mt-10) REVERT: B 16 MET cc_start: 0.6728 (ttt) cc_final: 0.6377 (mmt) REVERT: B 42 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7486 (mtmm) REVERT: B 73 ARG cc_start: 0.9058 (mtm180) cc_final: 0.8745 (mtm-85) REVERT: C 46 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8648 (mtm) REVERT: C 127 LYS cc_start: 0.8627 (tttt) cc_final: 0.8310 (tptm) REVERT: C 216 ARG cc_start: 0.7700 (mtp85) cc_final: 0.7444 (ttm110) REVERT: C 221 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7768 (tt) REVERT: D 211 TRP cc_start: 0.7902 (OUTLIER) cc_final: 0.7589 (m100) REVERT: H 228 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7487 (mm-30) REVERT: H 419 ASN cc_start: 0.6985 (m-40) cc_final: 0.6689 (m-40) REVERT: H 492 GLU cc_start: 0.8213 (tp30) cc_final: 0.7714 (tp30) REVERT: H 501 ARG cc_start: 0.8252 (ttt180) cc_final: 0.7897 (ttt-90) REVERT: H 512 ARG cc_start: 0.8733 (mmm160) cc_final: 0.8182 (tpp80) REVERT: H 525 LYS cc_start: 0.7864 (mptt) cc_final: 0.7653 (mptt) REVERT: I 94 MET cc_start: 0.8402 (tpt) cc_final: 0.8098 (tpt) REVERT: I 137 ASP cc_start: 0.8034 (t70) cc_final: 0.7677 (t0) REVERT: I 300 THR cc_start: 0.9439 (m) cc_final: 0.9161 (p) REVERT: I 405 ASN cc_start: 0.7535 (m110) cc_final: 0.7292 (m-40) REVERT: I 440 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8303 (mm-30) REVERT: I 523 MET cc_start: 0.7878 (ttm) cc_final: 0.7626 (ttm) REVERT: I 532 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8378 (m-30) REVERT: I 561 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8411 (t) outliers start: 98 outliers final: 85 residues processed: 629 average time/residue: 0.3010 time to fit residues: 301.4777 Evaluate side-chains 666 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 575 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 215 SER Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain H residue 298 SER Chi-restraints excluded: chain H residue 353 ASP Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 601 THR Chi-restraints excluded: chain H residue 626 HIS Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 239 LEU Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 274 TRP Chi-restraints excluded: chain I residue 316 THR Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 471 ASP Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 561 THR Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 187 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN C 23 ASN C 38 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 HIS ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21438 Z= 0.228 Angle : 0.633 11.205 29093 Z= 0.316 Chirality : 0.044 0.174 3253 Planarity : 0.004 0.090 3755 Dihedral : 6.462 82.904 2978 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.02 % Rotamer: Outliers : 3.94 % Allowed : 22.64 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % 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: -1.18 (0.16), residues: 2678 helix: 0.59 (0.19), residues: 773 sheet: -0.83 (0.22), residues: 582 loop : -1.60 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 98 HIS 0.005 0.001 HIS B 97 PHE 0.042 0.002 PHE H 250 TYR 0.015 0.002 TYR C 78 ARG 0.006 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 571 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8607 (tt) REVERT: A 174 HIS cc_start: 0.7859 (m-70) cc_final: 0.7464 (m90) REVERT: A 200 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7520 (mt-10) REVERT: A 244 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7397 (mt-10) REVERT: B 16 MET cc_start: 0.6742 (ttt) cc_final: 0.6347 (mmt) REVERT: B 73 ARG cc_start: 0.9030 (mtm180) cc_final: 0.8741 (mtm-85) REVERT: B 113 LEU cc_start: 0.8236 (tp) cc_final: 0.7697 (mp) REVERT: B 203 LYS cc_start: 0.7118 (ptpt) cc_final: 0.6908 (ptpt) REVERT: C 127 LYS cc_start: 0.8583 (tttt) cc_final: 0.8269 (tptm) REVERT: C 216 ARG cc_start: 0.7682 (mtp85) cc_final: 0.7413 (ttm110) REVERT: C 221 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7699 (tt) REVERT: D 211 TRP cc_start: 0.7850 (OUTLIER) cc_final: 0.7555 (m100) REVERT: H 228 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7454 (mm-30) REVERT: H 454 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8153 (mmtp) REVERT: H 501 ARG cc_start: 0.8306 (ttt180) cc_final: 0.7934 (ttt-90) REVERT: H 512 ARG cc_start: 0.8688 (mmm160) cc_final: 0.8172 (tpp80) REVERT: I 94 MET cc_start: 0.8380 (tpt) cc_final: 0.8112 (tpt) REVERT: I 137 ASP cc_start: 0.7905 (t70) cc_final: 0.7559 (t0) REVERT: I 300 THR cc_start: 0.9422 (m) cc_final: 0.9145 (p) REVERT: I 335 LYS cc_start: 0.8776 (ptmm) cc_final: 0.8474 (ptmm) REVERT: I 405 ASN cc_start: 0.7504 (m110) cc_final: 0.7133 (m-40) REVERT: I 422 LYS cc_start: 0.8308 (mttt) cc_final: 0.7812 (mttt) REVERT: I 440 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8297 (mm-30) REVERT: I 523 MET cc_start: 0.7841 (ttm) cc_final: 0.7614 (ttm) REVERT: I 532 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8320 (m-30) REVERT: I 561 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8437 (t) REVERT: I 634 MET cc_start: 0.7226 (mmm) cc_final: 0.6976 (tpt) outliers start: 88 outliers final: 76 residues processed: 615 average time/residue: 0.2921 time to fit residues: 283.5799 Evaluate side-chains 647 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 566 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 215 SER Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain H residue 298 SER Chi-restraints