Starting phenix.real_space_refine on Sat Aug 8 16:23:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10dq_75095/08_2026/10dq_75095.cif Found real_map, /net/cci-nas-00/data/ceres_data/10dq_75095/08_2026/10dq_75095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10dq_75095/08_2026/10dq_75095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10dq_75095/08_2026/10dq_75095.map" model { file = "/net/cci-nas-00/data/ceres_data/10dq_75095/08_2026/10dq_75095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10dq_75095/08_2026/10dq_75095.cif" } resolution = 3.9 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 54 5.49 5 S 109 5.16 5 C 17963 2.51 5 N 4863 2.21 5 O 5472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28461 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 822 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain: "B" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 1, 'TRANS': 105} Chain: "D" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 552 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "H" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1412 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 167} Chain breaks: 1 Chain: "I" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5496 Classifications: {'peptide': 679} Link IDs: {'PTRANS': 27, 'TRANS': 651} Chain breaks: 4 Chain: "K" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1762 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1941 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "N" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3166 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 369} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1979 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 6, 'TRANS': 234} Chain breaks: 1 Chain: "P" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2116 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 250} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "Q" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2144 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "T" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 761 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "U" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1485 Classifications: {'peptide': 184} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 181} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "W" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 551 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain breaks: 1 Chain: "Y" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1663 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "Z" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1180 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 148} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TYR:plan': 1, 'GLU:plan': 2, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Time building chain proxies: 6.20, per 1000 atoms: 0.22 Number of scatterers: 28461 At special positions: 0 Unit cell: (124.12, 187.25, 167.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 109 16.00 P 54 15.00 O 5472 8.00 N 4863 7.00 C 17963 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 - 3.00 Amino acid : True - 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: 2.78 Conformation dependent library (CDL) restraints added in 1.0 seconds 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6548 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 15 sheets defined 67.9% alpha, 9.0% beta 23 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 230 through 249 Processing helix chain 'A' and resid 255 through 320 Processing helix chain 'B' and resid 219 through 249 Processing helix chain 'B' and resid 255 through 324 Processing helix chain 'H' and resid 5 through 39 Processing helix chain 'H' and resid 46 through 74 removed outlier: 3.559A pdb=" N LEU H 52 " --> pdb=" O THR H 48 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 96 removed outlier: 3.599A pdb=" N THR H 84 " --> pdb=" O ASN H 80 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 133 removed outlier: 3.779A pdb=" N LEU H 101 " --> pdb=" O ASP H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 172 removed outlier: 3.711A pdb=" N GLU H 153 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 13 Processing helix chain 'I' and resid 26 through 38 Processing helix chain 'I' and resid 41 through 55 Processing helix chain 'I' and resid 59 through 70 Processing helix chain 'I' and resid 78 through 89 removed outlier: 3.545A pdb=" N LEU I 82 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 117 Processing helix chain 'I' and resid 131 through 140 Processing helix chain 'I' and resid 145 through 157 removed outlier: 3.929A pdb=" N THR I 150 " --> pdb=" O GLN I 146 " (cutoff:3.500A) Proline residue: I 151 - end of helix Processing helix chain 'I' and resid 159 through 163 removed outlier: 3.616A pdb=" N VAL I 163 " --> pdb=" O PRO I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 177 Processing helix chain 'I' and resid 182 through 199 removed outlier: 3.552A pdb=" N GLY I 199 " --> pdb=" O GLN I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 211 Processing helix chain 'I' and resid 215 through 223 removed outlier: 3.720A pdb=" N ASN I 223 " --> pdb=" O LYS I 219 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 241 Processing helix chain 'I' and resid 247 through 264 removed outlier: 3.756A pdb=" N ILE I 262 " --> pdb=" O TYR I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 267 No H-bonds generated for 'chain 'I' and resid 265 through 267' Processing helix chain 'I' and resid 295 through 302 removed outlier: 3.835A pdb=" N LEU I 299 " --> pdb=" O SER I 295 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA I 300 " --> pdb=" O LEU I 296 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN I 301 " --> pdb=" O GLU I 297 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN I 302 " --> pdb=" O GLN I 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 295 through 302' Processing helix chain 'I' and resid 311 through 317 Processing helix chain 'I' and resid 332 through 338 removed outlier: 3.821A pdb=" N LEU I 336 " --> pdb=" O ARG I 333 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS I 337 " --> pdb=" O ASP I 334 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N HIS I 338 " --> pdb=" O SER I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 348 Processing helix chain 'I' and resid 354 through 369 Processing helix chain 'I' and resid 378 through 388 removed outlier: 4.163A pdb=" N MET I 388 " --> pdb=" O SER I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 401 Processing helix chain 'I' and resid 402 through 409 removed outlier: 3.534A pdb=" N ASP I 409 " --> pdb=" O TYR I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 410 through 421 Processing helix chain 'I' and resid 422 through 424 No H-bonds generated for 'chain 'I' and resid 422 through 424' Processing helix chain 'I' and resid 431 through 450 removed outlier: 4.006A pdb=" N ASP I 450 " --> pdb=" O TRP I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 456 through 475 removed outlier: 3.724A pdb=" N ASP I 475 " --> pdb=" O ASN I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 494 Processing helix chain 'I' and resid 505 through 524 Processing helix chain 'I' and resid 531 through 535 removed outlier: 3.591A pdb=" N LEU I 535 " --> pdb=" O ILE I 532 " (cutoff:3.500A) Processing helix chain 'I' and resid 538 through 548 removed outlier: 3.623A pdb=" N MET I 542 " --> pdb=" O GLY I 538 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS I 544 " --> pdb=" O ASP I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 550 through 569 Processing helix chain 'I' and resid 577 through 593 Processing helix chain 'I' and resid 607 through 616 removed outlier: 3.913A pdb=" N PHE I 611 " --> pdb=" O SER I 607 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 655 Processing helix chain 'I' and resid 666 through 677 Processing helix chain 'I' and resid 677 through 684 Processing helix chain 'I' and resid 692 through 705 Processing helix chain 'I' and resid 711 through 721 removed outlier: 3.922A pdb=" N ALA I 715 " --> pdb=" O TYR I 711 " (cutoff:3.500A) Processing helix chain 'I' and resid 725 through 729 removed outlier: 3.788A pdb=" N SER I 729 " --> pdb=" O SER I 726 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 40 Processing helix chain 'K' and resid 49 through 58 Processing helix chain 'K' and resid 70 through 130 removed outlier: 3.844A pdb=" N SER K 130 " --> pdb=" O THR K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 159 Processing helix chain 'K' and resid 159 through 165 Processing helix chain 'K' and resid 166 through 169 Processing helix chain 'K' and resid 170 through 188 removed outlier: 3.791A pdb=" N LEU K 174 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU K 177 " --> pdb=" O SER K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 200 No H-bonds generated for 'chain 'K' and resid 198 through 200' Processing helix chain 'K' and resid 201 through 211 Processing helix chain 'L' and resid 19 through 28 removed outlier: 3.907A pdb=" N LEU L 23 " --> pdb=" O GLY L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 47 removed outlier: 3.554A pdb=" N GLY L 47 " --> pdb=" O PRO L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 108 removed outlier: 3.792A pdb=" N VAL L 98 " --> pdb=" O ASN L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 128 Processing helix chain 'L' and resid 153 through 157 Processing helix chain 'L' and resid 166 through 178 Processing helix chain 'L' and resid 182 through 187 Processing helix chain 'L' and resid 187 through 197 Processing helix chain 'L' and resid 229 through 240 Processing helix chain 'N' and resid 16 through 25 Processing helix chain 'N' and resid 28 through 43 Processing helix chain 'N' and resid 50 through 64 Processing helix chain 'N' and resid 67 through 78 removed outlier: 3.896A pdb=" N ILE N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 100 Processing helix chain 'N' and resid 101 through 104 removed outlier: 3.686A pdb=" N PHE N 104 " --> pdb=" O PRO N 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 101 through 104' Processing helix chain 'N' and resid 124 through 138 removed outlier: 3.847A pdb=" N LYS N 138 " --> pdb=" O THR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 218 through 234 removed outlier: 3.852A pdb=" N SER N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU N 234 " --> pdb=" O ARG N 230 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 259 Processing helix chain 'N' and resid 267 through 269 No H-bonds generated for 'chain 'N' and resid 267 through 269' Processing helix chain 'N' and resid 270 through 276 removed outlier: 3.711A pdb=" N ALA N 274 " --> pdb=" O TRP N 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 289 through 294 Processing helix chain 'N' and resid 318 through 335 Processing helix chain 'N' and resid 408 through 419 Processing helix chain 'N' and resid 428 through 433 Processing helix chain 'O' and resid 125 through 130 removed outlier: 4.198A pdb=" N ASP O 130 " --> pdb=" O PRO O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 134 through 139 removed outlier: 4.028A pdb=" N THR O 138 " --> pdb=" O THR O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 148 removed outlier: 3.575A pdb=" N ARG O 143 " --> pdb=" O SER O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 172 Processing helix chain 'O' and resid 182 through 184 No H-bonds generated for 'chain 'O' and resid 182 through 184' Processing helix chain 'O' and resid 245 through 253 Processing helix chain 'O' and resid 254 through 256 No H-bonds generated for 'chain 'O' and resid 254 through 256' Processing helix chain 'O' and resid 260 through 291 removed outlier: 3.518A pdb=" N GLN O 274 " --> pdb=" O ARG O 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 348 Processing helix chain 'O' and resid 351 through 364 removed outlier: 4.038A pdb=" N ALA O 364 " --> pdb=" O ASN O 360 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 112 Processing helix chain 'P' and resid 133 through 140 Processing helix chain 'P' and resid 149 through 160 Processing helix chain 'P' and resid 224 through 232 Processing helix chain 'P' and resid 236 through 266 Processing helix chain 'P' and resid 333 through 349 Processing helix chain 'P' and resid 350 through 363 Processing helix chain 'Q' and resid 129 through 142 removed outlier: 3.779A pdb=" N VAL Q 133 " --> pdb=" O GLU Q 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 155 through 181 Processing helix chain 'Q' and resid 181 through 190 removed outlier: 3.539A pdb=" N MET Q 185 " --> pdb=" O TYR Q 181 " (cutoff:3.500A) Processing helix chain 'Q' and resid 192 through 219 Processing helix chain 'Q' and resid 233 through 290 Processing helix chain 'Q' and resid 297 through 299 No H-bonds generated for 'chain 'Q' and resid 297 through 299' Processing helix chain 'Q' and resid 300 through 308 Processing helix chain 'Q' and resid 321 through 332 removed outlier: 3.668A pdb=" N HIS Q 330 " --> pdb=" O ARG Q 326 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 357 Processing helix chain 'Q' and resid 358 through 382 removed outlier: 4.194A pdb=" N GLU Q 362 " --> pdb=" O PRO Q 358 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 389 removed outlier: 3.567A pdb=" N VAL Q 389 " --> pdb=" O GLU Q 385 " (cutoff:3.500A) Processing helix chain 'T' and resid 274 through 289 removed outlier: 6.163A pdb=" N GLN T 284 " --> pdb=" O HIS T 280 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE T 285 " --> pdb=" O LEU T 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 294 through 316 removed outlier: 4.045A pdb=" N LEU T 306 " --> pdb=" O GLN T 302 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN T 307 " --> pdb=" O GLU T 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 320 through 331 removed outlier: 3.844A pdb=" N LEU T 324 " --> pdb=" O GLN T 320 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL T 325 " --> pdb=" O LYS T 321 " (cutoff:3.500A) Processing helix chain 'T' and resid 336 through 344 Processing helix chain 'T' and resid 349 through 360 Processing helix chain 'U' and resid 134 through 149 Processing helix chain 'U' and resid 150 through 161 Processing helix chain 'U' and resid 164 through 232 removed outlier: 3.759A pdb=" N ASN U 200 " --> pdb=" O ASN U 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 265 Processing helix chain 'U' and resid 286 through 299 Processing helix chain 'U' and resid 305 through 321 Processing helix chain 'W' and resid 2 through 15 Processing helix chain 'W' and resid 37 through 68 Processing helix chain 'W' and resid 74 through 89 Processing helix chain 'Y' and resid 3 through 16 removed outlier: 3.557A pdb=" N SER Y 7 " --> pdb=" O ASP Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 31 Processing helix chain 'Y' and resid 36 through 50 Processing helix chain 'Y' and resid 55 through 84 Processing helix chain 'Y' and resid 94 through 102 Processing helix chain 'Y' and resid 109 through 118 Processing helix chain 'Y' and resid 137 through 186 Processing helix chain 'Y' and resid 189 through 219 removed outlier: 3.818A pdb=" N PHE Y 194 " --> pdb=" O ILE Y 190 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA Y 195 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE Y 219 " --> pdb=" O ALA Y 215 " (cutoff:3.500A) Processing helix chain 'Y' and resid 221 through 238 Processing helix chain 'Z' and resid 4 through 13 Processing helix chain 'Z' and resid 15 through 20 Processing helix chain 'Z' and resid 21 through 29 Processing helix chain 'Z' and resid 35 through 84 Processing helix chain 'Z' and resid 86 through 127 Processing helix chain 'Z' and resid 134 through 153 removed outlier: 3.520A pdb=" N ASN Z 153 " --> pdb=" O LEU Z 149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 288 through 289 removed outlier: 6.479A pdb=" N VAL I 288 " --> pdb=" O HIS I 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 214 through 218 removed outlier: 3.745A pdb=" N LYS K 229 " --> pdb=" O THR K 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 34 through 39 removed outlier: 3.948A pdb=" N MET L 85 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP L 112 " --> pdb=" O GLY L 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 34 through 39 removed outlier: 3.948A pdb=" N MET L 85 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL N 385 " --> pdb=" O PHE N 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 130 through 133 removed outlier: 3.683A pdb=" N ILE L 137 " --> pdb=" O THR L 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 141 through 148 removed outlier: 3.912A pdb=" N HIS N 141 " --> pdb=" O PHE N 162 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR N 201 " --> pdb=" O SER N 214 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE N 210 " --> pdb=" O PRO N 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 295 through 298 Processing sheet with id=AA8, first strand: chain 'O' and resid 175 through 180 removed outlier: 3.885A pdb=" N LEU O 180 " --> pdb=" O MET O 201 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET O 201 " --> pdb=" O LEU O 180 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS O 225 " --> pdb=" O LEU O 235 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LEU O 235 " --> pdb=" O LYS O 225 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 186 through 188 Processing sheet with id=AB1, first strand: chain 'O' and resid 209 through 210 Processing sheet with id=AB2, first strand: chain 'O' and resid 298 through 299 removed outlier: 3.654A pdb=" N SER O 307 " --> pdb=" O ASP O 298 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS O 314 " --> pdb=" O ILE O 329 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE O 329 " --> pdb=" O LYS O 314 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU O 316 " --> pdb=" O CYS O 327 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N CYS O 327 " --> pdb=" O GLU O 316 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE O 318 " --> pdb=" O VAL O 325 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 165 through 171 removed outlier: 7.168A pdb=" N VAL P 184 " --> pdb=" O GLN P 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 165 through 171 removed outlier: 7.168A pdb=" N VAL P 184 " --> pdb=" O GLN P 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL P 185 " --> pdb=" O PHE P 201 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE P 197 " --> pdb=" O PHE P 189 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU P 198 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE P 220 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLN P 200 " --> pdb=" O LEU P 218 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS P 214 " --> pdb=" O PHE P 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 270 through 274 Processing sheet with id=AB6, first strand: chain 'P' and resid 270 through 274 removed outlier: 6.637A pdb=" N SER P 319 " --> pdb=" O MET Q 335 " (cutoff:3.500A) 1894 hydrogen bonds defined for protein. 5595 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9025 1.34 - 1.46: 5419 1.46 - 1.58: 14309 1.58 - 1.70: 106 1.70 - 1.82: 182 Bond restraints: 29041 Sorted by residual: bond pdb=" C3' DT E 14 " pdb=" C2' DT E 14 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.22e+00 bond pdb=" C3' DA D 128 " pdb=" C2' DA D 128 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.00e+00 bond pdb=" C1' DT E 2 " pdb=" N1 DT E 2 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.77e+00 bond pdb=" C3' DT E 11 " pdb=" C2' DT E 11 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.46e+00 bond pdb=" C3' DT D 147 " pdb=" C2' DT D 147 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.50e+00 ... (remaining 29036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 39168 3.12 - 6.25: 191 6.25 - 9.37: 30 9.37 - 12.49: 11 12.49 - 15.62: 3 Bond angle restraints: 39403 Sorted by residual: angle pdb=" CA MET K 103 " pdb=" CB MET K 103 " pdb=" CG MET K 103 " ideal model delta sigma weight residual 114.10 123.28 -9.18 2.00e+00 2.50e-01 2.11e+01 angle pdb=" CA LEU I 259 " pdb=" CB LEU I 259 " pdb=" CG LEU I 259 " ideal model delta sigma weight residual 116.30 131.92 -15.62 3.50e+00 8.16e-02 1.99e+01 angle pdb=" N3 DT E 6 " pdb=" C4 DT E 6 " pdb=" O4 DT E 6 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT D 147 " pdb=" C4 DT D 147 " pdb=" O4 DT D 147 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" CA LEU Z 57 " pdb=" CB LEU Z 57 " pdb=" CG LEU Z 57 " ideal model delta sigma weight residual 116.30 131.35 -15.05 3.50e+00 8.16e-02 1.85e+01 ... (remaining 39398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 15211 17.90 - 35.79: 1863 35.79 - 53.69: 512 53.69 - 71.59: 122 71.59 - 89.48: 42 Dihedral angle restraints: 17750 sinusoidal: 7743 harmonic: 10007 Sorted by residual: dihedral pdb=" CA ASP Y 187 " pdb=" C ASP Y 187 " pdb=" N ASP Y 188 " pdb=" CA ASP Y 188 " ideal model delta harmonic sigma weight residual 180.00 -147.15 -32.85 0 5.00e+00 4.00e-02 4.32e+01 dihedral pdb=" CA SER I 201 " pdb=" C SER I 201 " pdb=" N SER I 202 " pdb=" CA SER I 202 " ideal model delta harmonic sigma weight residual -180.00 -151.44 -28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA SER I 202 " pdb=" C SER I 202 " pdb=" N GLN I 203 " pdb=" CA GLN I 203 " ideal model delta harmonic sigma weight residual -180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 17747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4305 0.086 - 0.172: 221 0.172 - 0.258: 2 0.258 - 0.344: 1 0.344 - 0.430: 1 Chirality restraints: 4530 Sorted by residual: chirality pdb=" CG LEU Z 57 " pdb=" CB LEU Z 57 " pdb=" CD1 LEU Z 57 " pdb=" CD2 LEU Z 57 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CG LEU K 90 " pdb=" CB LEU K 90 " pdb=" CD1 LEU K 90 " pdb=" CD2 LEU K 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CB ILE N 92 " pdb=" CA ILE N 92 " pdb=" CG1 ILE N 92 " pdb=" CG2 ILE N 92 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.38e-01 ... (remaining 4527 not shown) Planarity restraints: 4802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR W 74 " 0.027 2.00e-02 2.50e+03 2.38e-02 1.14e+01 pdb=" CG TYR W 74 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR W 74 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR W 74 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR W 74 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR W 74 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR W 74 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR W 74 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE U 178 " -0.016 2.00e-02 2.50e+03 1.76e-02 5.44e+00 pdb=" CG PHE U 178 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE U 178 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE U 178 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE U 178 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE U 178 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE U 178 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG I 215 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C ARG I 215 " 0.031 2.00e-02 2.50e+03 pdb=" O ARG I 215 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS I 216 " -0.010 2.00e-02 2.50e+03 ... (remaining 4799 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1324 2.73 - 3.27: 30290 3.27 - 3.81: 49969 3.81 - 4.36: 56678 4.36 - 4.90: 94904 Nonbonded interactions: 233165 Sorted by model distance: nonbonded pdb=" O LEU H 53 " pdb=" ND1 HIS H 57 " model vdw 2.181 3.120 nonbonded pdb=" OD2 ASP N 93 " pdb=" OH TYR N 201 " model vdw 2.208 3.040 nonbonded pdb=" O LEU I 10 " pdb=" OG1 THR I 13 " model vdw 2.220 3.040 nonbonded pdb=" OE1 GLN H 107 " pdb=" NE2 GLN I 467 " model vdw 2.220 3.120 nonbonded pdb=" OH TYR U 302 " pdb=" OE2 GLU Y 183 " model vdw 2.224 3.040 ... (remaining 233160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 221 through 321) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 29.470 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29041 Z= 0.188 Angle : 0.675 15.617 39403 Z= 0.388 Chirality : 0.041 0.430 4530 Planarity : 0.003 0.040 4802 Dihedral : 17.480 89.484 11202 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.01 % Allowed : 14.77 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.15), residues: 3318 helix: 2.20 (0.11), residues: 2135 sheet: -0.18 (0.35), residues: 245 loop : -1.00 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 197 TYR 0.056 0.001 TYR W 74 PHE 0.041 0.001 PHE U 178 TRP 0.017 0.001 TRP L 102 HIS 0.004 0.001 HIS N 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.19 (29041) covalent geometry : angle 0.67480 / 0.39 (39403) hydrogen bonds : bond 0.10103 / 7.25 ( 1898) hydrogen bonds : angle 5.07297 / 4.22 ( 5699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 464 TYR cc_start: 0.8774 (m-80) cc_final: 0.8496 (m-80) REVERT: K 110 ILE cc_start: 0.8420 (tt) cc_final: 0.8011 (mm) REVERT: K 182 MET cc_start: 0.6154 (mmm) cc_final: 0.5448 (tmm) REVERT: L 184 TYR cc_start: 0.8939 (m-80) cc_final: 0.8437 (m-80) REVERT: N 425 ASP cc_start: 0.7904 (m-30) cc_final: 0.7458 (p0) REVERT: P 369 ARG cc_start: 0.5834 (mtt90) cc_final: 0.4471 (mmm160) REVERT: Q 188 MET cc_start: 0.5541 (tmm) cc_final: 0.4805 (tpp) REVERT: T 343 LEU cc_start: 0.5801 (tt) cc_final: 0.5363 (mp) REVERT: W 1 MET cc_start: 0.2624 (mtm) cc_final: 0.1767 (mmt) REVERT: W 62 ARG cc_start: 0.2853 (OUTLIER) cc_final: 0.2381 (tpt170) REVERT: Y 10 ASN cc_start: 0.8571 (m-40) cc_final: 0.8082 (p0) outliers start: 31 outliers final: 25 residues processed: 214 average time/residue: 0.1889 time to fit residues: 66.3273 Evaluate side-chains 206 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 253 ASN Chi-restraints excluded: chain I residue 389 ASP Chi-restraints excluded: chain I residue 518 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 142 CYS Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain P residue 209 ASP Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain Q residue 268 LEU Chi-restraints excluded: chain U residue 167 ARG Chi-restraints excluded: chain U residue 299 MET Chi-restraints excluded: chain W residue 62 ARG Chi-restraints excluded: chain Z residue 25 PHE Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 264 GLN ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 GLN ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 169 ASN Q 253 GLN Q 254 ASN ** Q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 330 HIS Z 9 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.089974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.069800 restraints weight = 173078.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.070225 restraints weight = 103773.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.070564 restraints weight = 70244.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.070635 restraints weight = 63831.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.070753 restraints weight = 54456.886| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29041 Z= 0.171 Angle : 0.605 12.196 39403 Z= 0.316 Chirality : 0.040 0.329 4530 Planarity : 0.004 0.042 4802 Dihedral : 13.172 71.437 4302 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.05 % Allowed : 13.63 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.15), residues: 3318 helix: 2.19 (0.11), residues: 2134 sheet: -0.37 (0.33), residues: 253 loop : -0.98 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 252 TYR 0.017 0.001 TYR Q 306 PHE 0.029 0.002 PHE U 178 TRP 0.011 0.001 TRP N 430 HIS 0.004 0.001 HIS I 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (29041) covalent geometry : angle 0.60532 / 0.32 (39403) hydrogen bonds : bond 0.04330 / 3.20 ( 1898) hydrogen bonds : angle 4.33640 / 3.67 ( 5699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 193 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 302 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8885 (tp) REVERT: I 496 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6547 (t70) REVERT: I 510 MET cc_start: 0.8339 (mmm) cc_final: 0.8120 (mmm) REVERT: I 691 ASN cc_start: 0.8073 (m-40) cc_final: 0.7647 (p0) REVERT: K 93 MET cc_start: 0.6146 (tmm) cc_final: 0.5928 (tmm) REVERT: L 85 MET cc_start: 0.8779 (tpp) cc_final: 0.8563 (tpp) REVERT: L 184 TYR cc_start: 0.8898 (m-80) cc_final: 0.8271 (m-80) REVERT: O 355 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8760 (tt) REVERT: P 369 ARG cc_start: 0.5960 (mtt90) cc_final: 0.4373 (mmm160) REVERT: Q 188 MET cc_start: 0.5866 (tmm) cc_final: 0.5163 (tpp) REVERT: T 343 LEU cc_start: 0.5903 (tt) cc_final: 0.5455 (mp) REVERT: W 1 MET cc_start: 0.2113 (mtm) cc_final: 0.1224 (mmt) REVERT: W 46 LEU cc_start: 0.5725 (tp) cc_final: 0.5470 (mt) REVERT: Y 54 MET cc_start: 0.7861 (tpp) cc_final: 0.7605 (tpp) outliers start: 63 outliers final: 34 residues processed: 244 average time/residue: 0.1698 time to fit residues: 69.2743 Evaluate side-chains 218 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain I residue 496 ASP Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 169 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 240 CYS Chi-restraints excluded: chain P residue 271 CYS Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 298 ILE Chi-restraints excluded: chain Q residue 243 PHE Chi-restraints excluded: chain Q residue 268 LEU Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Z residue 25 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 258 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 333 optimal weight: 0.9980 chunk 257 optimal weight: 0.0870 chunk 306 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 296 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 455 ASN ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 521 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 212 ASN O 215 GLN ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 14 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.090646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.070470 restraints weight = 173704.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.070548 restraints weight = 115329.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.070993 restraints weight = 74692.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.071219 restraints weight = 63070.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.071298 restraints weight = 55948.140| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29041 Z= 0.116 Angle : 0.556 11.001 39403 Z= 0.290 Chirality : 0.039 0.316 4530 Planarity : 0.003 0.039 4802 Dihedral : 12.989 72.926 4269 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.48 % Allowed : 14.15 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.15), residues: 3318 helix: 2.26 (0.11), residues: 2132 sheet: -0.37 (0.32), residues: 254 loop : -0.95 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG W 62 TYR 0.025 0.001 TYR W 74 PHE 0.030 0.001 PHE U 178 TRP 0.008 0.001 TRP B 219 HIS 0.004 0.001 HIS N 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (29041) covalent geometry : angle 0.55601 / 0.29 (39403) hydrogen bonds : bond 0.04017 / 2.98 ( 1898) hydrogen bonds : angle 4.13874 / 3.50 ( 5699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 187 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 316 MET cc_start: 0.8713 (mtt) cc_final: 0.8442 (mtt) REVERT: I 457 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7662 (t) REVERT: I 496 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6011 (t70) REVERT: I 510 MET cc_start: 0.8370 (mmm) cc_final: 0.8071 (mmm) REVERT: I 691 ASN cc_start: 0.8138 (m-40) cc_final: 0.7702 (p0) REVERT: K 234 ASN cc_start: 0.5066 (OUTLIER) cc_final: 0.4436 (p0) REVERT: L 184 TYR cc_start: 0.8932 (m-80) cc_final: 0.8299 (m-80) REVERT: N 21 PHE cc_start: 0.8814 (t80) cc_final: 0.8225 (m-80) REVERT: P 272 TYR cc_start: 0.8151 (p90) cc_final: 0.7827 (p90) REVERT: P 369 ARG cc_start: 0.5891 (mtt90) cc_final: 0.4393 (mmm160) REVERT: T 343 LEU cc_start: 0.5960 (tt) cc_final: 0.5550 (mp) REVERT: W 1 MET cc_start: 0.1753 (mtm) cc_final: 0.1411 (mmt) REVERT: W 46 LEU cc_start: 0.5762 (tp) cc_final: 0.5518 (mt) REVERT: Y 10 ASN cc_start: 0.8652 (m-40) cc_final: 0.8178 (p0) REVERT: Y 54 MET cc_start: 0.7915 (tpp) cc_final: 0.7652 (tpp) outliers start: 76 outliers final: 40 residues processed: 250 average time/residue: 0.1717 time to fit residues: 73.1721 Evaluate side-chains 212 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain I residue 455 ASN Chi-restraints excluded: chain I residue 457 THR Chi-restraints excluded: chain I residue 496 ASP Chi-restraints excluded: chain I residue 518 ILE Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 142 CYS Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 169 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 240 CYS Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain Q residue 268 LEU Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Z residue 25 PHE Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 173 optimal weight: 4.9990 chunk 312 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 212 optimal weight: 0.6980 chunk 323 optimal weight: 3.9990 chunk 309 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 305 optimal weight: 0.0570 chunk 13 optimal weight: 8.9990 chunk 196 optimal weight: 0.6980 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 8 GLN ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 ASN P 275 ASN ** Q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.090106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.069836 restraints weight = 173153.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.070404 restraints weight = 118072.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.070365 restraints weight = 73828.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.070599 restraints weight = 73740.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.070835 restraints weight = 59884.314| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29041 Z= 0.121 Angle : 0.557 11.388 39403 Z= 0.289 Chirality : 0.039 0.282 4530 Planarity : 0.003 0.040 4802 Dihedral : 12.985 75.180 4267 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.38 % Allowed : 15.59 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.15), residues: 3318 helix: 2.29 (0.11), residues: 2138 sheet: -0.37 (0.32), residues: 255 loop : -0.93 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 62 TYR 0.021 0.001 TYR W 74 PHE 0.034 0.001 PHE U 178 TRP 0.007 0.001 TRP N 430 HIS 0.003 0.001 HIS I 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (29041) covalent geometry : angle 0.55692 / 0.29 (39403) hydrogen bonds : bond 0.03908 / 2.90 ( 1898) hydrogen bonds : angle 4.07538 / 3.46 ( 5699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 180 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 316 MET cc_start: 0.8777 (mtt) cc_final: 0.8571 (mtt) REVERT: I 345 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8147 (pp) REVERT: I 460 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: I 496 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6013 (t70) REVERT: I 510 MET cc_start: 0.8333 (mmm) cc_final: 0.7983 (mmm) REVERT: I 691 ASN cc_start: 0.8176 (m-40) cc_final: 0.7753 (p0) REVERT: K 182 MET cc_start: 0.5936 (mmm) cc_final: 0.5376 (tmm) REVERT: L 85 MET cc_start: 0.8810 (tpp) cc_final: 0.8466 (tpp) REVERT: L 184 TYR cc_start: 0.8895 (m-80) cc_final: 0.8234 (m-80) REVERT: N 21 PHE cc_start: 0.8824 (t80) cc_final: 0.8259 (m-80) REVERT: P 369 ARG cc_start: 0.5858 (mtt90) cc_final: 0.4345 (mmm160) REVERT: Q 188 MET cc_start: 0.5560 (tmm) cc_final: 0.5036 (tpp) REVERT: T 276 MET cc_start: 0.6186 (tmm) cc_final: 0.5267 (tpt) REVERT: T 343 LEU cc_start: 0.5964 (tt) cc_final: 0.5544 (mp) REVERT: U 299 MET cc_start: 0.7385 (ptm) cc_final: 0.7118 (ppp) REVERT: W 1 MET cc_start: 0.1277 (mtm) cc_final: 0.0502 (mmt) REVERT: W 46 LEU cc_start: 0.5766 (tp) cc_final: 0.5535 (mt) REVERT: Y 6 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7129 (m110) REVERT: Y 10 ASN cc_start: 0.8620 (m-40) cc_final: 0.8178 (p0) REVERT: Y 54 MET cc_start: 0.7823 (tpp) cc_final: 0.7601 (tpp) outliers start: 73 outliers final: 45 residues processed: 239 average time/residue: 0.1668 time to fit residues: 68.4325 Evaluate side-chains 221 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 460 GLU Chi-restraints excluded: chain I residue 496 ASP Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 142 CYS Chi-restraints excluded: chain N residue 215 VAL Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 325 VAL Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 169 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 240 CYS Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 298 ILE Chi-restraints excluded: chain Q residue 268 LEU Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain T residue 358 SER Chi-restraints excluded: chain Y residue 6 ASN Chi-restraints excluded: chain Z residue 25 PHE Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 244 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 326 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 322 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 GLN ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 ASN Q 250 GLN ** Q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 289 ASN W 41 ASN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** 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 = 0.4056 r_free = 0.4056 target = 0.087935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.068026 restraints weight = 174554.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.067980 restraints weight = 121057.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.068162 restraints weight = 81989.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.068265 restraints weight = 75661.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.068602 restraints weight = 61740.266| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29041 Z= 0.181 Angle : 0.604 9.879 39403 Z= 0.312 Chirality : 0.040 0.255 4530 Planarity : 0.003 0.040 4802 Dihedral : 13.096 76.971 4267 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 3.29 % Allowed : 15.26 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.15), residues: 3318 helix: 2.17 (0.11), residues: 2142 sheet: -0.44 (0.32), residues: 261 loop : -0.93 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 648 TYR 0.025 0.002 TYR P 272 PHE 0.036 0.002 PHE U 178 TRP 0.009 0.001 TRP N 430 HIS 0.005 0.001 HIS I 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (29041) covalent geometry : angle 0.60390 / 0.31 (39403) hydrogen bonds : bond 0.04129 / 3.03 ( 1898) hydrogen bonds : angle 4.14692 / 3.53 ( 5699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 182 time to evaluate : 1.151 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: H 92 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8345 (tp30) REVERT: I 316 MET cc_start: 0.8796 (mtt) cc_final: 0.8588 (mtt) REVERT: I 510 MET cc_start: 0.8475 (mmm) cc_final: 0.8073 (mmm) REVERT: I 691 ASN cc_start: 0.8127 (m-40) cc_final: 0.7668 (p0) REVERT: K 234 ASN cc_start: 0.5059 (OUTLIER) cc_final: 0.4560 (p0) REVERT: L 85 MET cc_start: 0.8839 (tpp) cc_final: 0.8412 (tpp) REVERT: N 21 PHE cc_start: 0.8876 (t80) cc_final: 0.8412 (m-80) REVERT: P 369 ARG cc_start: 0.5958 (mtt90) cc_final: 0.4294 (mmm160) REVERT: Q 335 MET cc_start: 0.8674 (mtm) cc_final: 0.8420 (mtt) REVERT: T 343 LEU cc_start: 0.5918 (tt) cc_final: 0.5478 (mp) REVERT: W 1 MET cc_start: 0.1733 (mtm) cc_final: 0.1049 (mmt) REVERT: W 46 LEU cc_start: 0.5803 (tp) cc_final: 0.5569 (mt) REVERT: Y 6 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7282 (m-40) REVERT: Y 14 ASN cc_start: 0.8774 (p0) cc_final: 0.8418 (p0) REVERT: Y 54 MET cc_start: 0.7773 (tpp) cc_final: 0.7552 (tpp) outliers start: 101 outliers final: 60 residues processed: 268 average time/residue: 0.1713 time to fit residues: 77.5220 Evaluate side-chains 227 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 165 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 455 ASN Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 518 ILE Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain I residue 724 SER Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 142 CYS Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain O residue 172 MET Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 169 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 323 ILE Chi-restraints excluded: chain Q residue 268 LEU Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain T residue 358 SER Chi-restraints excluded: chain U residue 263 LEU Chi-restraints excluded: chain Y residue 6 ASN Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Z residue 6 LEU Chi-restraints excluded: chain Z residue 8 HIS Chi-restraints excluded: chain Z residue 25 PHE Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 40 optimal weight: 6.9990 chunk 262 optimal weight: 0.9980 chunk 94 optimal weight: 30.0000 chunk 325 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 287 optimal weight: 7.9990 chunk 110 optimal weight: 0.0000 chunk 166 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 204 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 GLN ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 521 GLN ** I 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.088508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.068522 restraints weight = 173153.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.068490 restraints weight = 106224.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.068759 restraints weight = 73795.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.068781 restraints weight = 73306.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.068923 restraints weight = 60838.554| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29041 Z= 0.123 Angle : 0.577 13.633 39403 Z= 0.296 Chirality : 0.039 0.246 4530 Planarity : 0.003 0.037 4802 Dihedral : 13.059 77.099 4267 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.74 % Allowed : 16.20 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.15), residues: 3318 helix: 2.23 (0.11), residues: 2142 sheet: -0.32 (0.33), residues: 249 loop : -0.89 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 55 TYR 0.032 0.001 TYR I 464 PHE 0.034 0.001 PHE U 178 TRP 0.020 0.001 TRP I 148 HIS 0.004 0.001 HIS I 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (29041) covalent geometry : angle 0.57725 / 0.30 (39403) hydrogen bonds : bond 0.03878 / 2.88 ( 1898) hydrogen bonds : angle 4.04692 / 3.45 ( 5699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 171 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8853 (mt0) REVERT: I 316 MET cc_start: 0.8792 (mtt) cc_final: 0.8529 (mtt) REVERT: I 496 ASP cc_start: 0.6263 (OUTLIER) cc_final: 0.4696 (m-30) REVERT: I 510 MET cc_start: 0.8488 (mmm) cc_final: 0.8060 (mmm) REVERT: I 691 ASN cc_start: 0.8214 (m-40) cc_final: 0.7756 (p0) REVERT: K 234 ASN cc_start: 0.5038 (OUTLIER) cc_final: 0.4579 (p0) REVERT: L 85 MET cc_start: 0.8821 (tpp) cc_final: 0.8444 (tpp) REVERT: N 21 PHE cc_start: 0.8859 (t80) cc_final: 0.8290 (m-80) REVERT: O 266 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9238 (mm) REVERT: P 272 TYR cc_start: 0.8069 (p90) cc_final: 0.7657 (p90) REVERT: P 369 ARG cc_start: 0.5877 (mtt90) cc_final: 0.4331 (mmm160) REVERT: Q 188 MET cc_start: 0.5446 (tmm) cc_final: 0.4953 (tpp) REVERT: T 343 LEU cc_start: 0.5951 (tt) cc_final: 0.5518 (mp) REVERT: W 1 MET cc_start: 0.1283 (mtm) cc_final: 0.0954 (mmt) REVERT: Y 6 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7427 (m-40) REVERT: Y 14 ASN cc_start: 0.8754 (p0) cc_final: 0.8359 (p0) REVERT: Y 54 MET cc_start: 0.7727 (tpp) cc_final: 0.7484 (tpp) outliers start: 84 outliers final: 55 residues processed: 242 average time/residue: 0.1691 time to fit residues: 69.9752 Evaluate side-chains 219 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 160 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 496 ASP Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 205 TYR Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 142 CYS Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain O residue 172 MET Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain P residue 169 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 318 MET Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain Q residue 268 LEU Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain T residue 358 SER Chi-restraints excluded: chain U residue 263 LEU Chi-restraints excluded: chain Y residue 6 ASN Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Z residue 6 LEU Chi-restraints excluded: chain Z residue 8 HIS Chi-restraints excluded: chain Z residue 25 PHE Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 147 optimal weight: 0.5980 chunk 196 optimal weight: 0.4980 chunk 194 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 312 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 GLN ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 10 ASN ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.088818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.068947 restraints weight = 174946.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.069111 restraints weight = 107069.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.069180 restraints weight = 74279.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.069451 restraints weight = 68781.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.069542 restraints weight = 59524.616| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29041 Z= 0.115 Angle : 0.584 14.813 39403 Z= 0.295 Chirality : 0.039 0.338 4530 Planarity : 0.003 0.041 4802 Dihedral : 13.008 78.603 4267 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.51 % Allowed : 16.63 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.15), residues: 3318 helix: 2.23 (0.11), residues: 2146 sheet: -0.22 (0.33), residues: 255 loop : -0.90 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 55 TYR 0.027 0.001 TYR L 191 PHE 0.036 0.001 PHE U 178 TRP 0.010 0.001 TRP I 148 HIS 0.003 0.001 HIS N 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (29041) covalent geometry : angle 0.58375 / 0.30 (39403) hydrogen bonds : bond 0.03818 / 2.83 ( 1898) hydrogen bonds : angle 3.99494 / 3.42 ( 5699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 168 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8829 (mt0) REVERT: H 125 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7628 (mpp) REVERT: I 496 ASP cc_start: 0.6287 (OUTLIER) cc_final: 0.4784 (m-30) REVERT: I 510 MET cc_start: 0.8518 (mmm) cc_final: 0.8079 (mmm) REVERT: I 691 ASN cc_start: 0.8160 (m-40) cc_final: 0.7735 (p0) REVERT: K 234 ASN cc_start: 0.5018 (OUTLIER) cc_final: 0.4379 (p0) REVERT: L 85 MET cc_start: 0.8815 (tpp) cc_final: 0.8433 (tpp) REVERT: N 21 PHE cc_start: 0.8864 (t80) cc_final: 0.8283 (m-80) REVERT: O 218 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9035 (ptmt) REVERT: O 266 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9226 (mm) REVERT: P 205 TYR cc_start: 0.7882 (m-80) cc_final: 0.7089 (t80) REVERT: P 272 TYR cc_start: 0.8039 (p90) cc_final: 0.7674 (p90) REVERT: P 316 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8744 (mt) REVERT: P 369 ARG cc_start: 0.5769 (mtt90) cc_final: 0.4247 (mmm160) REVERT: Q 188 MET cc_start: 0.5570 (tmm) cc_final: 0.5177 (tpp) REVERT: T 343 LEU cc_start: 0.5947 (tt) cc_final: 0.5486 (mp) REVERT: W 1 MET cc_start: 0.1124 (mtm) cc_final: 0.0872 (mmt) REVERT: Y 6 ASN cc_start: 0.7713 (OUTLIER) cc_final: 0.7358 (m-40) REVERT: Y 13 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: Y 14 ASN cc_start: 0.8710 (p0) cc_final: 0.8473 (p0) REVERT: Y 54 MET cc_start: 0.7655 (tpp) cc_final: 0.7419 (tpp) outliers start: 77 outliers final: 55 residues processed: 231 average time/residue: 0.1658 time to fit residues: 64.7673 Evaluate side-chains 222 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 159 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 496 ASP Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 518 ILE Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 205 TYR Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 142 CYS Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain O residue 172 MET Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 218 LYS Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain P residue 169 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 316 LEU Chi-restraints excluded: chain P residue 318 MET Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain Q residue 268 LEU Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain U residue 263 LEU Chi-restraints excluded: chain Y residue 6 ASN Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Z residue 6 LEU Chi-restraints excluded: chain Z residue 25 PHE Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 172 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 297 optimal weight: 7.9990 chunk 227 optimal weight: 0.6980 chunk 189 optimal weight: 0.6980 chunk 243 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 335 optimal weight: 40.0000 chunk 334 optimal weight: 30.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 GLN ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.088478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.068707 restraints weight = 175663.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.068840 restraints weight = 107699.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.068998 restraints weight = 73363.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.069291 restraints weight = 63494.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.069387 restraints weight = 56561.969| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29041 Z= 0.120 Angle : 0.584 14.331 39403 Z= 0.296 Chirality : 0.039 0.310 4530 Planarity : 0.003 0.041 4802 Dihedral : 12.998 79.778 4267 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.61 % Allowed : 16.66 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.15), residues: 3318 helix: 2.25 (0.11), residues: 2152 sheet: -0.14 (0.33), residues: 251 loop : -0.87 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 55 TYR 0.026 0.001 TYR L 191 PHE 0.038 0.001 PHE U 178 TRP 0.009 0.001 TRP B 219 HIS 0.003 0.001 HIS I 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (29041) covalent geometry : angle 0.58392 / 0.30 (39403) hydrogen bonds : bond 0.03785 / 2.81 ( 1898) hydrogen bonds : angle 3.96686 / 3.39 ( 5699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 163 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8829 (mt0) REVERT: I 355 SER cc_start: 0.9315 (OUTLIER) cc_final: 0.9042 (p) REVERT: I 496 ASP cc_start: 0.6404 (OUTLIER) cc_final: 0.4960 (m-30) REVERT: I 510 MET cc_start: 0.8495 (mmm) cc_final: 0.8046 (mmm) REVERT: I 677 HIS cc_start: 0.5980 (m90) cc_final: 0.5762 (m90) REVERT: I 691 ASN cc_start: 0.8145 (m-40) cc_final: 0.7723 (p0) REVERT: K 182 MET cc_start: 0.5820 (mmm) cc_final: 0.5239 (tmm) REVERT: K 234 ASN cc_start: 0.5010 (OUTLIER) cc_final: 0.4511 (p0) REVERT: L 85 MET cc_start: 0.8771 (tpp) cc_final: 0.8398 (tpp) REVERT: N 21 PHE cc_start: 0.8858 (t80) cc_final: 0.8407 (m-80) REVERT: O 218 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.9035 (ptmt) REVERT: O 266 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9232 (mm) REVERT: P 205 TYR cc_start: 0.7884 (m-80) cc_final: 0.7076 (t80) REVERT: P 272 TYR cc_start: 0.8037 (p90) cc_final: 0.7683 (p90) REVERT: P 369 ARG cc_start: 0.5747 (mtt90) cc_final: 0.4182 (mmm160) REVERT: Q 188 MET cc_start: 0.5659 (tmm) cc_final: 0.5207 (tpp) REVERT: T 343 LEU cc_start: 0.6006 (tt) cc_final: 0.5549 (mp) REVERT: W 1 MET cc_start: 0.1347 (mtm) cc_final: 0.0867 (mmt) REVERT: Y 6 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7321 (m-40) REVERT: Y 13 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: Y 14 ASN cc_start: 0.8738 (p0) cc_final: 0.8509 (p0) REVERT: Y 54 MET cc_start: 0.7561 (tpp) cc_final: 0.7319 (tpp) outliers start: 80 outliers final: 55 residues processed: 229 average time/residue: 0.1692 time to fit residues: 65.4865 Evaluate side-chains 223 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 161 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 313 ASP Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain I residue 496 ASP Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 518 ILE Chi-restraints excluded: chain I residue 553 LEU Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 205 TYR Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 142 CYS Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain O residue 172 MET Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 218 LYS Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 128 ILE Chi-restraints excluded: chain P residue 169 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 318 MET Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain Q residue 268 LEU Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain Y residue 6 ASN Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Z residue 6 LEU Chi-restraints excluded: chain Z residue 25 PHE Chi-restraints excluded: chain Z residue 57 LEU Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 214 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 127 optimal weight: 0.2980 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 318 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 GLN I 203 GLN ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 188 HIS ** N 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.087177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.067086 restraints weight = 175010.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.067031 restraints weight = 126024.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.067199 restraints weight = 85104.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.067412 restraints weight = 74649.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.067505 restraints weight = 64298.237| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29041 Z= 0.165 Angle : 0.616 14.793 39403 Z= 0.313 Chirality : 0.040 0.317 4530 Planarity : 0.003 0.040 4802 Dihedral : 13.082 80.114 4267 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.28 % Allowed : 16.79 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.15), residues: 3318 helix: 2.19 (0.11), residues: 2148 sheet: -0.26 (0.33), residues: 251 loop : -0.89 (0.21), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 39 TYR 0.023 0.001 TYR L 191 PHE 0.037 0.002 PHE U 178 TRP 0.008 0.001 TRP B 219 HIS 0.005 0.001 HIS I 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (29041) covalent geometry : angle 0.61634 / 0.31 (39403) hydrogen bonds : bond 0.03979 / 2.93 ( 1898) hydrogen bonds : angle 4.06692 / 3.47 ( 5699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 164 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 284 GLN cc_start: 0.9519 (OUTLIER) cc_final: 0.8800 (tm-30) REVERT: H 125 MET cc_start: 0.8071 (mtt) cc_final: 0.7622 (mpp) REVERT: I 171 ILE cc_start: 0.4888 (tp) cc_final: 0.4672 (tp) REVERT: I 355 SER cc_start: 0.9394 (OUTLIER) cc_final: 0.9125 (p) REVERT: I 496 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.5117 (m-30) REVERT: I 510 MET cc_start: 0.8568 (mmm) cc_final: 0.8045 (mmm) REVERT: I 691 ASN cc_start: 0.8134 (m-40) cc_final: 0.7715 (p0) REVERT: K 93 MET cc_start: 0.6805 (tmm) cc_final: 0.6565 (tmm) REVERT: K 234 ASN cc_start: 0.5022 (OUTLIER) cc_final: 0.4509 (p0) REVERT: L 85 MET cc_start: 0.8817 (tpp) cc_final: 0.8458 (tpp) REVERT: N 21 PHE cc_start: 0.8825 (t80) cc_final: 0.8356 (m-80) REVERT: O 266 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9269 (mm) REVERT: P 205 TYR cc_start: 0.8037 (m-80) cc_final: 0.7302 (t80) REVERT: P 272 TYR cc_start: 0.8148 (p90) cc_final: 0.7803 (p90) REVERT: P 369 ARG cc_start: 0.5846 (mtt90) cc_final: 0.4228 (mmm160) REVERT: Q 158 MET cc_start: 0.6932 (ptp) cc_final: 0.6436 (pmm) REVERT: T 343 LEU cc_start: 0.5958 (tt) cc_final: 0.5486 (mp) REVERT: W 1 MET cc_start: 0.1687 (mtm) cc_final: 0.1126 (mmt) REVERT: Y 6 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7545 (m-40) REVERT: Y 14 ASN cc_start: 0.8771 (p0) cc_final: 0.8467 (p0) REVERT: Y 54 MET cc_start: 0.7590 (tpp) cc_final: 0.7375 (tpp) outliers start: 70 outliers final: 53 residues processed: 221 average time/residue: 0.1638 time to fit residues: 61.6041 Evaluate side-chains 218 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 159 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain I residue 496 ASP Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 518 ILE Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 109 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 142 CYS Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain O residue 172 MET Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 169 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 318 MET Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain Q residue 268 LEU Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain T residue 358 SER Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain Y residue 6 ASN Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Z residue 6 LEU Chi-restraints excluded: chain Z residue 8 HIS Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 140 optimal weight: 0.0570 chunk 205 optimal weight: 0.9990 chunk 251 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 266 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 190 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN Q 169 ASN ** Q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 172 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.087963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.068003 restraints weight = 174442.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.068218 restraints weight = 108869.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.068478 restraints weight = 72655.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.068674 restraints weight = 64445.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.068713 restraints weight = 56865.860| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29041 Z= 0.116 Angle : 0.601 13.891 39403 Z= 0.302 Chirality : 0.040 0.472 4530 Planarity : 0.003 0.037 4802 Dihedral : 13.000 80.325 4265 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.05 % Allowed : 16.99 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.15), residues: 3318 helix: 2.23 (0.11), residues: 2146 sheet: -0.18 (0.33), residues: 242 loop : -0.84 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 579 TYR 0.034 0.001 TYR L 191 PHE 0.040 0.001 PHE U 178 TRP 0.008 0.001 TRP B 219 HIS 0.003 0.001 HIS I 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (29041) covalent geometry : angle 0.60107 / 0.30 (39403) hydrogen bonds : bond 0.03804 / 2.84 ( 1898) hydrogen bonds : angle 3.98935 / 3.40 ( 5699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 162 time to evaluate : 1.069 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: B 222 GLN cc_start: 0.9150 (mm-40) cc_final: 0.8800 (mt0) REVERT: B 284 GLN cc_start: 0.9521 (OUTLIER) cc_final: 0.8795 (tm-30) REVERT: H 125 MET cc_start: 0.8233 (mtt) cc_final: 0.7874 (mpp) REVERT: I 355 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.9075 (p) REVERT: I 496 ASP cc_start: 0.6426 (OUTLIER) cc_final: 0.5165 (m-30) REVERT: I 510 MET cc_start: 0.8487 (mmm) cc_final: 0.7981 (mmm) REVERT: I 691 ASN cc_start: 0.8140 (m-40) cc_final: 0.7727 (p0) REVERT: K 234 ASN cc_start: 0.4981 (OUTLIER) cc_final: 0.4496 (p0) REVERT: L 85 MET cc_start: 0.8790 (tpp) cc_final: 0.8424 (tpp) REVERT: L 111 MET cc_start: 0.8505 (mmp) cc_final: 0.8085 (mmp) REVERT: N 21 PHE cc_start: 0.8821 (t80) cc_final: 0.8331 (m-80) REVERT: O 266 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9233 (mm) REVERT: P 205 TYR cc_start: 0.7900 (m-80) cc_final: 0.7228 (t80) REVERT: P 369 ARG cc_start: 0.5801 (mtt90) cc_final: 0.4280 (mmm160) REVERT: Q 158 MET cc_start: 0.6763 (ptp) cc_final: 0.6317 (pmm) REVERT: Q 188 MET cc_start: 0.5446 (tmm) cc_final: 0.4843 (tpp) REVERT: T 343 LEU cc_start: 0.6007 (tt) cc_final: 0.5529 (mp) REVERT: W 1 MET cc_start: 0.1783 (mtm) cc_final: 0.1251 (mmt) REVERT: Y 6 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7586 (m-40) REVERT: Y 13 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: Y 14 ASN cc_start: 0.8864 (p0) cc_final: 0.8638 (p0) REVERT: Y 54 MET cc_start: 0.7471 (tpp) cc_final: 0.7255 (tpp) outliers start: 63 outliers final: 48 residues processed: 214 average time/residue: 0.1584 time to fit residues: 58.0555 Evaluate side-chains 211 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 156 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain I residue 59 ASP Chi-restraints excluded: chain I residue 345 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain I residue 496 ASP Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 518 ILE Chi-restraints excluded: chain I residue 707 THR Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 221 ILE Chi-restraints excluded: chain L residue 222 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 40 PHE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 142 CYS Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain O residue 172 MET Chi-restraints excluded: chain O residue 197 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain O residue 361 HIS Chi-restraints excluded: chain P residue 169 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 282 VAL Chi-restraints excluded: chain P residue 318 MET Chi-restraints excluded: chain P residue 341 CYS Chi-restraints excluded: chain Q residue 268 LEU Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 246 LEU Chi-restraints excluded: chain Y residue 6 ASN Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Z residue 6 LEU Chi-restraints excluded: chain Z residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 232 optimal weight: 6.9990 chunk 162 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 301 optimal weight: 4.9990 chunk 44 optimal weight: 0.0970 chunk 37 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 311 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.086384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.066173 restraints weight = 175357.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.066472 restraints weight = 122542.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.066432 restraints weight = 90261.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.066783 restraints weight = 69115.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.067103 restraints weight = 57039.819| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29041 Z= 0.192 Angle : 0.640 14.298 39403 Z= 0.324 Chirality : 0.041 0.367 4530 Planarity : 0.003 0.034 4802 Dihedral : 13.054 80.268 4263 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.05 % Allowed : 17.05 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.15), residues: 3318 helix: 2.16 (0.11), residues: 2142 sheet: -0.31 (0.33), residues: 244 loop : -0.93 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 199 TYR 0.037 0.002 TYR L 191 PHE 0.039 0.002 PHE U 178 TRP 0.009 0.001 TRP I 155 HIS 0.005 0.001 HIS Z 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (29041) covalent geometry : angle 0.64008 / 0.32 (39403) hydrogen bonds : bond 0.04052 / 3.03 ( 1898) hydrogen bonds : angle 4.11158 / 3.52 ( 5699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4611.31 seconds wall clock time: 81 minutes 9.42 seconds (4869.42 seconds total)