Starting phenix.real_space_refine (version: 1.21rc1) on Sat May 13 00:20:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/05_2023/7qba_13885_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/05_2023/7qba_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_13885/05_2023/7qba_13885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/05_2023/7qba_13885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/05_2023/7qba_13885_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/05_2023/7qba_13885_updated.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 13.23, per 1000 atoms: 0.63 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: 8.55 Conformation dependent library (CDL) restraints added in 3.9 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: 2.34 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: 7.41 Time building geometry restraints manager: 9.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 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: 11488 17.94 - 35.88: 983 35.88 - 53.81: 166 53.81 - 71.75: 28 71.75 - 89.69: 20 Dihedral angle restraints: 12685 sinusoidal: 5027 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 12682 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 5.290 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 57.290 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.490 ------------------------------------------------------------------------------- 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 : 13.925 89.692 7793 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 % 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 *********************** 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 : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 767 average time/residue: 0.3022 time to fit residues: 358.1077 Evaluate side-chains 644 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 641 time to evaluate : 1.790 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1549 time to fit residues: 3.4628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 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: 0.0170 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: 0.9938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: