Starting phenix.real_space_refine on Fri Mar 6 08:02:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vap_31857/03_2026/7vap_31857.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vap_31857/03_2026/7vap_31857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vap_31857/03_2026/7vap_31857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vap_31857/03_2026/7vap_31857.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vap_31857/03_2026/7vap_31857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vap_31857/03_2026/7vap_31857.map" } resolution = 3.0 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 29558 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.52, per 1000 atoms: 0.22 Number of scatterers: 29558 At special positions: 0 Unit cell: (136.4, 147.84, 176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 9 15.00 Mg 2 11.99 O 5578 8.00 N 5131 7.00 C 18735 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: 2.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 24 sheets defined 47.8% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 4.021A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.106A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.564A pdb=" N ASP A 390 " --> pdb=" O PRO A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.602A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.550A pdb=" N ARG A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.790A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 532 Processing helix chain 'A' and resid 535 through 540 Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.982A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 576 removed outlier: 3.531A pdb=" N TYR A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 removed outlier: 3.566A pdb=" N PHE B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 5.015A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.692A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.917A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 464 removed outlier: 3.553A pdb=" N LEU B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 477 through 494 removed outlier: 3.928A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 533 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.682A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 577 removed outlier: 3.582A pdb=" N TYR B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.827A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.201A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 4.132A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.542A pdb=" N ASP C 390 " --> pdb=" O PRO C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.552A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.551A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.015A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.552A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.695A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.608A pdb=" N TYR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN C 571 " --> pdb=" O MET C 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.757A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.576A pdb=" N ARG D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.528A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.965A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.750A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.508A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 285 No H-bonds generated for 'chain 'D' and resid 284 through 285' Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 removed outlier: 3.645A pdb=" N ILE D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.774A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 467 through 472 Processing helix chain 'E' and resid 85 through 89 removed outlier: 4.200A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 175 through 179 removed outlier: 3.627A pdb=" N GLY E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 4.043A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 215 Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.970A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.909A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.568A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 331 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 365 Processing helix chain 'E' and resid 374 through 400 removed outlier: 4.029A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.505A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 89' Processing helix chain 'F' and resid 120 through 124 Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.823A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.656A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 361 through 366 removed outlier: 3.945A pdb=" N GLY F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL F 366 " --> pdb=" O MET F 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 361 through 366' Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.516A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.564A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 470 removed outlier: 3.503A pdb=" N GLU F 469 " --> pdb=" O LYS F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.794A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 3.636A pdb=" N VAL G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 209 removed outlier: 3.572A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 6 through 16 removed outlier: 3.604A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.921A pdb=" N LEU H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 64 removed outlier: 5.889A pdb=" N ARG H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 83 removed outlier: 4.118A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 98 Processing helix chain 'I' and resid 82 through 105 Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'J' and resid 62 through 93 Processing helix chain 'J' and resid 94 through 97 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.790A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 139 removed outlier: 4.560A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.589A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 119 removed outlier: 3.625A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU K 119 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 92 Processing helix chain 'L' and resid 93 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 128 through 130 No H-bonds generated for 'chain 'L' and resid 128 through 130' Processing helix chain 'L' and resid 131 through 139 Processing helix chain 'L' and resid 166 through 187 removed outlier: 5.082A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.587A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 5.664A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 6.751A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.826A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 50 removed outlier: 5.461A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 5.820A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 21 current: chain 'F' and resid 42 through 51 removed outlier: 5.784A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 55 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 141 through 144 current: chain 'L' and resid 161 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 82 through 84 current: chain 'A' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 290 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 148 removed outlier: 6.587A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 3.625A pdb=" N GLY A 155 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 288 current: chain 'B' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 428 through 429 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 148 removed outlier: 3.808A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 164 " --> pdb=" O TRP B 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.795A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB2, first strand: chain 'C' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.604A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.560A pdb=" N GLY C 155 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.718A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 91 through 93 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 91 through 93 current: chain 'D' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 217 through 223 current: chain 'D' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 307 through 315 current: chain 'D' and resid 358 through 359 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.716A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AB9, first strand: chain 'E' and resid 91 through 93 removed outlier: 6.737A pdb=" N ARG E 91 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU E 221 