excluded: chain H residue 353 ASP Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 601 THR Chi-restraints excluded: chain H residue 626 HIS Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 471 ASP Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 561 THR Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 243 optimal weight: 10.0000 chunk 211 optimal weight: 0.0980 chunk 21 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN C 38 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 419 ASN ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 HIS ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21438 Z= 0.193 Angle : 0.616 10.121 29093 Z= 0.306 Chirality : 0.043 0.171 3253 Planarity : 0.004 0.085 3755 Dihedral : 6.288 89.987 2978 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 3.68 % Allowed : 23.17 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % 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: -1.05 (0.16), residues: 2678 helix: 0.76 (0.19), residues: 776 sheet: -0.78 (0.22), residues: 576 loop : -1.55 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 98 HIS 0.008 0.001 HIS H 78 PHE 0.030 0.002 PHE H 262 TYR 0.013 0.001 TYR C 78 ARG 0.003 0.000 ARG H 512 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 564 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8562 (tt) REVERT: A 82 LEU cc_start: 0.8558 (tp) cc_final: 0.8340 (tp) REVERT: A 174 HIS cc_start: 0.7821 (m-70) cc_final: 0.7453 (m90) REVERT: A 200 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7481 (mt-10) REVERT: A 244 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7369 (mt-10) REVERT: A 425 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7423 (mt-10) REVERT: B 16 MET cc_start: 0.6719 (ttt) cc_final: 0.6283 (mmt) REVERT: B 73 ARG cc_start: 0.9013 (mtm180) cc_final: 0.8736 (mtm-85) REVERT: B 88 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8319 (mm110) REVERT: B 113 LEU cc_start: 0.8196 (tp) cc_final: 0.7674 (mp) REVERT: C 127 LYS cc_start: 0.8522 (tttt) cc_final: 0.8205 (tptm) REVERT: C 221 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7631 (tt) REVERT: D 211 TRP cc_start: 0.7833 (OUTLIER) cc_final: 0.7585 (m100) REVERT: D 236 MET cc_start: 0.6286 (mmp) cc_final: 0.4813 (mmm) REVERT: H 168 MET cc_start: 0.8888 (ttt) cc_final: 0.8640 (ttt) REVERT: H 419 ASN cc_start: 0.7045 (OUTLIER) cc_final: 0.6797 (m110) REVERT: H 501 ARG cc_start: 0.8319 (ttt180) cc_final: 0.7959 (ttt-90) REVERT: H 512 ARG cc_start: 0.8640 (mmm160) cc_final: 0.8126 (tpp80) REVERT: I 94 MET cc_start: 0.8379 (tpt) cc_final: 0.8139 (tpt) REVERT: I 137 ASP cc_start: 0.7940 (t70) cc_final: 0.7609 (t0) REVERT: I 300 THR cc_start: 0.9400 (m) cc_final: 0.9120 (p) REVERT: I 335 LYS cc_start: 0.8774 (ptmm) cc_final: 0.8475 (ptmm) REVERT: I 405 ASN cc_start: 0.7457 (m110) cc_final: 0.7055 (m110) REVERT: I 422 LYS cc_start: 0.8253 (mttt) cc_final: 0.7694 (mttt) REVERT: I 440 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8304 (mm-30) REVERT: I 532 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8354 (m-30) REVERT: I 634 MET cc_start: 0.7174 (mmm) cc_final: 0.6926 (tpt) outliers start: 82 outliers final: 70 residues processed: 609 average time/residue: 0.3112 time to fit residues: 299.1263 Evaluate side-chains 628 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 552 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 215 SER Chi-restraints excluded: chain H residue 270 ASN Chi-restraints excluded: chain H residue 298 SER Chi-restraints excluded: chain H residue 332 SER Chi-restraints excluded: chain H residue 353 ASP Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 419 ASN Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 441 THR Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 601 THR Chi-restraints excluded: chain H residue 626 HIS Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 471 ASP Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 194 optimal weight: 0.0570 chunk 31 optimal weight: 0.0030 chunk 58 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 217 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 overall best weight: 1.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 108 GLN C 23 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 419 ASN H 589 ASN ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 HIS ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.145056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.115760 restraints weight = 40225.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.119612 restraints weight = 17655.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.122029 restraints weight = 9611.014| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21438 Z= 0.205 Angle : 0.625 10.372 29093 Z= 0.309 Chirality : 0.044 0.171 3253 Planarity : 0.004 0.084 3755 Dihedral : 6.217 87.764 2978 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.25 % Rotamer: Outliers : 3.54 % Allowed : 23.49 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % 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: -1.02 (0.16), residues: 2678 helix: 0.79 (0.19), residues: 776 sheet: -0.74 (0.22), residues: 576 loop : -1.54 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 141 HIS 0.007 0.001 HIS H 78 PHE 0.034 0.002 PHE H 250 TYR 0.012 0.001 TYR I 216 ARG 0.003 0.000 ARG H 512 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5551.33 seconds wall clock time: 102 minutes 58.78 seconds (6178.78 seconds total)