Starting phenix.real_space_refine on Thu Mar 5 19:33:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v8o_21107/03_2026/6v8o_21107.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v8o_21107/03_2026/6v8o_21107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v8o_21107/03_2026/6v8o_21107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v8o_21107/03_2026/6v8o_21107.map" model { file = "/net/cci-nas-00/data/ceres_data/6v8o_21107/03_2026/6v8o_21107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v8o_21107/03_2026/6v8o_21107.cif" } resolution = 3.07 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= -0.000 sd= 0.005 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 Zn 1 6.06 5 S 91 5.16 5 C 15930 2.51 5 N 4277 2.21 5 O 4804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25103 Number of models: 1 Model: "" Number of chains: 23 Chain: "C" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 493 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "D" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 772 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain breaks: 1 Chain: "E" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 536 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 7, 'TRANS': 59} Chain breaks: 1 Chain: "G" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 422 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "H" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1083 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain breaks: 1 Chain: "I" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2416 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "J" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'TRANS': 114} Chain: "K" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 878 Classifications: {'peptide': 109} Link IDs: {'TRANS': 108} Chain breaks: 1 Chain: "L" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2445 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 2 Chain: "M" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2474 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 16, 'TRANS': 293} Chain breaks: 3 Chain: "N" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3275 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 18, 'TRANS': 393} Chain breaks: 1 Chain: "O" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3145 Classifications: {'peptide': 384} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 361} Chain breaks: 3 Chain: "Q" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2137 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 12, 'TRANS': 251} Chain breaks: 2 Chain: "R" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2126 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain breaks: 1 Chain: "S" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 278 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "2" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 Chain: "3" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "4" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "5" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "6" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "7" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 245 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'UNK:plan-1': 49} Unresolved non-hydrogen planarities: 49 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5813 SG CYS I 260 150.361 54.662 77.002 1.00 50.60 S ATOM 5836 SG CYS I 263 153.627 52.802 78.258 1.00 55.54 S ATOM 5999 SG CYS I 283 152.020 55.587 80.436 1.00 54.74 S ATOM 6022 SG CYS I 286 153.971 56.119 76.846 1.00 50.21 S Time building chain proxies: 5.25, per 1000 atoms: 0.21 Number of scatterers: 25103 At special positions: 0 Unit cell: (208.655, 130.949, 198.582, 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) Zn 1 29.99 S 91 16.00 O 4804 8.00 N 4277 7.00 C 15930 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: 2.20 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 601 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 260 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 263 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 286 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 283 " Number of angles added : 6 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6118 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 17 sheets defined 56.4% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'C' and resid 20 through 40 Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 54 through 75 Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 72 through 79 Processing helix chain 'D' and resid 93 through 99 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.601A pdb=" N PHE D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 125 Processing helix chain 'E' and resid 318 through 343 Processing helix chain 'E' and resid 400 through 404 removed outlier: 4.236A pdb=" N SER E 403 " --> pdb=" O THR E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 411 removed outlier: 4.272A pdb=" N TYR E 410 " --> pdb=" O PRO E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 433 Processing helix chain 'F' and resid 862 through 867 Processing helix chain 'F' and resid 871 through 881 removed outlier: 3.765A pdb=" N MET F 881 " --> pdb=" O HIS F 877 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 196 removed outlier: 3.906A pdb=" N ILE G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 468 Processing helix chain 'I' and resid 58 through 72 Processing helix chain 'I' and resid 95 through 102 Processing helix chain 'I' and resid 103 through 106 Processing helix chain 'I' and resid 114 through 132 removed outlier: 3.756A pdb=" N SER I 132 " --> pdb=" O THR I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 146 removed outlier: 3.845A pdb=" N VAL I 142 " --> pdb=" O THR I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 163 removed outlier: 3.512A pdb=" N TRP I 163 " --> pdb=" O PHE I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 175 removed outlier: 4.099A pdb=" N LYS I 175 " --> pdb=" O PRO I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 244 Processing helix chain 'I' and resid 246 through 251 Processing helix chain 'I' and resid 283 through 289 Processing helix chain 'I' and resid 297 through 299 No H-bonds generated for 'chain 'I' and resid 297 through 299' Processing helix chain 'I' and resid 316 through 330 Processing helix chain 'I' and resid 333 through 342 removed outlier: 3.847A pdb=" N GLY I 342 " --> pdb=" O ALA I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 356 Processing helix chain 'I' and resid 360 through 368 Processing helix chain 'J' and resid 388 through 403 removed outlier: 3.624A pdb=" N CYS J 392 " --> pdb=" O LYS J 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 406 through 490 removed outlier: 3.834A pdb=" N VAL J 410 " --> pdb=" O LYS J 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 402 Processing helix chain 'K' and resid 421 through 489 Processing helix chain 'L' and resid 59 through 76 Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 96 through 102 Processing helix chain 'L' and resid 114 through 131 Processing helix chain 'L' and resid 138 through 145 removed outlier: 4.076A pdb=" N VAL L 142 " --> pdb=" O THR L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 163 Processing helix chain 'L' and resid 171 through 175 removed outlier: 3.541A pdb=" N LYS L 175 " --> pdb=" O PRO L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 292 Processing helix chain 'L' and resid 298 through 304 Processing helix chain 'L' and resid 316 through 330 Processing helix chain 'L' and resid 333 through 342 Processing helix chain 'L' and resid 346 through 356 Processing helix chain 'L' and resid 360 through 377 removed outlier: 3.583A pdb=" N ILE L 364 " --> pdb=" O GLU L 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 51 Processing helix chain 'M' and resid 237 through 242 removed outlier: 3.629A pdb=" N LEU M 241 " --> pdb=" O ASN M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 263 Processing helix chain 'M' and resid 268 through 275 Processing helix chain 'M' and resid 316 through 324 Processing helix chain 'M' and resid 331 through 342 removed outlier: 3.623A pdb=" N VAL M 335 " --> pdb=" O PRO M 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 372 through 377 Processing helix chain 'M' and resid 387 through 425 Processing helix chain 'M' and resid 425 through 445 Processing helix chain 'M' and resid 452 through 457 Processing helix chain 'M' and resid 470 through 472 No H-bonds generated for 'chain 'M' and resid 470 through 472' Processing helix chain 'M' and resid 473 through 480 Processing helix chain 'N' and resid 40 through 46 Processing helix chain 'N' and resid 65 through 70 removed outlier: 3.923A pdb=" N SER N 70 " --> pdb=" O VAL N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 92 removed outlier: 3.995A pdb=" N GLY N 92 " --> pdb=" O ALA N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 111 Processing helix chain 'N' and resid 123 through 140 removed outlier: 3.664A pdb=" N PHE N 127 " --> pdb=" O LEU N 123 " (cutoff:3.500A) Proline residue: N 133 - end of helix Processing helix chain 'N' and resid 148 through 170 Processing helix chain 'N' and resid 171 through 180 removed outlier: 3.691A pdb=" N LYS N 180 " --> pdb=" O GLN N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 201 Processing helix chain 'N' and resid 208 through 210 No H-bonds generated for 'chain 'N' and resid 208 through 210' Processing helix chain 'N' and resid 211 through 231 removed outlier: 3.878A pdb=" N SER N 231 " --> pdb=" O GLU N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 240 through 253 Processing helix chain 'N' and resid 255 through 269 removed outlier: 3.614A pdb=" N VAL N 259 " --> pdb=" O ASP N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 284 removed outlier: 3.521A pdb=" N ASP N 282 " --> pdb=" O SER N 279 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU N 284 " --> pdb=" O ALA N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 285 through 298 removed outlier: 3.565A pdb=" N LEU N 298 " --> pdb=" O SER N 294 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 317 Processing helix chain 'N' and resid 320 through 329 removed outlier: 4.334A pdb=" N SER N 329 " --> pdb=" O GLU N 325 " (cutoff:3.500A) Processing helix chain 'N' and resid 329 through 345 Proline residue: N 341 - end of helix removed outlier: 3.681A pdb=" N SER N 345 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 353 through 359 removed outlier: 3.800A pdb=" N GLN N 357 " --> pdb=" O TYR N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 524 through 539 removed outlier: 3.651A pdb=" N ASN N 539 " --> pdb=" O CYS N 535 " (cutoff:3.500A) Processing helix chain 'N' and resid 546 through 564 removed outlier: 3.749A pdb=" N CYS N 550 " --> pdb=" O GLY N 546 " (cutoff:3.500A) Proline residue: N 555 - end of helix Processing helix chain 'N' and resid 564 through 571 removed outlier: 3.513A pdb=" N THR N 568 " --> pdb=" O ILE N 564 " (cutoff:3.500A) Processing helix chain 'N' and resid 571 through 577 Processing helix chain 'O' and resid 10 through 25 Processing helix chain 'O' and resid 29 through 33 Processing helix chain 'O' and resid 43 through 45 No H-bonds generated for 'chain 'O' and resid 43 through 45' Processing helix chain 'O' and resid 46 through 61 Processing helix chain 'O' and resid 75 through 82 removed outlier: 3.518A pdb=" N ARG O 79 " --> pdb=" O THR O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 110 removed outlier: 3.500A pdb=" N PHE O 92 " --> pdb=" O ILE O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 138 removed outlier: 3.532A pdb=" N GLN O 118 " --> pdb=" O THR O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 179 Processing helix chain 'O' and resid 243 through 248 removed outlier: 4.029A pdb=" N VAL O 247 " --> pdb=" O ARG O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 314 Processing helix chain 'O' and resid 389 through 394 Processing helix chain 'O' and resid 403 through 412 removed outlier: 3.659A pdb=" N ILE O 407 " --> pdb=" O GLY O 403 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 436 removed outlier: 3.656A pdb=" N ASN O 436 " --> pdb=" O GLU O 432 " (cutoff:3.500A) Processing helix chain 'O' and resid 442 through 462 Processing helix chain 'Q' and resid 3 through 7 Processing helix chain 'Q' and resid 15 through 22 Processing helix chain 'Q' and resid 161 through 167 Processing helix chain 'Q' and resid 168 through 177 Processing helix chain 'Q' and resid 231 through 244 Processing helix chain 'Q' and resid 247 through 265 removed outlier: 3.553A pdb=" N LEU Q 265 " --> pdb=" O GLN Q 261 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 270 removed outlier: 3.629A pdb=" N ALA Q 270 " --> pdb=" O GLU Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 319 Processing helix chain 'Q' and resid 323 through 345 removed outlier: 4.018A pdb=" N LEU Q 327 " --> pdb=" O GLU Q 323 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER Q 329 " --> pdb=" O ILE Q 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 66 Processing helix chain 'R' and resid 68 through 73 Processing helix chain 'R' and resid 74 through 102 removed outlier: 3.502A pdb=" N ALA R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 127 Processing helix chain 'R' and resid 132 through 136 removed outlier: 4.081A pdb=" N LEU R 136 " --> pdb=" O ASP R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 172 removed outlier: 3.548A pdb=" N LEU R 172 " --> pdb=" O LYS R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 179 removed outlier: 4.106A pdb=" N PHE R 178 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 208 Processing helix chain 'R' and resid 236 through 250 Processing helix chain 'R' and resid 250 through 267 Processing helix chain 'R' and resid 268 through 273 Processing helix chain 'R' and resid 273 through 278 Processing helix chain 'R' and resid 279 through 290 removed outlier: 3.635A pdb=" N GLN R 290 " --> pdb=" O GLN R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 318 Processing helix chain 'S' and resid 204 through 227 removed outlier: 3.744A pdb=" N GLN S 227 " --> pdb=" O LEU S 223 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 20 Processing helix chain '4' and resid 1 through 18 Processing helix chain '5' and resid 4 through 16 Processing helix chain '6' and resid 421 through 434 Processing sheet with id=AA1, first strand: chain 'E' and resid 349 through 351 removed outlier: 3.734A pdb=" N GLY L 180 " --> pdb=" O ILE E 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 368 through 373 removed outlier: 6.977A pdb=" N VAL E 368 " --> pdb=" O ASP I 192 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP I 192 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY E 370 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL E 385 " --> pdb=" O PHE I 187 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL I 189 " --> pdb=" O VAL E 385 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU E 387 " --> pdb=" O VAL I 189 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU I 191 " --> pdb=" O GLU E 387 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL E 389 " --> pdb=" O LEU I 191 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS I 231 " --> pdb=" O THR E 388 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE E 390 " --> pdb=" O THR I 229 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR I 229 " --> pdb=" O ILE E 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 157 through 160 removed outlier: 3.503A pdb=" N SER S 201 " --> pdb=" O ASN G 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 589 through 594 removed outlier: 4.072A pdb=" N HIS H 514 " --> pdb=" O GLN H 453 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLN H 453 " --> pdb=" O HIS H 514 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER H 458 " --> pdb=" O VAL H 482 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL H 482 " --> pdb=" O SER H 458 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP H 481 " --> pdb=" O ILE L 259 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N HIS L 261 " --> pdb=" O TRP H 481 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU H 483 " --> pdb=" O HIS L 261 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR L 262 " --> pdb=" O ASN L 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 522 through 526 removed outlier: 6.052A pdb=" N PHE H 498 " --> pdb=" O TRP H 620 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ASN H 622 " --> pdb=" O PHE H 498 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE H 500 " --> pdb=" O ASN H 622 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA H 497 " --> pdb=" O ILE O 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 80 through 83 Processing sheet with id=AA7, first strand: chain 'I' and resid 256 through 257 removed outlier: 3.664A pdb=" N VAL N 47 " --> pdb=" O VAL I 257 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 281 through 282 Processing sheet with id=AA9, first strand: chain 'K' and resid 493 through 497 Processing sheet with id=AB1, first strand: chain 'M' and resid 368 through 369 removed outlier: 3.543A pdb=" N LEU M 368 " --> pdb=" O ILE M 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG M 75 " --> pdb=" O UNK 7 24 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR M 77 " --> pdb=" O UNK 7 26 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR M 79 " --> pdb=" O UNK 7 28 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 349 through 352 removed outlier: 6.582A pdb=" N SER M 219 " --> pdb=" O UNK 7 62 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N UNK 7 64 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR M 221 " --> pdb=" O UNK 7 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 246 through 247 Processing sheet with id=AB4, first strand: chain 'M' and resid 313 through 314 removed outlier: 3.531A pdb=" N LEU M 330 " --> pdb=" O VAL M 313 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 476 through 477 Processing sheet with id=AB6, first strand: chain 'Q' and resid 13 through 14 removed outlier: 3.566A pdb=" N LYS Q 179 " --> pdb=" O SER Q 14 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 203 through 212 Processing sheet with id=AB8, first strand: chain 'Q' and resid 278 through 286 1297 hydrogen bonds defined for protein. 3765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8274 1.34 - 1.46: 4234 1.46 - 1.57: 12890 1.57 - 1.69: 0 1.69 - 1.81: 145 Bond restraints: 25543 Sorted by residual: bond pdb=" CB TRP I 163 " pdb=" CG TRP I 163 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.30e+00 bond pdb=" CA LEU N 132 " pdb=" C LEU N 132 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.26e-02 6.30e+03 1.20e+00 bond pdb=" C TYR O 85 " pdb=" N GLU O 86 " ideal model delta sigma weight residual 1.329 1.297 0.031 3.03e-02 1.09e+03 1.08e+00 bond pdb=" C LEU N 132 " pdb=" O LEU N 132 " ideal model delta sigma weight residual 1.238 1.251 -0.013 1.28e-02 6.10e+03 1.07e+00 bond pdb=" C PHE R 135 " pdb=" N LEU R 136 " ideal model delta sigma weight residual 1.332 1.318 0.014 1.40e-02 5.10e+03 9.94e-01 ... (remaining 25538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 34433 2.96 - 5.92: 112 5.92 - 8.87: 8 8.87 - 11.83: 1 11.83 - 14.79: 1 Bond angle restraints: 34555 Sorted by residual: angle pdb=" N SER Q 374 " pdb=" CA SER Q 374 " pdb=" C SER Q 374 " ideal model delta sigma weight residual 110.80 120.59 -9.79 2.13e+00 2.20e-01 2.11e+01 angle pdb=" C ILE H 528 " pdb=" N ASN H 529 " pdb=" CA ASN H 529 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C GLY Q 373 " pdb=" N SER Q 374 " pdb=" CA SER Q 374 " ideal model delta sigma weight residual 121.54 129.11 -7.57 1.91e+00 2.74e-01 1.57e+01 angle pdb=" N PRO O 415 " pdb=" CA PRO O 415 " pdb=" C PRO O 415 " ideal model delta sigma weight residual 114.18 110.44 3.74 1.39e+00 5.18e-01 7.23e+00 angle pdb=" C SER Q 374 " pdb=" CA SER Q 374 " pdb=" CB SER Q 374 " ideal model delta sigma weight residual 110.42 105.22 5.20 1.99e+00 2.53e-01 6.84e+00 ... (remaining 34550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 14796 17.77 - 35.54: 707 35.54 - 53.31: 140 53.31 - 71.09: 34 71.09 - 88.86: 6 Dihedral angle restraints: 15683 sinusoidal: 6343 harmonic: 9340 Sorted by residual: dihedral pdb=" CA GLU Q 371 " pdb=" C GLU Q 371 " pdb=" N LEU Q 372 " pdb=" CA LEU Q 372 " ideal model delta harmonic sigma weight residual -180.00 -153.93 -26.07 