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE E 93 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS E 223 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET E 194 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.504A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.510A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 94 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 92 through 94 current: chain 'F' and resid 217 through 221 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 217 through 221 current: chain 'F' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 307 through 315 current: chain 'F' and resid 358 through 359 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.794A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 91 through 96 Processing sheet with id=AC6, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.778A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) 1274 hydrogen bonds defined for protein. 3651 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: 5.16 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9959 1.34 - 1.46: 4212 1.46 - 1.57: 15740 1.57 - 1.69: 9 1.69 - 1.81: 194 Bond restraints: 30114 Sorted by residual: bond pdb=" O4 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.568 1.449 0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" O3 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.569 1.474 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" O1 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.565 1.473 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" O3B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.430 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" O2 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.567 1.496 0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 30109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 40432 2.23 - 4.46: 326 4.46 - 6.69: 48 6.69 - 8.92: 6 8.92 - 11.15: 1 Bond angle restraints: 40813 Sorted by residual: angle pdb=" C THR E 371 " pdb=" CA THR E 371 " pdb=" CB THR E 371 " ideal model delta sigma weight residual 117.23 110.39 6.84 1.36e+00 5.41e-01 2.53e+01 angle pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" O3B ADP A 601 " ideal model delta sigma weight residual 108.20 97.05 11.15 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA THR E 371 " pdb=" C THR E 371 " pdb=" N ARG E 372 " ideal model delta sigma weight residual 119.98 117.37 2.61 8.50e-01 1.38e+00 9.40e+00 angle pdb=" CA ILE A 402 " pdb=" C ILE A 402 " pdb=" N VAL A 403 " ideal model delta sigma weight residual 116.60 120.71 -4.11 1.45e+00 4.76e-01 8.05e+00 angle pdb=" C PHE C 419 " pdb=" N PRO C 420 " pdb=" CA PRO C 420 " ideal model delta sigma weight residual 127.00 133.66 -6.66 2.40e+00 1.74e-01 7.70e+00 ... (remaining 40808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.14: 17865 30.14 - 60.27: 450 60.27 - 90.41: 67 90.41 - 120.55: 0 120.55 - 150.69: 1 Dihedral angle restraints: 18383 sinusoidal: 7561 harmonic: 10822 Sorted by residual: dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual 300.00 149.32 150.69 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" CA ARG E 372 " pdb=" C ARG E 372 " pdb=" N GLU E 373 " pdb=" CA GLU E 373 " ideal model delta harmonic sigma weight residual 180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 -134.15 74.14 1 2.00e+01 2.50e-03 1.74e+01 ... (remaining 18380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3437 0.045 - 0.091: 837 0.091 - 0.136: 287 0.136 - 0.181: 9 0.181 - 0.227: 2 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CB ILE C 83 " pdb=" CA ILE C 83 " pdb=" CG1 ILE C 83 " pdb=" CG2 ILE C 83 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" C3' ADP A 601 " pdb=" O2' ADP A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 4569 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 393 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 394 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 323 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO D 324 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 324 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 324 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 393 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 394 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 394 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 394 " 0.023 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.30: 14 2.30 - 2.95: 12825 2.95 - 3.60: 42092 3.60 - 4.25: 67651 4.25 - 4.90: 116962 Nonbonded interactions: 239544 Sorted by model distance: nonbonded pdb=" OG SER A 235 " pdb="MG MG A 602 " model vdw 1.645 2.170 nonbonded pdb=" O2B ADP A 601 " pdb="MG MG A 602 " model vdw 1.882 2.170 nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 1.953 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 2.003 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 2.078 2.170 ... (remaining 239539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } 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: 1.870 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 25.220 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 0.119 30114 Z= 0.181 Angle : 0.538 11.153 40813 Z= 0.282 Chirality : 0.043 0.227 4572 Planarity : 0.004 0.048 5333 Dihedral : 13.606 150.687 11465 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.43 (0.14), residues: 3764 helix: 2.09 (0.14), residues: 1537 sheet: 0.27 (0.23), residues: 570 loop : 0.20 (0.16), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 364 TYR 0.011 0.001 TYR D 463 PHE 0.016 0.001 PHE A 230 TRP 0.008 0.001 TRP C 119 HIS 0.006 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00410 (30114) covalent geometry : angle 0.53781 (40813) hydrogen bonds : bond 0.14406 ( 1274) hydrogen bonds : angle 5.81521 ( 3651) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 597 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7281 (mt0) cc_final: 0.6916 (mt0) REVERT: A 38 GLU cc_start: 0.7692 (tt0) cc_final: 0.7111 (tt0) REVERT: A 97 LYS cc_start: 0.6905 (mttt) cc_final: 0.6603 (mttt) REVERT: A 115 LYS cc_start: 0.8168 (tttp) cc_final: 0.7826 (tttt) REVERT: A 209 MET cc_start: 0.7207 (mtp) cc_final: 0.6840 (mtt) REVERT: A 240 SER cc_start: 0.8399 (m) cc_final: 0.8098 (p) REVERT: A 273 THR cc_start: 0.8227 (m) cc_final: 0.7982 (t) REVERT: A 343 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7056 (mt-10) REVERT: A 344 MET cc_start: 0.7568 (tpt) cc_final: 0.6584 (tmm) REVERT: A 441 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6937 (mm-30) REVERT: A 456 GLU cc_start: 0.5773 (mt-10) cc_final: 0.5470 (mt-10) REVERT: A 466 GLU cc_start: 0.6202 (mt-10) cc_final: 0.5770 (tt0) REVERT: A 491 ARG cc_start: 0.6800 (mmt180) cc_final: 0.5666 (mtm-85) REVERT: A 538 GLU cc_start: 0.5273 (tm-30) cc_final: 0.5071 (tm-30) REVERT: A 555 SER cc_start: 0.7320 (t) cc_final: 0.6953 (p) REVERT: B 96 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6665 (mt-10) REVERT: B 124 LYS cc_start: 0.7096 (mtmm) cc_final: 0.6280 (mptt) REVERT: B 152 ASP cc_start: 0.6506 (m-30) cc_final: 0.6238 (p0) REVERT: B 156 ARG cc_start: 0.6803 (ttm170) cc_final: 0.6358 (ttm110) REVERT: B 159 GLU cc_start: 0.6766 (tm-30) cc_final: 0.6303 (mm-30) REVERT: B 165 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7148 (mm-30) REVERT: B 179 THR cc_start: 0.7030 (m) cc_final: 0.6586 (t) REVERT: B 220 MET cc_start: 0.7598 (ttp) cc_final: 0.7326 (ttm) REVERT: B 241 LEU cc_start: 0.7435 (mt) cc_final: 0.7126 (tt) REVERT: B 264 ASP cc_start: 0.6822 (m-30) cc_final: 0.6543 (m-30) REVERT: B 268 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6620 (mt-10) REVERT: B 276 LYS cc_start: 0.6474 (mttt) cc_final: 0.5664 (ttpp) REVERT: B 294 MET cc_start: 0.7623 (mtp) cc_final: 0.7378 (mmm) REVERT: B 323 MET cc_start: 0.8237 (mtt) cc_final: 0.8017 (mtm) REVERT: B 374 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7177 (mt-10) REVERT: B 393 GLU cc_start: 0.6535 (tt0) cc_final: 0.6217 (tt0) REVERT: B 397 GLN cc_start: 0.7216 (mm-40) cc_final: 0.6844 (mt0) REVERT: B 408 ARG cc_start: 0.7213 (ttm170) cc_final: 0.6857 (tpp80) REVERT: B 460 ARG cc_start: 0.6023 (mtp180) cc_final: 0.5742 (mmm160) REVERT: B 488 ARG cc_start: 0.5607 (ttp-110) cc_final: 0.5400 (tmm160) REVERT: B 489 ILE cc_start: 0.6381 (mt) cc_final: 0.6081 (mt) REVERT: B 541 GLN cc_start: 0.5415 (mp10) cc_final: 0.4656 (mt0) REVERT: B 547 ARG cc_start: 0.5101 (mmm-85) cc_final: 0.4548 (mmt180) REVERT: B 558 GLU cc_start: 0.5619 (tt0) cc_final: 0.5096 (tp30) REVERT: C 107 VAL cc_start: 0.8674 (m) cc_final: 0.8355 (t) REVERT: C 146 LYS cc_start: 0.7859 (mttp) cc_final: 0.7617 (mtpp) REVERT: C 154 ARG cc_start: 0.7086 (mtp-110) cc_final: 0.6850 (mtm-85) REVERT: C 159 GLU cc_start: 0.7352 (pt0) cc_final: 0.6722 (pp20) REVERT: C 165 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6815 (mt-10) REVERT: C 342 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7207 (mm-30) REVERT: C 412 SER cc_start: 0.7893 (m) cc_final: 0.7597 (p) REVERT: C 424 TRP cc_start: 0.7406 (p90) cc_final: 0.6980 (p-90) REVERT: C 480 GLU cc_start: 0.6601 (mp0) cc_final: 0.6220 (mm-30) REVERT: C 481 ARG cc_start: 0.6234 (mmm-85) cc_final: 0.5796 (mmm-85) REVERT: C 492 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6933 (mt-10) REVERT: C 530 ILE cc_start: 0.6711 (mt) cc_final: 0.6363 (mt) REVERT: C 538 GLU cc_start: 0.6385 (mt-10) cc_final: 0.5399 (mm-30) REVERT: C 565 GLU cc_start: 0.6220 (mm-30) cc_final: 0.5795 (mt-10) REVERT: C 571 GLN cc_start: 0.6583 (mp10) cc_final: 0.6205 (mt0) REVERT: D 6 LYS cc_start: 0.6866 (tttp) cc_final: 0.6620 (tptp) REVERT: D 34 ASP cc_start: 0.7200 (m-30) cc_final: 0.6813 (p0) REVERT: D 49 GLU cc_start: 0.7029 (tt0) cc_final: 0.6726 (tt0) REVERT: D 77 GLU cc_start: 0.6652 (tt0) cc_final: 0.6415 (mt-10) REVERT: D 98 LYS cc_start: 0.7694 (mmmm) cc_final: 0.7281 (mmpt) REVERT: D 175 PRO cc_start: 0.7294 (Cg_endo) cc_final: 0.6952 (Cg_exo) REVERT: D 223 LYS cc_start: 0.7446 (mtpp) cc_final: 0.6814 (mtpt) REVERT: D 260 MET cc_start: 0.7931 (mmm) cc_final: 0.7688 (mmm) REVERT: D 264 CYS cc_start: 0.7552 (m) cc_final: 0.7128 (m) REVERT: D 305 LYS cc_start: 0.7700 (mtmm) cc_final: 0.7304 (mtmm) REVERT: D 321 ARG cc_start: 0.7436 (mtp180) cc_final: 0.7210 (tpp80) REVERT: D 362 MET cc_start: 0.8446 (ttt) cc_final: 0.8054 (ttt) REVERT: D 421 PHE cc_start: 0.7374 (m-80) cc_final: 0.6883 (m-10) REVERT: D 452 LYS cc_start: 0.7310 (mmtp) cc_final: 0.7018 (mmtp) REVERT: E 7 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6729 (OUTLIER) REVERT: E 26 ASP cc_start: 0.7523 (p0) cc_final: 0.7287 (p0) REVERT: E 49 GLU cc_start: 0.7589 (tt0) cc_final: 0.7288 (tt0) REVERT: E 81 ARG cc_start: 0.7426 (mtt-85) cc_final: 0.7045 (mtt-85) REVERT: E 302 GLU cc_start: 0.7062 (tt0) cc_final: 0.6830 (tp30) REVERT: E 305 LYS cc_start: 0.7664 (mtmm) cc_final: 0.7377 (mmtp) REVERT: E 353 ASP cc_start: 0.7883 (t0) cc_final: 0.7667 (t70) REVERT: E 376 LYS cc_start: 0.6996 (tttm) cc_final: 0.6493 (ttpt) REVERT: E 420 ARG cc_start: 0.6852 (mtm110) cc_final: 0.6418 (mtm-85) REVERT: E 427 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7899 (mm110) REVERT: E 428 GLN cc_start: 0.6899 (tt0) cc_final: 0.6663 (mt0) REVERT: E 465 GLN cc_start: 0.6090 (tt0) cc_final: 0.5623 (mm110) REVERT: F 7 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7197 (mt-10) REVERT: F 9 THR cc_start: 0.7851 (m) cc_final: 0.7456 (p) REVERT: F 53 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6323 (mp0) REVERT: F 81 ARG cc_start: 0.8004 (mtt-85) cc_final: 0.7549 (mtt-85) REVERT: F 110 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7691 (mtmt) REVERT: F 129 GLN cc_start: 0.7696 (mm110) cc_final: 0.7481 (tp-100) REVERT: F 248 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7275 (mt-10) REVERT: F 305 LYS cc_start: 0.7782 (mmtm) cc_final: 0.7201 (mttm) REVERT: F 409 ARG cc_start: 0.7047 (ttm-80) cc_final: 0.6712 (ttm-80) REVERT: F 410 ARG cc_start: 0.6927 (mtm-85) cc_final: 0.6552 (mtt90) REVERT: F 437 GLN cc_start: 0.7004 (tt0) cc_final: 0.5981 (mm-40) REVERT: F 445 MET cc_start: 0.8208 (mtt) cc_final: 0.7775 (mtp) REVERT: F 452 LYS cc_start: 0.7261 (mmtp) cc_final: 0.6735 (mtmt) REVERT: F 457 ASP cc_start: 0.5956 (m-30) cc_final: 0.5657 (t0) REVERT: G 17 GLN cc_start: 0.6420 (mm-40) cc_final: 0.6108 (tp40) REVERT: G 155 LYS cc_start: 0.5485 (mttt) cc_final: 0.4815 (tppt) REVERT: G 160 ARG cc_start: 0.5448 (mmm-85) cc_final: 0.5204 (tpp80) REVERT: G 197 ILE cc_start: 0.6132 (pt) cc_final: 0.5430 (mm) REVERT: G 200 LYS cc_start: 0.5440 (mttm) cc_final: 0.5226 (mtpp) REVERT: J 158 GLU cc_start: 0.4026 (tp30) cc_final: 0.3796 (mt-10) REVERT: J 170 ARG cc_start: 0.3064 (mtp85) cc_final: 0.2812 (mtp85) REVERT: L 158 GLU cc_start: 0.4564 (mm-30) cc_final: 0.3968 (pt0) outliers start: 0 outliers final: 3 residues processed: 597 average time/residue: 0.8964 time to fit residues: 601.3432 Evaluate side-chains 361 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 359 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain B residue 515 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN C 283 HIS D 170 GLN D 252 HIS D 310 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 GLN E 222 ASN E 407 ASN F 388 ASN ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.108287 restraints weight = 38354.701| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.82 r_work: 