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ASN H 529 " pdb=" C ASN H 529 " pdb=" N LYS H 530 " pdb=" CA LYS H 530 " ideal model delta harmonic sigma weight residual 180.00 155.34 24.66 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLY Q 373 " pdb=" C GLY Q 373 " pdb=" N SER Q 374 " pdb=" CA SER Q 374 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 15680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2642 0.033 - 0.066: 973 0.066 - 0.099: 233 0.099 - 0.133: 118 0.133 - 0.166: 5 Chirality restraints: 3971 Sorted by residual: chirality pdb=" CA ILE E 359 " pdb=" N ILE E 359 " pdb=" C ILE E 359 " pdb=" CB ILE E 359 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ILE N 514 " pdb=" N ILE N 514 " pdb=" C ILE N 514 " pdb=" CB ILE N 514 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA SER Q 374 " pdb=" N SER Q 374 " pdb=" C SER Q 374 " pdb=" CB SER Q 374 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 3968 not shown) Planarity restraints: 4440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE N 564 " -0.048 5.00e-02 4.00e+02 7.37e-02 8.70e+00 pdb=" N PRO N 565 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO N 565 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO N 565 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN M 6 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO M 7 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO M 7 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO M 7 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU N 124 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO N 125 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO N 125 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO N 125 " -0.025 5.00e-02 4.00e+02 ... (remaining 4437 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 668 2.70 - 3.25: 25129 3.25 - 3.80: 37366 3.80 - 4.35: 48918 4.35 - 4.90: 82429 Nonbonded interactions: 194510 Sorted by model distance: nonbonded pdb=" O GLU N 227 " pdb=" OG SER N 230 " model vdw 2.149 3.040 nonbonded pdb=" OH TYR Q 184 " pdb=" OD1 ASP Q 242 " model vdw 2.150 3.040 nonbonded pdb=" OE2 GLU O 41 " pdb=" OG SER O 50 " model vdw 2.163 3.040 nonbonded pdb=" O LYS H 449 " pdb=" OG1 THR H 516 " model vdw 2.164 3.040 nonbonded pdb=" OD1 ASN Q 282 " pdb=" ND2 ASN Q 295 " model vdw 2.201 3.120 ... (remaining 194505 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 '3' selection = chain '4' } ncs_group { reference = chain '5' selection = (chain '6' and resid 421 through 434) } ncs_group { reference = (chain 'I' and (resid 58 through 304 or resid 312 through 368)) selection = (chain 'L' and (resid 58 through 202 or resid 222 through 368)) } ncs_group { reference = (chain 'J' and (resid 387 through 402 or resid 420 through 501)) selection = (chain 'K' and resid 387 through 501) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.650 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 : 0.004 0.068 25547 Z= 0.189 Angle : 0.554 14.790 34561 Z= 0.299 Chirality : 0.039 0.166 3971 Planarity : 0.003 0.074 4440 Dihedral : 11.206 88.857 9565 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.89 % Favored : 93.01 % Rotamer: Outliers : 2.31 % Allowed : 5.62 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.57 (0.14), residues: 2946 helix: 0.34 (0.13), residues: 1511 sheet: -0.89 (0.36), residues: 187 loop : -2.91 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 19 TYR 0.015 0.001 TYR I 272 PHE 0.012 0.001 PHE I 85 TRP 0.020 0.001 TRP O 273 HIS 0.004 0.001 HIS N 220 Details of bonding type rmsd covalent geometry : bond 0.00417 (25543) covalent geometry : angle 0.54855 (34555) hydrogen bonds : bond 0.13786 ( 1297) hydrogen bonds : angle 5.58856 ( 3765) metal coordination : bond 0.06372 ( 4) metal coordination : angle 6.00010 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 682 time to evaluate : 0.965 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: C 48 ARG cc_start: 0.7326 (ttt90) cc_final: 0.7065 (tmt170) REVERT: D 94 ARG cc_start: 0.6705 (ttt180) cc_final: 0.6442 (ttt-90) REVERT: D 107 HIS cc_start: 0.7234 (t70) cc_final: 0.6968 (t-90) REVERT: E 329 ARG cc_start: 0.7079 (mtm110) cc_final: 0.6538 (mmt180) REVERT: E 353 TYR cc_start: 0.8604 (m-80) cc_final: 0.8031 (m-80) REVERT: E 407 LYS cc_start: 0.7526 (mttt) cc_final: 0.7170 (ptmm) REVERT: E 430 LYS cc_start: 0.8227 (mttt) cc_final: 0.8021 (mtmt) REVERT: F 817 ARG cc_start: 0.6858 (mtp180) cc_final: 0.6477 (mtp85) REVERT: G 167 MET cc_start: 0.8383 (ttm) cc_final: 0.7455 (mtp) REVERT: G 189 LEU cc_start: 0.7023 (mt) cc_final: 0.6773 (mt) REVERT: I 191 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7780 (pp) REVERT: I 255 HIS cc_start: 0.6476 (p-80) cc_final: 0.6195 (m170) REVERT: I 281 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8571 (m-40) REVERT: J 388 LYS cc_start: 0.7808 (mttt) cc_final: 0.7329 (mppt) REVERT: J 390 MET cc_start: 0.7978 (mmm) cc_final: 0.7726 (mmm) REVERT: J 394 ASN cc_start: 0.8741 (m-40) cc_final: 0.8443 (m110) REVERT: J 437 MET cc_start: 0.7769 (mmm) cc_final: 0.7246 (mmt) REVERT: K 475 LEU cc_start: 0.7844 (tp) cc_final: 0.7631 (mm) REVERT: K 485 SER cc_start: 0.7064 (t) cc_final: 0.6521 (p) REVERT: K 503 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6530 (p0) REVERT: L 317 ASP cc_start: 0.7461 (m-30) cc_final: 0.7225 (m-30) REVERT: M 40 ASP cc_start: 0.8293 (t70) cc_final: 0.8087 (t70) REVERT: M 391 THR cc_start: 0.6244 (m) cc_final: 0.5833 (p) REVERT: N 85 MET cc_start: 0.8801 (mtm) cc_final: 0.8128 (mtm) REVERT: N 102 LYS cc_start: 0.8000 (mttt) cc_final: 0.7671 (mtpp) REVERT: N 104 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.6829 (m-10) REVERT: N 170 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8455 (mp10) REVERT: N 293 VAL cc_start: 0.8319 (t) cc_final: 0.8015 (t) REVERT: N 329 SER cc_start: 0.8300 (t) cc_final: 0.7857 (m) REVERT: N 551 GLN cc_start: 0.8485 (mt0) cc_final: 0.8267 (mt0) REVERT: N 553 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8390 (tp) REVERT: O 122 LYS cc_start: 0.6901 (tttt) cc_final: 0.6296 (tmtt) REVERT: Q 173 ASP cc_start: 0.6972 (m-30) cc_final: 0.6600 (t0) REVERT: Q 203 MET cc_start: 0.8732 (mmt) cc_final: 0.8357 (mmt) REVERT: Q 266 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7333 (pt0) REVERT: Q 294 ASP cc_start: 0.7805 (t0) cc_final: 0.7350 (t0) REVERT: Q 303 LYS cc_start: 0.8529 (mttt) cc_final: 0.8305 (mmtt) REVERT: R 193 ILE cc_start: 0.8099 (mt) cc_final: 0.7824 (pt) REVERT: R 306 GLU cc_start: 0.6363 (mt-10) cc_final: 0.6038 (pt0) REVERT: S 218 ASN cc_start: 0.6751 (m-40) cc_final: 0.6270 (t0) outliers start: 64 outliers final: 16 residues processed: 729 average time/residue: 0.1786 time to fit residues: 199.4690 Evaluate side-chains 406 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 384 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 281 ASN Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain K residue 503 ASP Chi-restraints excluded: chain M residue 316 ASP Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 170 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain Q residue 342 ASP Chi-restraints excluded: chain Q residue 345 ASP Chi-restraints excluded: chain Q residue 368 ASP Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 262 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 HIS D 64 HIS D 108 HIS D 122 HIS E 331 ASN E 425 GLN E 432 ASN F 816 ASN F 855 ASN H 452 GLN ** H 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 494 ASN H 506 GLN H 514 HIS H 529 ASN H 601 HIS I 167 ASN I 314 ASN J 430 GLN L 145 ASN L 318 GLN M 340 ASN M 378 GLN M 380 GLN N 43 GLN N 69 GLN N 286 HIS N 512 ASN N 559 HIS O 18 GLN O 22 ASN O 97 HIS O 193 GLN O 482 ASN O 484 ASN Q 5 ASN ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 158 GLN Q 164 ASN Q 220 GLN Q 261 GLN Q 352 HIS R 116 ASN R 123 GLN R 204 ASN R 270 HIS R 290 GLN S 227 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.161346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117293 restraints weight = 36509.333| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.53 r_work: 0.3247 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25547 Z= 0.136 Angle : 0.571 14.662 34561 Z= 0.291 Chirality : 0.040 0.246 3971 Planarity : 0.004 0.073 4440 Dihedral : 5.318 59.533 3399 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.60 % Favored : 94.33 % Rotamer: Outliers : 2.59 % Allowed : 10.99 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.10 (0.15), residues: 2946 helix: 1.62 (0.13), residues: 1529 sheet: -0.53 (0.35), residues: 196 loop : -2.32 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 249 TYR 0.021 0.001 TYR O 178 PHE 0.032 0.001 PHE R 83 TRP 0.014 0.001 TRP O 273 HIS 0.009 0.001 HIS N 220 Details of bonding type rmsd covalent geometry : bond 0.00290 (25543) covalent geometry : angle 0.56896 (34555) hydrogen bonds : bond 0.05273 ( 1297) hydrogen bonds : angle 4.14882 ( 3765) metal coordination : bond 0.00624 ( 4) metal coordination : angle 3.56674 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 418 time to evaluate : 0.999 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: C 48 ARG cc_start: 0.7414 (ttt90) cc_final: 0.7105 (tmt170) REVERT: D 94 ARG cc_start: 0.7201 (ttt180) cc_final: 0.6685 (ttt-90) REVERT: D 107 HIS cc_start: 0.7522 (t70) cc_final: 0.7185 (t-90) REVERT: E 329 ARG cc_start: 0.7671 (mtm110) cc_final: 0.6479 (mmt180) REVERT: E 407 LYS cc_start: 0.7623 (mttt) cc_final: 0.7117 (ptmm) REVERT: E 408 GLU cc_start: 0.8692 (mp0) cc_final: 0.8472 (mp0) REVERT: F 817 ARG cc_start: 0.7068 (mtp180) cc_final: 0.6223 (mtp85) REVERT: G 167 MET cc_start: 0.8289 (ttm) cc_final: 0.7494 (mtp) REVERT: H 446 LYS cc_start: 0.8036 (ttmm) cc_final: 0.7817 (ttmm) REVERT: H 453 GLN cc_start: 0.7387 (mt0) cc_final: 0.7108 (pt0) REVERT: H 613 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6752 (mt-10) REVERT: I 239 GLN cc_start: 0.8385 (mp10) cc_final: 0.8035 (mp10) REVERT: I 312 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7511 (tptt) REVERT: I 317 ASP cc_start: 0.8161 (m-30) cc_final: 0.7849 (m-30) REVERT: J 388 LYS cc_start: 0.7903 (mttt) cc_final: 0.7518 (mppt) REVERT: J 395 ASP cc_start: 0.8682 (m-30) cc_final: 0.8409 (m-30) REVERT: J 437 MET cc_start: 0.8565 (mmm) cc_final: 0.7962 (mmt) REVERT: J 463 LYS cc_start: 0.8106 (mmmt) cc_final: 0.7624 (mmmt) REVERT: K 464 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7244 (tt0) REVERT: K 471 ASP cc_start: 0.6802 (m-30) cc_final: 0.6575 (m-30) REVERT: K 499 SER cc_start: 0.7773 (m) cc_final: 0.6988 (p) REVERT: L 149 ASP cc_start: 0.7820 (p0) cc_final: 0.7457 (p0) REVERT: L 239 GLN cc_start: 0.8776 (mt0) cc_final: 0.8565 (mt0) REVERT: L 312 LYS cc_start: 0.7246 (mttt) cc_final: 0.6418 (tptt) REVERT: L 317 ASP cc_start: 0.8566 (m-30) cc_final: 0.8172 (m-30) REVERT: N 69 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7969 (mm110) REVERT: N 102 LYS cc_start: 0.8847 (mttt) cc_final: 0.8501 (mtpp) REVERT: N 104 TYR cc_start: 0.9287 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: N 170 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8655 (mp10) REVERT: N 293 VAL cc_start: 0.8319 (t) cc_final: 0.8068 (t) REVERT: N 517 VAL cc_start: 0.7890 (t) cc_final: 0.7666 (m) REVERT: N 521 GLN cc_start: 0.8074 (pm20) cc_final: 0.7818 (mp10) REVERT: N 522 GLU cc_start: 0.8455 (pt0) cc_final: 0.8241 (pm20) REVERT: N 553 ILE cc_start: 0.8529 (tt) cc_final: 0.8308 (tp) REVERT: O 122 LYS cc_start: 0.6987 (tttt) cc_final: 0.6151 (tmtt) REVERT: O 137 ARG cc_start: 0.6898 (ttm-80) cc_final: 0.6609 (ttt180) REVERT: O 196 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8257 (tt0) REVERT: O 215 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6858 (t0) REVERT: O 265 MET cc_start: 0.8460 (mtt) cc_final: 0.7808 (mtt) REVERT: O 405 ASP cc_start: 0.8088 (p0) cc_final: 0.7168 (p0) REVERT: Q 167 ARG cc_start: 0.8998 (mtp180) cc_final: 0.8728 (mtp180) REVERT: Q 173 ASP cc_start: 0.7741 (m-30) cc_final: 0.7223 (t0) REVERT: Q 266 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7517 (pt0) REVERT: Q 303 LYS cc_start: 0.8610 (mttt) cc_final: 0.8240 (mmtt) REVERT: Q 343 TRP cc_start: 0.7901 (t60) cc_final: 0.7642 (t60) REVERT: R 134 TYR cc_start: 0.6795 (p90) cc_final: 0.6488 (p90) REVERT: R 221 CYS cc_start: 0.8835 (m) cc_final: 0.8430 (p) REVERT: R 234 MET cc_start: 0.8930 (mmm) cc_final: 0.7556 (mmm) REVERT: R 306 GLU cc_start: 0.6263 (mt-10) cc_final: 0.5847 (pt0) REVERT: S 218 ASN cc_start: 0.6651 (m-40) cc_final: 0.6212 (t0) outliers start: 72 outliers final: 41 residues processed: 467 average time/residue: 0.1652 time to fit residues: 120.6592 Evaluate side-chains 392 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 347 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 237 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 244 MET Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 170 GLN Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 321 GLN Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain O residue 215 ASP Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 264 MET Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain Q residue 268 ILE Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain S residue 213 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 209 optimal weight: 5.9990 chunk 287 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 294 optimal weight: 6.9990 chunk 300 optimal weight: 20.0000 chunk 235 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 289 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 23 GLN D 122 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 HIS ** H 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 506 GLN H 514 HIS I 60 GLN I 253 GLN J 394 ASN M 4 GLN M 270 GLN M 378 GLN M 380 GLN N 551 GLN O 97 HIS O 225 ASN O 234 GLN ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 297 GLN R 123 GLN S 227 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.155182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111988 restraints weight = 36458.356| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.42 r_work: 0.3152 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25547 Z= 0.205 Angle : 0.621 14.037 34561 Z= 0.316 Chirality : 0.043 0.198 3971 Planarity : 0.004 0.075 4440 Dihedral : 5.175 58.554 3377 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.87 % Favored : 94.06 % Rotamer: Outliers : 2.92 % Allowed : 11.89 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.22 (0.15), residues: 2946 helix: 1.84 (0.13), residues: 1524 sheet: -0.12 (0.36), residues: 190 loop : -2.13 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 379 TYR 0.020 0.002 TYR M 17 PHE 0.025 0.002 PHE R 83 TRP 0.018 0.002 TRP O 273 HIS 0.008 0.001 HIS N 220 Details of bonding type rmsd covalent geometry : bond 0.00483 (25543) covalent geometry : angle 0.61756 (34555) hydrogen bonds : bond 0.05937 ( 1297) hydrogen bonds : angle 4.19247 ( 3765) metal coordination : bond 0.01067 ( 4) metal coordination : angle 4.83924 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 384 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 GLU cc_start: 0.8510 (tp30) cc_final: 0.8285 (tp30) REVERT: C 48 ARG cc_start: 0.7559 (ttt90) cc_final: 0.7049 (tmt170) REVERT: C 64 GLU cc_start: 0.7698 (tp30) cc_final: 0.7307 (mp0) REVERT: D 94 ARG cc_start: 0.7401 (ttt180) cc_final: 0.7040 (ttt-90) REVERT: D 107 HIS cc_start: 0.7743 (t70) cc_final: 0.7436 (t-90) REVERT: E 329 ARG cc_start: 0.7595 (mtm110) cc_final: 0.6290 (mmt180) REVERT: E 420 ARG cc_start: 0.7725 (mtp180) cc_final: 0.7290 (ttp80) REVERT: F 817 ARG cc_start: 0.7055 (mtp180) cc_final: 0.6483 (mtp85) REVERT: H 613 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7324 (mt-10) REVERT: I 63 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8112 (mm-40) REVERT: I 192 ASP cc_start: 0.8076 (t0) cc_final: 0.7873 (t0) REVERT: I 317 ASP cc_start: 0.8433 (m-30) cc_final: 0.8213 (m-30) REVERT: I 346 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7246 (mtp85) REVERT: I 360 GLU cc_start: 0.8730 (tt0) cc_final: 0.8525 (tt0) REVERT: J 388 LYS cc_start: 0.8067 (mttt) cc_final: 0.7580 (mppt) REVERT: J 395 ASP cc_start: 0.8741 (m-30) cc_final: 0.8411 (m-30) REVERT: J 437 MET cc_start: 0.8752 (mmm) cc_final: 0.8073 (mmt) REVERT: K 464 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7347 (tt0) REVERT: K 468 MET cc_start: 0.7192 (tmm) cc_final: 0.6788 (tmm) REVERT: K 499 SER cc_start: 0.7681 (m) cc_final: 0.6900 (p) REVERT: L 66 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6837 (mt-10) REVERT: L 149 ASP cc_start: 0.7844 (p0) cc_final: 0.7148 (p0) REVERT: L 239 GLN cc_start: 0.8767 (mt0) cc_final: 0.8494 (mt0) REVERT: M 445 GLN cc_start: 0.8397 (pt0) cc_final: 0.7768 (pp30) REVERT: N 28 MET cc_start: 0.4872 (tmm) cc_final: 0.4467 (tmm) REVERT: N 102 LYS cc_start: 0.8907 (mttt) cc_final: 0.8587 (mtpp) REVERT: N 170 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8489 (mp10) REVERT: N 522 GLU cc_start: 0.8488 (pt0) cc_final: 0.8068 (tt0) REVERT: N 553 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8442 (tp) REVERT: O 80 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.7023 (t80) REVERT: O 122 LYS cc_start: 0.7038 (tttt) cc_final: 0.6208 (tmtt) REVERT: O 129 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7283 (pt0) REVERT: O 240 GLU cc_start: 0.7697 (tp30) cc_final: 0.7248 (pm20) REVERT: Q 303 LYS cc_start: 0.8746 (mttt) cc_final: 0.8262 (mmtt) REVERT: Q 341 LYS cc_start: 0.7807 (tttp) cc_final: 0.7458 (tptt) REVERT: R 50 ARG cc_start: 0.7542 (ttt90) cc_final: 0.6936 (mtp-110) REVERT: R 101 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7475 (mtt90) REVERT: R 108 PHE cc_start: 0.6361 (t80) cc_final: 0.5948 (t80) REVERT: R 134 TYR cc_start: 0.6867 (p90) cc_final: 0.6443 (p90) REVERT: R 234 MET cc_start: 0.8976 (mmm) cc_final: 0.7547 (mmm) REVERT: R 306 GLU cc_start: 0.6147 (mt-10) cc_final: 0.5745 (pt0) REVERT: S 218 ASN cc_start: 0.6609 (m-40) cc_final: 0.6130 (t0) outliers start: 81 outliers final: 55 residues processed: 439 average time/residue: 0.1773 time to fit residues: 119.0458 Evaluate side-chains 392 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 334 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain F residue 798 ILE Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 530 LYS Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 237 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 504 SER Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 170 GLN Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 348 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 279 THR Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 268 ILE Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain S residue 198 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 12 optimal weight: 4.9990 chunk 238 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 305 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 242 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 23 GLN D 122 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 GLN H 493 GLN H 496 ASN H 506 GLN H 514 HIS J 394 ASN K 430 GLN ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN O 97 HIS O 196 GLN ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN S 227 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.155573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111777 restraints weight = 36344.307| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.52 r_work: 0.3165 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25547 Z= 0.161 Angle : 0.556 14.560 34561 Z= 0.285 Chirality : 0.041 0.219 3971 Planarity : 0.004 0.078 4440 Dihedral : 5.003 58.030 3375 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 2.88 % Allowed : 12.97 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.52 (0.16), residues: 2946 helix: 2.08 (0.13), residues: 1535 sheet: 0.02 (0.36), residues: 192 loop : -2.01 (0.16), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 379 TYR 0.015 0.002 TYR H 455 PHE 0.020 0.001 PHE R 83 TRP 0.019 0.001 TRP O 273 HIS 0.007 0.001 HIS N 220 Details of bonding type rmsd covalent geometry : bond 0.00375 (25543) covalent geometry : angle 0.55421 (34555) hydrogen bonds : bond 0.05345 ( 1297) hydrogen bonds : angle 4.00059 ( 3765) metal coordination : bond 0.00910 ( 4) metal coordination : angle 3.75900 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 370 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 GLU cc_start: 0.8488 (tp30) cc_final: 0.8218 (tp30) REVERT: C 48 ARG cc_start: 0.7507 (ttt90) cc_final: 0.7017 (tmt170) REVERT: C 64 GLU cc_start: 0.7792 (tp30) cc_final: 0.7324 (mp0) REVERT: D 94 ARG cc_start: 0.7561 (ttt180) cc_final: 0.7171 (ttt-90) REVERT: D 107 HIS cc_start: 0.7786 (t70) cc_final: 0.7482 (t-90) REVERT: E 329 ARG cc_start: 0.7534 (mtm110) cc_final: 0.6163 (mmt180) REVERT: E 353 TYR cc_start: 0.9215 (m-80) cc_final: 0.9004 (m-80) REVERT: E 407 LYS cc_start: 0.7420 (pttp) cc_final: 0.7151 (ptmm) REVERT: E 420 ARG cc_start: 0.7766 (mtp180) cc_final: 0.7352 (ttp80) REVERT: F 817 ARG cc_start: 0.7042 (mtp180) cc_final: 0.6042 (mtp85) REVERT: G 176 GLU cc_start: 0.3494 (OUTLIER) cc_final: 0.2567 (tt0) REVERT: H 534 LYS cc_start: 0.7115 (ptpp) cc_final: 0.6847 (ptpp) REVERT: H 613 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7224 (mt-10) REVERT: I 192 ASP cc_start: 0.8101 (t0) cc_final: 0.7876 (t0) REVERT: I 255 HIS cc_start: 0.7222 (p90) cc_final: 0.7018 (m170) REVERT: I 257 VAL cc_start: 0.8950 (t) cc_final: 0.8711 (p) REVERT: I 269 ASN cc_start: 0.8626 (m-40) cc_final: 0.8391 (t0) REVERT: I 312 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7402 (pttt) REVERT: I 317 ASP cc_start: 0.8461 (m-30) cc_final: 0.8201 (m-30) REVERT: I 346 ARG cc_start: 0.7495 (mtp85) cc_final: 0.7231 (mtp85) REVERT: J 388 LYS cc_start: 0.8065 (mttt) cc_final: 0.7565 (mppt) REVERT: J 395 ASP cc_start: 0.8592 (m-30) cc_final: 0.8253 (m-30) REVERT: J 437 MET cc_start: 0.8717 (mmm) cc_final: 0.8030 (mmt) REVERT: K 430 GLN cc_start: 0.7954 (mt0) cc_final: 0.7720 (tp40) REVERT: K 464 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7247 (tt0) REVERT: K 499 SER cc_start: 0.7730 (m) cc_final: 0.6967 (p) REVERT: K 501 GLN cc_start: 0.6923 (mt0) cc_final: 0.6717 (mt0) REVERT: L 66 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6802 (mt-10) REVERT: L 149 ASP cc_start: 0.7710 (p0) cc_final: 0.7020 (p0) REVERT: M 445 GLN cc_start: 0.8319 (pt0) cc_final: 0.7814 (pp30) REVERT: M 468 ARG cc_start: 0.7417 (mmm-85) cc_final: 0.6389 (mpt180) REVERT: N 102 LYS cc_start: 0.8869 (mttt) cc_final: 0.8543 (tttm) REVERT: N 104 TYR cc_start: 0.9440 (OUTLIER) cc_final: 0.8072 (m-80) REVERT: N 321 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: N 331 GLU cc_start: 0.8411 (pm20) cc_final: 0.8158 (pm20) REVERT: N 522 GLU cc_start: 0.8370 (pt0) cc_final: 0.7969 (tt0) REVERT: N 553 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8115 (tp) REVERT: O 48 TYR cc_start: 0.6430 (t80) cc_final: 0.5853 (t80) REVERT: O 80 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7182 (t80) REVERT: O 122 LYS cc_start: 0.7000 (tttt) cc_final: 0.6155 (tmtt) REVERT: O 129 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7274 (pt0) REVERT: O 202 MET cc_start: 0.6794 (pmm) cc_final: 0.6535 (pmm) REVERT: O 215 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6977 (t0) REVERT: O 220 GLU cc_start: 0.6799 (tp30) cc_final: 0.6319 (tm-30) REVERT: O 240 GLU cc_start: 0.7689 (tp30) cc_final: 0.7113 (pm20) REVERT: O 421 ASP cc_start: 0.7874 (t0) cc_final: 0.7600 (t0) REVERT: Q 268 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7965 (mm) REVERT: Q 302 ASP cc_start: 0.8476 (t0) cc_final: 0.8085 (t0) REVERT: Q 303 LYS cc_start: 0.8821 (mttt) cc_final: 0.8191 (mmtt) REVERT: Q 341 LYS cc_start: 0.7902 (tttp) cc_final: 0.7673 (tptt) REVERT: R 50 ARG cc_start: 0.7631 (ttt90) cc_final: 0.7000 (mtp-110) REVERT: R 101 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7346 (mtt90) REVERT: R 229 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7830 (t0) REVERT: R 259 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8411 (pt0) REVERT: R 306 GLU cc_start: 0.6351 (mt-10) cc_final: 0.5931 (pt0) REVERT: S 218 ASN cc_start: 0.6694 (m-40) cc_final: 0.6262 (t0) outliers start: 80 outliers final: 54 residues processed: 421 average time/residue: 0.1708 time to fit residues: 111.9900 Evaluate side-chains 406 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 342 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain F residue 798 ILE Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 530 LYS Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 237 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 230 ILE Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 321 GLN Chi-restraints excluded: chain N residue 348 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 188 THR Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain O residue 215 ASP Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 279 THR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 268 ILE Chi-restraints excluded: chain Q residue 344 VAL Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 252 THR Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain S residue 198 LEU Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 300 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 210 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 23 GLN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 855 ASN H 506 GLN I 95 HIS J 394 ASN L 242 ASN ** N 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS O 196 GLN ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 297 GLN ** R 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.153053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.109876 restraints weight = 36213.614| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.42 r_work: 0.3124 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 25547 Z= 0.213 Angle : 0.620 15.324 34561 Z= 0.316 Chirality : 0.043 0.200 3971 Planarity : 0.004 0.081 4440 Dihedral : 4.987 54.709 3370 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 3.64 % Allowed : 13.26 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.53 (0.16), residues: 2946 helix: 2.08 (0.13), residues: 1526 sheet: 0.01 (0.36), residues: 192 loop : -1.98 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 379 TYR 0.020 0.002 TYR M 17 PHE 0.021 0.002 PHE I 85 TRP 0.022 0.002 TRP O 273 HIS 0.007 0.001 HIS N 220 Details of bonding type rmsd covalent geometry : bond 0.00512 (25543) covalent geometry : angle 0.61774 (34555) hydrogen bonds : bond 0.05952 ( 1297) hydrogen bonds : angle 4.14521 ( 3765) metal coordination : bond 0.01261 ( 4) metal coordination : angle 4.21098 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 349 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 38 GLU cc_start: 0.8543 (tp30) cc_final: 0.8210 (tp30) REVERT: C 48 ARG cc_start: 0.7554 (ttt90) cc_final: 0.7070 (tmt170) REVERT: C 63 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7566 (mm-30) REVERT: C 64 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: D 94 ARG cc_start: 0.7486 (ttt180) cc_final: 0.7059 (ttt-90) REVERT: D 107 HIS cc_start: 0.7884 (t70) cc_final: 0.7602 (t-90) REVERT: E 407 LYS cc_start: 0.7485 (pttp) cc_final: 0.7180 (ptmm) REVERT: F 817 ARG cc_start: 0.7064 (mtp180) cc_final: 0.6021 (mtp85) REVERT: G 176 GLU cc_start: 0.3643 (OUTLIER) cc_final: 0.2665 (tt0) REVERT: H 613 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7249 (mt-10) REVERT: I 63 GLN cc_start: 0.8360 (mm-40) cc_final: 0.7579 (tm-30) REVERT: I 183 PHE cc_start: 0.7675 (t80) cc_final: 0.6692 (p90) REVERT: I 191 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8777 (pp) REVERT: I 346 ARG cc_start: 0.7531 (mtp85) cc_final: 0.7291 (mtp85) REVERT: J 388 LYS cc_start: 0.8068 (mttt) cc_final: 0.7540 (mppt) REVERT: J 395 ASP cc_start: 0.8624 (m-30) cc_final: 0.8252 (m-30) REVERT: J 437 MET cc_start: 0.8796 (mmm) cc_final: 0.8083 (mmt) REVERT: K 464 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7279 (tt0) REVERT: K 499 SER cc_start: 0.7680 (m) cc_final: 0.6843 (p) REVERT: L 66 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6645 (mt-10) REVERT: L 149 ASP cc_start: 0.7990 (p0) cc_final: 0.7093 (p0) REVERT: M 343 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8286 (t) REVERT: M 445 GLN cc_start: 0.8465 (pt0) cc_final: 0.7948 (pp30) REVERT: N 28 MET cc_start: 0.5167 (tmm) cc_final: 0.4156 (tmm) REVERT: N 84 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8719 (ttm-80) REVERT: N 102 LYS cc_start: 0.8925 (mttt) cc_final: 0.8633 (tttm) REVERT: N 331 GLU cc_start: 0.8471 (pm20) cc_final: 0.8175 (pm20) REVERT: N 553 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8444 (tp) REVERT: O 48 TYR cc_start: 0.6415 (t80) cc_final: 0.5807 (t80) REVERT: O 80 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.6995 (t80) REVERT: O 122 LYS cc_start: 0.6620 (tttt) cc_final: 0.5862 (tmtt) REVERT: O 129 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7350 (pt0) REVERT: O 240 GLU cc_start: 0.7713 (tp30) cc_final: 0.7192 (pm20) REVERT: O 421 ASP cc_start: 0.8060 (t0) cc_final: 0.7738 (t0) REVERT: Q 265 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8165 (mt) REVERT: Q 268 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8155 (mm) REVERT: Q 334 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8155 (mt-10) REVERT: R 50 ARG cc_start: 0.7789 (ttt90) cc_final: 0.7177 (mtp85) REVERT: R 77 LYS cc_start: 0.8517 (tttt) cc_final: 0.8204 (ttpp) REVERT: R 101 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.7605 (mtt90) REVERT: R 229 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8075 (t0) REVERT: R 259 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8490 (pt0) REVERT: R 261 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8855 (tp) REVERT: R 306 GLU cc_start: 0.6178 (mt-10) cc_final: 0.5939 (pt0) REVERT: S 198 LEU cc_start: 0.8880 (tp) cc_final: 0.8500 (tt) REVERT: S 218 ASN cc_start: 0.6853 (m-40) cc_final: 0.6220 (t0) outliers start: 101 outliers final: 67 residues processed: 418 average time/residue: 0.1799 time to fit residues: 115.9963 Evaluate side-chains 407 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 328 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain F residue 798 ILE Chi-restraints excluded: chain F residue 800 ASN Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain F residue 811 LEU Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain J residue 486 LEU Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 504 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 230 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 256 ILE Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain M residue 343 VAL Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 84 ARG Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 348 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 116 ASN Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 188 THR Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 279 THR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 268 ILE Chi-restraints excluded: chain Q residue 344 VAL Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 252 THR Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 287 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 289 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 278 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 855 ASN H 506 GLN H 514 HIS J 394 ASN K 501 GLN ** L 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN O 97 HIS ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 352 HIS R 264 ASN S 227 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.155978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111770 restraints weight = 36191.835| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.44 r_work: 0.3168 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25547 Z= 0.125 Angle : 0.536 16.832 34561 Z= 0.271 Chirality : 0.039 0.181 3971 Planarity : 0.004 0.076 4440 Dihedral : 4.701 52.039 3370 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.87 % Rotamer: Outliers : 2.63 % Allowed : 14.55 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.86 (0.16), residues: 2946 helix: 2.37 (0.13), residues: 1526 sheet: 0.21 (0.37), residues: 192 loop : -1.84 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 379 TYR 0.013 0.001 TYR N 257 PHE 0.020 0.001 PHE R 83 TRP 0.018 0.001 TRP O 273 HIS 0.006 0.001 HIS N 220 Details of bonding type rmsd covalent geometry : bond 0.00277 (25543) covalent geometry : angle 0.53451 (34555) hydrogen bonds : bond 0.04975 ( 1297) hydrogen bonds : angle 3.90106 ( 3765) metal coordination : bond 0.00601 ( 4) metal coordination : angle 3.15967 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 367 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 GLU cc_start: 0.8545 (tp30) cc_final: 0.8182 (tp30) REVERT: C 48 ARG cc_start: 0.7553 (ttt90) cc_final: 0.7088 (tmt170) REVERT: C 63 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7521 (mm-30) REVERT: C 64 GLU cc_start: 0.7721 (tp30) cc_final: 0.7177 (mp0) REVERT: D 94 ARG cc_start: 0.7396 (ttt180) cc_final: 0.7050 (ttt-90) REVERT: D 107 HIS cc_start: 0.7808 (t70) cc_final: 0.7524 (t-90) REVERT: D 124 VAL cc_start: 0.6107 (t) cc_final: 0.5802 (m) REVERT: E 353 TYR cc_start: 0.9179 (m-80) cc_final: 0.8962 (m-80) REVERT: E 407 LYS cc_start: 0.7402 (pttp) cc_final: 0.7157 (ptmm) REVERT: F 817 ARG cc_start: 0.7048 (mtp180) cc_final: 0.5945 (mtp85) REVERT: G 176 GLU cc_start: 0.3392 (OUTLIER) cc_final: 0.2501 (tt0) REVERT: H 531 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7577 (tp30) REVERT: H 613 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7033 (mt-10) REVERT: H 616 PHE cc_start: 0.8636 (m-80) cc_final: 0.8371 (m-10) REVERT: I 63 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7575 (tm-30) REVERT: I 183 PHE cc_start: 0.7639 (t80) cc_final: 0.6654 (p90) REVERT: I 191 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8764 (pp) REVERT: I 255 HIS cc_start: 0.7392 (p90) cc_final: 0.7119 (m170) REVERT: I 283 CYS cc_start: 0.8135 (m) cc_final: 0.7916 (m) REVERT: I 346 ARG cc_start: 0.7444 (mtp85) cc_final: 0.7192 (mtp85) REVERT: J 388 LYS cc_start: 0.7994 (mttt) cc_final: 0.7449 (mppt) REVERT: J 395 ASP cc_start: 0.8603 (m-30) cc_final: 0.8222 (m-30) REVERT: K 464 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7180 (tt0) REVERT: K 499 SER cc_start: 0.7633 (m) cc_final: 0.6829 (p) REVERT: L 66 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6693 (mt-10) REVERT: L 149 ASP cc_start: 0.7800 (p0) cc_final: 0.6932 (p0) REVERT: L 362 ASN cc_start: 0.8774 (m-40) cc_final: 0.8548 (m-40) REVERT: M 244 MET cc_start: 0.9255 (ptt) cc_final: 0.8841 (ptp) REVERT: M 445 GLN cc_start: 0.8326 (pt0) cc_final: 0.7820 (pp30) REVERT: N 28 MET cc_start: 0.5100 (tmm) cc_final: 0.4254 (tmm) REVERT: N 102 LYS cc_start: 0.8872 (mttt) cc_final: 0.8538 (tttm) REVERT: N 553 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8136 (tp) REVERT: O 48 TYR cc_start: 0.6376 (t80) cc_final: 0.5857 (t80) REVERT: O 80 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.7090 (t80) REVERT: O 122 LYS cc_start: 0.6510 (tttt) cc_final: 0.5746 (tmtt) REVERT: O 129 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7234 (pt0) REVERT: O 240 GLU cc_start: 0.7736 (tp30) cc_final: 0.7138 (pm20) REVERT: O 421 ASP cc_start: 0.8019 (t0) cc_final: 0.7814 (t70) REVERT: Q 334 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8127 (mt-10) REVERT: R 50 ARG cc_start: 0.7606 (ttt90) cc_final: 0.7011 (mtp85) REVERT: R 101 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7627 (mtt90) REVERT: R 229 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8027 (t0) REVERT: R 234 MET cc_start: 0.9024 (tpp) cc_final: 0.8822 (tpp) REVERT: R 259 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8356 (pt0) REVERT: R 261 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8789 (tt) REVERT: S 218 ASN cc_start: 0.6758 (m-40) cc_final: 0.6162 (t0) outliers start: 73 outliers final: 52 residues processed: 409 average time/residue: 0.1699 time to fit residues: 108.8938 Evaluate side-chains 408 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 348 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 531 GLU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 402 GLN Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 147 CYS Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 107 ILE Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 344 VAL Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 194 optimal weight: 0.1980 chunk 144 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 284 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS ** E 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 506 GLN J 394 ASN K 402 GLN ** L 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 352 HIS S 227 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.155392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111190 restraints weight = 36409.296| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.42 r_work: 0.3151 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25547 Z= 0.151 Angle : 0.557 15.083 34561 Z= 0.282 Chirality : 0.040 0.196 3971 Planarity : 0.004 0.077 4440 Dihedral : 4.631 50.923 3368 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.97 % Favored : 93.99 % Rotamer: Outliers : 2.77 % Allowed : 14.99 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.90 (0.16), residues: 2946 helix: 2.38 (0.13), residues: 1526 sheet: 0.24 (0.37), residues: 192 loop : -1.80 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 379 TYR 0.014 0.002 TYR Q 225 PHE 0.025 0.001 PHE O 109 TRP 0.018 0.001 TRP O 273 HIS 0.006 0.001 HIS N 220 Details of bonding type rmsd covalent geometry : bond 0.00352 (25543) covalent geometry : angle 0.55507 (34555) hydrogen bonds : bond 0.05185 ( 1297) hydrogen bonds : angle 3.93038 ( 3765) metal coordination : bond 0.00857 ( 4) metal coordination : angle 3.55710 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 351 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 ARG cc_start: 0.7630 (ttt90) cc_final: 0.7179 (tmt170) REVERT: C 63 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7343 (mm-30) REVERT: D 94 ARG cc_start: 0.7449 (ttt180) cc_final: 0.7103 (ttt-90) REVERT: D 107 HIS cc_start: 0.7853 (t70) cc_final: 0.7567 (t-90) REVERT: E 353 TYR cc_start: 0.9192 (m-80) cc_final: 0.8980 (m-80) REVERT: E 407 LYS cc_start: 0.7439 (pttp) cc_final: 0.7202 (ptmm) REVERT: F 817 ARG cc_start: 0.7090 (mtp180) cc_final: 0.5969 (mtp85) REVERT: G 176 GLU cc_start: 0.3502 (OUTLIER) cc_final: 0.2581 (tt0) REVERT: H 531 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: H 613 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7181 (mt-10) REVERT: H 616 PHE cc_start: 0.8649 (m-80) cc_final: 0.8387 (m-10) REVERT: I 63 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7596 (tm-30) REVERT: I 183 PHE cc_start: 0.7613 (t80) cc_final: 0.6657 (p90) REVERT: I 191 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8771 (pp) REVERT: I 346 ARG cc_start: 0.7511 (mtp85) cc_final: 0.7261 (mtp85) REVERT: J 388 LYS cc_start: 0.8024 (mttt) cc_final: 0.7448 (mppt) REVERT: J 437 MET cc_start: 0.8772 (mmm) cc_final: 0.8024 (mmt) REVERT: K 464 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7194 (tt0) REVERT: K 499 SER cc_start: 0.7643 (m) cc_final: 0.6852 (p) REVERT: L 66 GLU cc_start: 0.6426 (mt-10) cc_final: 0.6189 (mt-10) REVERT: L 362 ASN cc_start: 0.8770 (m-40) cc_final: 0.8532 (m-40) REVERT: M 445 GLN cc_start: 0.8439 (pt0) cc_final: 0.7895 (pp30) REVERT: N 28 MET cc_start: 0.4822 (tmm) cc_final: 0.3966 (tmm) REVERT: N 102 LYS cc_start: 0.8862 (mttt) cc_final: 0.8596 (tttm) REVERT: N 310 ASP cc_start: 0.8718 (m-30) cc_final: 0.8407 (m-30) REVERT: N 553 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8197 (tp) REVERT: O 48 TYR cc_start: 0.5880 (t80) cc_final: 0.5357 (t80) REVERT: O 80 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.7088 (t80) REVERT: O 122 LYS cc_start: 0.6532 (tttt) cc_final: 0.5739 (tmtt) REVERT: O 129 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7287 (pt0) REVERT: O 240 GLU cc_start: 0.7825 (tp30) cc_final: 0.7243 (pm20) REVERT: O 421 ASP cc_start: 0.8209 (t0) cc_final: 0.7993 (t70) REVERT: Q 334 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8174 (mt-10) REVERT: Q 338 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7709 (tptt) REVERT: Q 379 ARG cc_start: 0.8343 (ptp90) cc_final: 0.8099 (ptp90) REVERT: R 50 ARG cc_start: 0.7768 (ttt90) cc_final: 0.7247 (mtp85) REVERT: R 101 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7760 (mtt90) REVERT: R 229 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8055 (t0) REVERT: R 259 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8408 (pt0) REVERT: R 261 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8896 (tp) REVERT: S 218 ASN cc_start: 0.6837 (m-40) cc_final: 0.6239 (t0) outliers start: 77 outliers final: 61 residues processed: 399 average time/residue: 0.1659 time to fit residues: 104.1186 Evaluate side-chains 406 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 337 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 798 ILE Chi-restraints excluded: chain F residue 800 ASN Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain F residue 811 LEU Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 531 GLU Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 313 VAL Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 357 GLN Chi-restraints excluded: chain N residue 553 ILE Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 107 ILE Chi-restraints excluded: chain O residue 116 ASN Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 344 VAL Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 255 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 234 optimal weight: 0.8980 chunk 208 optimal weight: 0.0970 chunk 240 optimal weight: 3.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS E 331 ASN H 506 GLN J 394 ASN ** L 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS O 234 GLN O 484 ASN ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 352 HIS S 227 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.156306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.111758 restraints weight = 36444.265| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.19 r_work: 0.3189 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25547 Z= 0.119 Angle : 0.524 14.025 34561 Z= 0.267 Chirality : 0.039 0.148 3971 Planarity : 0.004 0.073 4440 Dihedral : 4.473 48.607 3368 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.98 % Rotamer: Outliers : 2.70 % Allowed : 15.38 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.08 (0.16), residues: 2946 helix: 2.55 (0.13), residues: 1521 sheet: 0.16 (0.37), residues: 195 loop : -1.70 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 290 TYR 0.014 0.001 TYR Q 225 PHE 0.023 0.001 PHE O 109 TRP 0.018 0.001 TRP O 273 HIS 0.005 0.001 HIS N 220 Details of bonding type rmsd covalent geometry : bond 0.00262 (25543) covalent geometry : angle 0.52314 (34555) hydrogen bonds : bond 0.04705 ( 1297) hydrogen bonds : angle 3.80630 ( 3765) metal coordination : bond 0.00758 ( 4) metal coordination : angle 2.71202 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 363 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 GLU cc_start: 0.8666 (tp30) cc_final: 0.8362 (tp30) REVERT: C 48 ARG cc_start: 0.7552 (ttt90) cc_final: 0.7141 (tmt170) REVERT: C 63 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7437 (mm-30) REVERT: C 64 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: D 94 ARG cc_start: 0.7477 (ttt180) cc_final: 0.7094 (ttt-90) REVERT: D 107 HIS cc_start: 0.7833 (t70) cc_final: 0.7538 (t-90) REVERT: D 116 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7778 (ttmt) REVERT: E 353 TYR cc_start: 0.9069 (m-80) cc_final: 0.8863 (m-80) REVERT: F 817 ARG cc_start: 0.7060 (mtp180) cc_final: 0.5884 (mtp85) REVERT: G 176 GLU cc_start: 0.3290 (OUTLIER) cc_final: 0.2522 (tt0) REVERT: H 531 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7671 (tp30) REVERT: H 613 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7068 (mt-10) REVERT: H 616 PHE cc_start: 0.8539 (m-80) cc_final: 0.8335 (m-10) REVERT: I 63 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7750 (tm-30) REVERT: I 183 PHE cc_start: 0.7556 (t80) cc_final: 0.6442 (p90) REVERT: I 191 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8795 (pp) REVERT: I 255 HIS cc_start: 0.7420 (p90) cc_final: 0.7157 (m170) REVERT: I 346 ARG cc_start: 0.7502 (mtp85) cc_final: 0.7263 (mtp85) REVERT: J 388 LYS cc_start: 0.8019 (mttt) cc_final: 0.7397 (mppt) REVERT: J 437 MET cc_start: 0.8684 (mmm) cc_final: 0.8475 (mmm) REVERT: J 493 LYS cc_start: 0.6944 (pttp) cc_final: 0.6351 (pttp) REVERT: K 464 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7186 (tt0) REVERT: K 499 SER cc_start: 0.7656 (m) cc_final: 0.6876 (p) REVERT: L 66 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6432 (mt-10) REVERT: L 362 ASN cc_start: 0.8749 (m-40) cc_final: 0.8505 (m-40) REVERT: M 445 GLN cc_start: 0.8186 (pt0) cc_final: 0.7708 (pp30) REVERT: N 28 MET cc_start: 0.4626 (tmm) cc_final: 0.4273 (tmm) REVERT: N 32 MET cc_start: 0.7817 (mtp) cc_final: 0.7588 (mtp) REVERT: N 102 LYS cc_start: 0.8846 (mttt) cc_final: 0.8585 (tttm) REVERT: N 104 TYR cc_start: 0.9412 (OUTLIER) cc_final: 0.8030 (m-80) REVERT: N 310 ASP cc_start: 0.8676 (m-30) cc_final: 0.8379 (m-30) REVERT: N 553 ILE cc_start: 0.8586 (tt) cc_final: 0.8174 (tp) REVERT: O 33 GLU cc_start: 0.4744 (mm-30) cc_final: 0.4343 (mm-30) REVERT: O 48 TYR cc_start: 0.5832 (t80) cc_final: 0.5357 (t80) REVERT: O 80 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.7098 (t80) REVERT: O 122 LYS cc_start: 0.6327 (tttt) cc_final: 0.5671 (tmtt) REVERT: O 129 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7269 (pt0) REVERT: O 240 GLU cc_start: 0.7793 (tp30) cc_final: 0.7257 (pm20) REVERT: O 421 ASP cc_start: 0.8176 (t0) cc_final: 0.7971 (t70) REVERT: Q 245 MET cc_start: 0.7715 (mmm) cc_final: 0.7375 (mmt) REVERT: Q 334 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8138 (mt-10) REVERT: Q 338 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7728 (tptt) REVERT: R 50 ARG cc_start: 0.7667 (ttt90) cc_final: 0.7150 (mtp85) REVERT: R 101 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7779 (mtt90) REVERT: R 229 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.7926 (t0) REVERT: R 259 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8325 (pt0) REVERT: R 261 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8827 (tp) REVERT: S 198 LEU cc_start: 0.8630 (tt) cc_final: 0.8302 (tt) REVERT: S 199 MET cc_start: 0.8745 (ptp) cc_final: 0.8474 (pmm) REVERT: S 218 ASN cc_start: 0.6818 (m-40) cc_final: 0.6263 (t0) outliers start: 75 outliers final: 55 residues processed: 411 average time/residue: 0.1604 time to fit residues: 103.3978 Evaluate side-chains 407 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 343 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 356 ILE Chi-restraints excluded: chain F residue 800 ASN Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 524 THR Chi-restraints excluded: chain H residue 530 LYS Chi-restraints excluded: chain H residue 531 GLU Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 452 THR Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 139 ILE Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain L residue 359 ILE Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 147 CYS Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 107 ILE Chi-restraints excluded: chain O residue 116 ASN Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 176 ILE Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 344 VAL Chi-restraints excluded: chain Q residue 369 ILE Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 42 optimal weight: 7.9990 chunk 182 optimal weight: 0.0670 chunk 294 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 193 optimal weight: 0.5980 chunk 160 optimal weight: 0.0670 chunk 195 optimal weight: 0.5980 chunk 127 optimal weight: 0.6980 chunk 240 optimal weight: 2.9990 chunk 114 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS H 506 GLN ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS ** O 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 352 HIS S 227 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.158462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115111 restraints weight = 36646.249| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.42 r_work: 0.3210 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25547 Z= 0.104 Angle : 0.505 13.378 34561 Z= 0.256 Chirality : 0.038 0.182 3971 Planarity : 0.004 0.070 4440 Dihedral : 4.255 46.934 3368 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.30 % Favored : 94.67 % Rotamer: Outliers : 2.45 % Allowed : 15.99 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.29 (0.16), residues: 2946 helix: 2.69 (0.13), residues: 1525 sheet: 0.27 (0.38), residues: 191 loop : -1.55 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 379 TYR 0.012 0.001 TYR N 257 PHE 0.023 0.001 PHE O 109 TRP 0.016 0.001 TRP E 319 HIS 0.005 0.001 HIS Q 160 Details of bonding type rmsd covalent geometry : bond 0.00214 (25543) covalent geometry : angle 0.50379 (34555) hydrogen bonds : bond 0.04285 ( 1297) hydrogen bonds : angle 3.70387 ( 3765) metal coordination : bond 0.00794 ( 4) metal coordination : angle 2.15855 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 362 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: C 48 ARG cc_start: 0.7508 (ttt90) cc_final: 0.7092 (tmt170) REVERT: C 64 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: D 94 ARG cc_start: 0.7489 (ttt180) cc_final: 0.7089 (ttt-90) REVERT: D 107 HIS cc_start: 0.7814 (t70) cc_final: 0.7534 (t-90) REVERT: E 353 TYR cc_start: 0.9104 (m-80) cc_final: 0.8896 (m-80) REVERT: E 395 LEU cc_start: 0.7377 (tt) cc_final: 0.6999 (tp) REVERT: E 407 LYS cc_start: 0.7427 (pttp) cc_final: 0.7207 (ptmm) REVERT: F 817 ARG cc_start: 0.6973 (mtp180) cc_final: 0.6041 (mtp85) REVERT: G 176 GLU cc_start: 0.3132 (OUTLIER) cc_final: 0.2402 (tt0) REVERT: H 531 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7702 (tp30) REVERT: H 603 MET cc_start: 0.7197 (mtm) cc_final: 0.6813 (mtt) REVERT: H 613 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6720 (mm-30) REVERT: H 616 PHE cc_start: 0.8624 (m-80) cc_final: 0.8414 (m-10) REVERT: I 63 GLN cc_start: 0.8401 (mm-40) cc_final: 0.7737 (tm-30) REVERT: I 183 PHE cc_start: 0.7456 (t80) cc_final: 0.6293 (p90) REVERT: I 191 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8796 (pp) REVERT: I 255 HIS cc_start: 0.7487 (p90) cc_final: 0.7148 (m170) REVERT: I 346 ARG cc_start: 0.7485 (mtp85) cc_final: 0.7247 (mtp85) REVERT: J 388 LYS cc_start: 0.7816 (mttt) cc_final: 0.7309 (mppt) REVERT: J 437 MET cc_start: 0.8690 (mmm) cc_final: 0.8482 (mmm) REVERT: J 463 LYS cc_start: 0.8010 (mmmt) cc_final: 0.7691 (mttm) REVERT: J 493 LYS cc_start: 0.7110 (pttp) cc_final: 0.6794 (pttp) REVERT: K 464 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7271 (mp0) REVERT: K 499 SER cc_start: 0.7298 (m) cc_final: 0.6394 (p) REVERT: L 66 GLU cc_start: 0.6279 (mt-10) cc_final: 0.6050 (mt-10) REVERT: L 362 ASN cc_start: 0.8737 (m-40) cc_final: 0.8518 (m-40) REVERT: M 44 ASP cc_start: 0.9209 (m-30) cc_final: 0.8841 (m-30) REVERT: M 445 GLN cc_start: 0.8211 (pt0) cc_final: 0.7712 (pp30) REVERT: N 28 MET cc_start: 0.4526 (tmm) cc_final: 0.4213 (tmm) REVERT: N 32 MET cc_start: 0.7809 (mtp) cc_final: 0.7593 (mtp) REVERT: N 73 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8677 (mtmt) REVERT: N 102 LYS cc_start: 0.8854 (mttt) cc_final: 0.8567 (tttm) REVERT: N 104 TYR cc_start: 0.9401 (OUTLIER) cc_final: 0.7942 (m-80) REVERT: N 293 VAL cc_start: 0.8383 (t) cc_final: 0.8056 (t) REVERT: N 310 ASP cc_start: 0.8669 (m-30) cc_final: 0.8371 (m-30) REVERT: N 551 GLN cc_start: 0.8631 (mt0) cc_final: 0.8353 (mm-40) REVERT: N 553 ILE cc_start: 0.8596 (tt) cc_final: 0.8168 (tp) REVERT: O 33 GLU cc_start: 0.4649 (mm-30) cc_final: 0.4230 (mm-30) REVERT: O 48 TYR cc_start: 0.5799 (t80) cc_final: 0.5324 (t80) REVERT: O 122 LYS cc_start: 0.6304 (tttt) cc_final: 0.5643 (tmtt) REVERT: O 129 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7237 (pt0) REVERT: O 240 GLU cc_start: 0.7803 (tp30) cc_final: 0.7260 (pm20) REVERT: O 421 ASP cc_start: 0.8213 (t0) cc_final: 0.8000 (t70) REVERT: Q 245 MET cc_start: 0.7596 (mmm) cc_final: 0.7241 (mmt) REVERT: Q 338 LYS cc_start: 0.8092 (ttmt) cc_final: 0.7717 (tptt) REVERT: R 50 ARG cc_start: 0.7713 (ttt90) cc_final: 0.7197 (mtp85) REVERT: R 101 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7551 (mtt90) REVERT: R 229 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8011 (t0) REVERT: R 259 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8311 (pt0) REVERT: R 261 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8798 (tp) REVERT: S 198 LEU cc_start: 0.8568 (tt) cc_final: 0.8289 (tt) REVERT: S 199 MET cc_start: 0.8725 (ptp) cc_final: 0.8435 (pmm) REVERT: S 218 ASN cc_start: 0.6677 (m-40) cc_final: 0.6174 (t0) outliers start: 68 outliers final: 45 residues processed: 402 average time/residue: 0.1719 time to fit residues: 108.1732 Evaluate side-chains 395 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 342 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 531 GLU Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain L residue 359 ILE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 50 ARG Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 147 CYS Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 344 VAL Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 214 optimal weight: 7.9990 chunk 218 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 279 optimal weight: 0.0980 chunk 112 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS H 506 GLN K 394 ASN ** L 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 HIS ** O 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.157528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114908 restraints weight = 36487.824| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.35 r_work: 0.3192 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25547 Z= 0.117 Angle : 0.522 12.952 34561 Z= 0.266 Chirality : 0.039 0.265 3971 Planarity : 0.004 0.068 4440 Dihedral : 4.136 45.664 3365 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 1.98 % Allowed : 16.46 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.31 (0.16), residues: 2946 helix: 2.70 (0.13), residues: 1523 sheet: 0.26 (0.38), residues: 192 loop : -1.52 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 118 TYR 0.013 0.001 TYR R 93 PHE 0.022 0.001 PHE O 109 TRP 0.015 0.001 TRP E 319 HIS 0.005 0.001 HIS N 220 Details of bonding type rmsd covalent geometry : bond 0.00257 (25543) covalent geometry : angle 0.52138 (34555) hydrogen bonds : bond 0.04449 ( 1297) hydrogen bonds : angle 3.72389 ( 3765) metal coordination : bond 0.00778 ( 4) metal coordination : angle 2.49423 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 353 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 ARG cc_start: 0.7519 (ttt90) cc_final: 0.7109 (tmt170) REVERT: C 64 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: D 94 ARG cc_start: 0.7475 (ttt180) cc_final: 0.7090 (ttt-90) REVERT: D 107 HIS cc_start: 0.7852 (t70) cc_final: 0.7561 (t-90) REVERT: D 116 LYS cc_start: 0.7853 (ttmt) cc_final: 0.7432 (mtmm) REVERT: E 353 TYR cc_start: 0.9127 (m-80) cc_final: 0.8913 (m-80) REVERT: E 407 LYS cc_start: 0.7451 (pttp) cc_final: 0.7228 (ptmm) REVERT: F 817 ARG cc_start: 0.7013 (mtp180) cc_final: 0.6067 (mtp85) REVERT: G 176 GLU cc_start: 0.3185 (OUTLIER) cc_final: 0.2443 (tt0) REVERT: H 531 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: H 603 MET cc_start: 0.7247 (mtm) cc_final: 0.6840 (mtt) REVERT: H 613 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7141 (mt-10) REVERT: I 63 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7775 (tm-30) REVERT: I 183 PHE cc_start: 0.7434 (t80) cc_final: 0.6273 (p90) REVERT: I 191 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8812 (pp) REVERT: I 255 HIS cc_start: 0.7477 (p90) cc_final: 0.7159 (m170) REVERT: I 346 ARG cc_start: 0.7489 (mtp85) cc_final: 0.7270 (mtp85) REVERT: J 388 LYS cc_start: 0.7872 (mttt) cc_final: 0.7354 (mppt) REVERT: J 437 MET cc_start: 0.8696 (mmm) cc_final: 0.8486 (mmm) REVERT: J 463 LYS cc_start: 0.7984 (mmmt) cc_final: 0.7699 (mttm) REVERT: J 493 LYS cc_start: 0.7120 (pttp) cc_final: 0.6794 (pttp) REVERT: K 464 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7211 (tt0) REVERT: L 66 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6380 (mt-10) REVERT: L 362 ASN cc_start: 0.8764 (m-40) cc_final: 0.8544 (m-40) REVERT: M 445 GLN cc_start: 0.8171 (pt0) cc_final: 0.7685 (pp30) REVERT: N 28 MET cc_start: 0.4455 (tmm) cc_final: 0.4153 (tmm) REVERT: N 73 LYS cc_start: 0.8925 (mtpt) cc_final: 0.8716 (mtmt) REVERT: N 102 LYS cc_start: 0.8876 (mttt) cc_final: 0.8613 (tttm) REVERT: N 293 VAL cc_start: 0.8429 (t) cc_final: 0.8061 (t) REVERT: N 310 ASP cc_start: 0.8698 (m-30) cc_final: 0.8410 (m-30) REVERT: N 355 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7901 (tp) REVERT: N 551 GLN cc_start: 0.8660 (mt0) cc_final: 0.8380 (mm-40) REVERT: N 553 ILE cc_start: 0.8613 (tt) cc_final: 0.8183 (tp) REVERT: O 18 GLN cc_start: 0.8503 (tt0) cc_final: 0.8010 (tp40) REVERT: O 33 GLU cc_start: 0.4450 (mm-30) cc_final: 0.4045 (mm-30) REVERT: O 48 TYR cc_start: 0.5772 (t80) cc_final: 0.5303 (t80) REVERT: O 122 LYS cc_start: 0.6375 (tttt) cc_final: 0.5704 (tmtt) REVERT: O 129 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7337 (pt0) REVERT: O 240 GLU cc_start: 0.7818 (tp30) cc_final: 0.7289 (pm20) REVERT: O 421 ASP cc_start: 0.8199 (t0) cc_final: 0.7990 (t70) REVERT: Q 245 MET cc_start: 0.7662 (mmm) cc_final: 0.7305 (mmt) REVERT: Q 334 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8216 (mt-10) REVERT: Q 338 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7724 (tptt) REVERT: R 50 ARG cc_start: 0.7759 (ttt90) cc_final: 0.7269 (mtp85) REVERT: R 101 ARG cc_start: 0.7827 (ttm-80) cc_final: 0.7562 (mtt90) REVERT: R 229 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8021 (t0) REVERT: R 259 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8341 (pt0) REVERT: R 261 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8840 (tp) REVERT: S 198 LEU cc_start: 0.8584 (tt) cc_final: 0.8313 (tt) REVERT: S 199 MET cc_start: 0.8751 (ptp) cc_final: 0.8472 (pmm) REVERT: S 218 ASN cc_start: 0.6783 (m-40) cc_final: 0.6244 (t0) outliers start: 55 outliers final: 44 residues processed: 387 average time/residue: 0.1694 time to fit residues: 102.2859 Evaluate side-chains 398 residues out of total 2776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 346 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain F residue 804 ILE Chi-restraints excluded: chain F residue 811 LEU Chi-restraints excluded: chain G residue 176 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 531 GLU Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 312 LYS Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 352 GLU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain L residue 359 ILE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 309 GLU Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 147 CYS Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 355 LEU Chi-restraints excluded: chain N residue 568 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 132 LEU Chi-restraints excluded: chain O residue 219 HIS Chi-restraints excluded: chain O residue 274 TYR Chi-restraints excluded: chain O residue 397 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 376 TRP Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ASP Chi-restraints excluded: chain R residue 229 ASP Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 211 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 112 optimal weight: 2.9990 chunk 250 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 285 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 HIS E 393 ASN K 394 ASN ** L 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 512 ASN O 97 HIS ** O 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.155005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111000 restraints weight = 36371.019| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.32 r_work: 0.3164 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25547 Z= 0.155 Angle : 0.560 14.189 34561 Z= 0.285 Chirality : 0.040 0.259 3971 Planarity : 0.004 0.073 4440 Dihedral : 4.305 48.935 3365 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.84 % Favored : 94.09 % Rotamer: Outliers : 2.23 % Allowed : 16.28 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.19 (0.16), residues: 2946 helix: 2.59 (0.13), residues: 1520 sheet: 0.19 (0.37), residues: 192 loop : -1.56 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 379 TYR 0.014 0.002 TYR O 117 PHE 0.022 0.001 PHE O 109 TRP 0.016 0.001 TRP O 273 HIS 0.006 0.001 HIS N 220 Details of bonding type rmsd covalent geometry : bond 0.00362 (25543) covalent geometry : angle 0.55811 (34555) hydrogen bonds : bond 0.05009 ( 1297) hydrogen bonds : angle 3.85848 ( 3765) metal coordination : bond 0.01169 ( 4) metal coordination : angle 3.64778 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8680.78 seconds wall clock time: 148 minutes 14.79 seconds (8894.79 seconds total)