0.2973 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 30114 Z= 0.248 Angle : 0.696 8.951 40813 Z= 0.360 Chirality : 0.050 0.184 4572 Planarity : 0.006 0.052 5333 Dihedral : 7.058 153.822 4263 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.92 % Allowed : 8.43 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.59 (0.14), residues: 3764 helix: 1.29 (0.13), residues: 1563 sheet: 0.02 (0.22), residues: 557 loop : -0.25 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 460 TYR 0.020 0.002 TYR A 25 PHE 0.028 0.003 PHE C 230 TRP 0.024 0.002 TRP C 119 HIS 0.019 0.002 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00599 (30114) covalent geometry : angle 0.69639 (40813) hydrogen bonds : bond 0.06028 ( 1274) hydrogen bonds : angle 4.95517 ( 3651) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 359 time to evaluate : 1.138 Fit side-chains REVERT: A 3 GLN cc_start: 0.7908 (mt0) cc_final: 0.7528 (mt0) REVERT: A 38 GLU cc_start: 0.8601 (tt0) cc_final: 0.8154 (tt0) REVERT: A 97 LYS cc_start: 0.7608 (mttt) cc_final: 0.7391 (mttt) REVERT: A 209 MET cc_start: 0.8404 (mtp) cc_final: 0.8126 (mtt) REVERT: A 344 MET cc_start: 0.7755 (tpt) cc_final: 0.7156 (tmm) REVERT: A 348 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: A 441 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7902 (mm-30) REVERT: A 461 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: A 466 GLU cc_start: 0.6428 (mt-10) cc_final: 0.6092 (tt0) REVERT: A 491 ARG cc_start: 0.7731 (mmt180) cc_final: 0.6942 (mtm-85) REVERT: A 570 ILE cc_start: 0.6540 (mt) cc_final: 0.6334 (mm) REVERT: B 33 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7286 (mt-10) REVERT: B 85 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8121 (p0) REVERT: B 156 ARG cc_start: 0.7658 (ttm170) cc_final: 0.7323 (ttp-110) REVERT: B 159 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6931 (mm-30) REVERT: B 165 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7392 (mm-30) REVERT: B 241 LEU cc_start: 0.8313 (mt) cc_final: 0.8004 (tt) REVERT: B 264 ASP cc_start: 0.7673 (m-30) cc_final: 0.7360 (m-30) REVERT: B 268 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7597 (mt-10) REVERT: B 325 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7516 (t0) REVERT: B 393 GLU cc_start: 0.7005 (tt0) cc_final: 0.6769 (tt0) REVERT: B 397 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7810 (mt0) REVERT: B 408 ARG cc_start: 0.7980 (ttm170) cc_final: 0.7751 (tpp80) REVERT: B 525 GLU cc_start: 0.5950 (mt-10) cc_final: 0.5252 (tp30) REVERT: B 541 GLN cc_start: 0.5425 (mp10) cc_final: 0.4612 (mt0) REVERT: B 547 ARG cc_start: 0.5831 (mmm-85) cc_final: 0.5240 (mmt180) REVERT: B 553 TYR cc_start: 0.5915 (m-80) cc_final: 0.5381 (m-80) REVERT: C 154 ARG cc_start: 0.7652 (mtp-110) cc_final: 0.7442 (mtm-85) REVERT: C 159 GLU cc_start: 0.7818 (pt0) cc_final: 0.7570 (pp20) REVERT: C 342 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7842 (mm-30) REVERT: C 375 GLU cc_start: 0.7773 (tt0) cc_final: 0.7235 (mt-10) REVERT: C 424 TRP cc_start: 0.7965 (p90) cc_final: 0.7627 (p-90) REVERT: C 480 GLU cc_start: 0.7533 (mp0) cc_final: 0.6983 (mm-30) REVERT: C 481 ARG cc_start: 0.6974 (mmm-85) cc_final: 0.6545 (mmm-85) REVERT: C 530 ILE cc_start: 0.7343 (mt) cc_final: 0.6969 (mt) REVERT: C 538 GLU cc_start: 0.6401 (mt-10) cc_final: 0.5485 (mm-30) REVERT: C 565 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6975 (mt-10) REVERT: C 571 GLN cc_start: 0.6542 (mp10) cc_final: 0.6282 (mt0) REVERT: D 39 THR cc_start: 0.7722 (p) cc_final: 0.7411 (t) REVERT: D 49 GLU cc_start: 0.7920 (tt0) cc_final: 0.7710 (tt0) REVERT: D 185 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6646 (mm-30) REVERT: D 338 GLN cc_start: 0.8433 (tt0) cc_final: 0.8226 (tp40) REVERT: D 406 GLU cc_start: 0.5971 (mm-30) cc_final: 0.5655 (pm20) REVERT: D 416 ASP cc_start: 0.7937 (t0) cc_final: 0.7665 (t70) REVERT: D 421 PHE cc_start: 0.8236 (m-80) cc_final: 0.8009 (m-80) REVERT: D 452 LYS cc_start: 0.7774 (mmtp) cc_final: 0.7458 (mmtp) REVERT: E 81 ARG cc_start: 0.8317 (mtt-85) cc_final: 0.8070 (mtt-85) REVERT: E 276 GLU cc_start: 0.5931 (OUTLIER) cc_final: 0.4846 (mp0) REVERT: E 321 ARG cc_start: 0.7952 (ttm110) cc_final: 0.7665 (ttt-90) REVERT: E 353 ASP cc_start: 0.7969 (t0) cc_final: 0.7691 (t70) REVERT: E 376 LYS cc_start: 0.8161 (tttm) cc_final: 0.7692 (ttpt) REVERT: E 420 ARG cc_start: 0.8072 (mtm110) cc_final: 0.7742 (mtm-85) REVERT: E 465 GLN cc_start: 0.6600 (tt0) cc_final: 0.6294 (mm110) REVERT: F 7 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8077 (mt-10) REVERT: F 9 THR cc_start: 0.8217 (m) cc_final: 0.7947 (p) REVERT: F 81 ARG cc_start: 0.8753 (mtt-85) cc_final: 0.8401 (mtt-85) REVERT: F 248 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7891 (mt-10) REVERT: F 437 GLN cc_start: 0.8373 (tt0) cc_final: 0.7790 (mm-40) REVERT: F 452 LYS cc_start: 0.7936 (mmtp) cc_final: 0.7532 (mtmt) REVERT: G 155 LYS cc_start: 0.6018 (mttt) cc_final: 0.5419 (tptp) REVERT: G 164 LEU cc_start: 0.5531 (OUTLIER) cc_final: 0.5266 (tp) REVERT: H 1 MET cc_start: 0.2984 (pmm) cc_final: 0.2071 (tmt) REVERT: J 164 GLU cc_start: 0.6032 (OUTLIER) cc_final: 0.5044 (tm-30) REVERT: J 170 ARG cc_start: 0.3499 (mtp85) cc_final: 0.3175 (mtp85) REVERT: L 82 GLU cc_start: 0.2772 (OUTLIER) cc_final: 0.2449 (mp0) REVERT: L 158 GLU cc_start: 0.4484 (mm-30) cc_final: 0.4236 (pm20) outliers start: 90 outliers final: 40 residues processed: 420 average time/residue: 0.8924 time to fit residues: 422.7216 Evaluate side-chains 343 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 295 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 49 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 270 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 307 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 251 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 407 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.109794 restraints weight = 38484.098| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.67 r_work: 0.2999 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30114 Z= 0.136 Angle : 0.537 6.938 40813 Z= 0.277 Chirality : 0.044 0.163 4572 Planarity : 0.005 0.048 5333 Dihedral : 6.709 160.729 4261 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.69 % Allowed : 11.32 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.84 (0.14), residues: 3764 helix: 1.59 (0.13), residues: 1575 sheet: 0.04 (0.23), residues: 558 loop : -0.18 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 460 TYR 0.014 0.001 TYR H 89 PHE 0.017 0.001 PHE A 230 TRP 0.017 0.001 TRP C 119 HIS 0.004 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00315 (30114) covalent geometry : angle 0.53691 (40813) hydrogen bonds : bond 0.04715 ( 1274) hydrogen bonds : angle 4.64278 ( 3651) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 319 time to evaluate : 1.189 Fit side-chains REVERT: A 3 GLN cc_start: 0.7835 (mt0) cc_final: 0.7458 (mt0) REVERT: A 38 GLU cc_start: 0.8546 (tt0) cc_final: 0.8111 (tt0) REVERT: A 93 ARG cc_start: 0.8504 (mmm160) cc_final: 0.8288 (mmp80) REVERT: A 209 MET cc_start: 0.8365 (mtp) cc_final: 0.8060 (mtt) REVERT: A 343 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7452 (mt-10) REVERT: A 344 MET cc_start: 0.7735 (tpt) cc_final: 0.7208 (tmm) REVERT: A 348 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: A 466 GLU cc_start: 0.6374 (mt-10) cc_final: 0.6077 (tt0) REVERT: A 491 ARG cc_start: 0.7734 (mmt180) cc_final: 0.6969 (mtm-85) REVERT: A 548 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6689 (tt) REVERT: B 85 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8069 (p0) REVERT: B 156 ARG cc_start: 0.7622 (ttm170) cc_final: 0.7295 (ttp-110) REVERT: B 159 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6864 (mm-30) REVERT: B 165 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7349 (mm-30) REVERT: B 241 LEU cc_start: 0.8242 (mt) cc_final: 0.7984 (tt) REVERT: B 264 ASP cc_start: 0.7619 (m-30) cc_final: 0.7359 (m-30) REVERT: B 268 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7651 (mt-10) REVERT: B 294 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8376 (mtt) REVERT: B 397 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7814 (mt0) REVERT: B 408 ARG cc_start: 0.7976 (ttm170) cc_final: 0.7714 (tpp80) REVERT: B 517 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.5839 (mmtm) REVERT: B 525 GLU cc_start: 0.5869 (mt-10) cc_final: 0.5262 (tp30) REVERT: B 541 GLN cc_start: 0.5407 (mp10) cc_final: 0.4624 (mt0) REVERT: B 547 ARG cc_start: 0.5838 (mmm-85) cc_final: 0.5144 (mmt180) REVERT: B 550 ARG cc_start: 0.6012 (tpp-160) cc_final: 0.5574 (tpm170) REVERT: B 553 TYR cc_start: 0.6002 (m-80) cc_final: 0.5501 (m-80) REVERT: C 159 GLU cc_start: 0.7795 (pt0) cc_final: 0.7524 (pp20) REVERT: C 342 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7738 (mm-30) REVERT: C 375 GLU cc_start: 0.7744 (tt0) cc_final: 0.7228 (mt-10) REVERT: C 424 TRP cc_start: 0.7922 (p90) cc_final: 0.7581 (p-90) REVERT: C 456 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: C 480 GLU cc_start: 0.7465 (mp0) cc_final: 0.6861 (mm-30) REVERT: C 530 ILE cc_start: 0.7344 (mt) cc_final: 0.6965 (mt) REVERT: C 565 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6694 (mt-10) REVERT: D 39 THR cc_start: 0.7710 (p) cc_final: 0.7438 (t) REVERT: D 61 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6656 (mt-10) REVERT: D 185 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6647 (mm-30) REVERT: D 230 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7790 (mt-10) REVERT: D 338 GLN cc_start: 0.8359 (tt0) cc_final: 0.8149 (tp40) REVERT: D 406 GLU cc_start: 0.5982 (mm-30) cc_final: 0.5642 (pm20) REVERT: D 416 ASP cc_start: 0.8172 (t0) cc_final: 0.7958 (t70) REVERT: D 421 PHE cc_start: 0.8218 (m-80) cc_final: 0.8010 (m-80) REVERT: D 452 LYS cc_start: 0.7767 (mmtp) cc_final: 0.7562 (mmtm) REVERT: E 321 ARG cc_start: 0.7956 (ttm110) cc_final: 0.7735 (ttm-80) REVERT: E 353 ASP cc_start: 0.7922 (t0) cc_final: 0.7660 (t70) REVERT: E 376 LYS cc_start: 0.8101 (tttm) cc_final: 0.7643 (ttpt) REVERT: E 420 ARG cc_start: 0.8052 (mtm110) cc_final: 0.7672 (mtm-85) REVERT: E 427 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: E 465 GLN cc_start: 0.6544 (tt0) cc_final: 0.6228 (mm110) REVERT: F 7 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7984 (mt-10) REVERT: F 9 THR cc_start: 0.8076 (m) cc_final: 0.7750 (p) REVERT: F 81 ARG cc_start: 0.8722 (mtt-85) cc_final: 0.8423 (mtm180) REVERT: F 87 GLU cc_start: 0.7273 (pt0) cc_final: 0.6974 (pt0) REVERT: F 394 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7462 (pttm) REVERT: F 437 GLN cc_start: 0.8399 (tt0) cc_final: 0.7807 (mm-40) REVERT: F 452 LYS cc_start: 0.7985 (mmtp) cc_final: 0.7602 (mtmt) REVERT: G 155 LYS cc_start: 0.6091 (mttt) cc_final: 0.5468 (tptp) REVERT: G 197 ILE cc_start: 0.6804 (pt) cc_final: 0.6306 (mm) REVERT: H 1 MET cc_start: 0.2935 (pmm) cc_final: 0.2203 (tmt) REVERT: J 141 GLU cc_start: 0.3860 (OUTLIER) cc_final: 0.3397 (mt-10) REVERT: J 164 GLU cc_start: 0.5907 (OUTLIER) cc_final: 0.4964 (tm-30) REVERT: J 170 ARG cc_start: 0.3363 (mtp85) cc_final: 0.3155 (mtp85) REVERT: L 82 GLU cc_start: 0.2777 (OUTLIER) cc_final: 0.2529 (mp0) REVERT: L 158 GLU cc_start: 0.4455 (mm-30) cc_final: 0.4240 (pm20) outliers start: 83 outliers final: 38 residues processed: 375 average time/residue: 0.8668 time to fit residues: 367.6089 Evaluate side-chains 343 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 293 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 260 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 293 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 311 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 342 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.109239 restraints weight = 38237.378| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.84 r_work: 0.3018 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30114 Z= 0.147 Angle : 0.543 7.535 40813 Z= 0.280 Chirality : 0.044 0.210 4572 Planarity : 0.005 0.049 5333 Dihedral : 6.694 173.268 4261 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.34 % Allowed : 12.39 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.82 (0.14), residues: 3764 helix: 1.59 (0.13), residues: 1576 sheet: 0.01 (0.23), residues: 554 loop : -0.21 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 159 TYR 0.013 0.001 TYR A 25 PHE 0.018 0.002 PHE C 230 TRP 0.016 0.001 TRP C 119 HIS 0.005 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00348 (30114) covalent geometry : angle 0.54293 (40813) hydrogen bonds : bond 0.04680 ( 1274) hydrogen bonds : angle 4.59559 ( 3651) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 302 time to evaluate : 1.201 Fit side-chains REVERT: A 3 GLN cc_start: 0.7844 (mt0) cc_final: 0.7451 (mt0) REVERT: A 38 GLU cc_start: 0.8494 (tt0) cc_final: 0.8092 (tt0) REVERT: A 93 ARG cc_start: 0.8524 (mmm160) cc_final: 0.8280 (mmp80) REVERT: A 209 MET cc_start: 0.8349 (mtp) cc_final: 0.8041 (mtt) REVERT: A 343 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7466 (mt-10) REVERT: A 344 MET cc_start: 0.7709 (tpt) cc_final: 0.7142 (tmm) REVERT: A 348 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: A 461 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: A 466 GLU cc_start: 0.6402 (mt-10) cc_final: 0.6067 (tt0) REVERT: A 491 ARG cc_start: 0.7737 (mmt180) cc_final: 0.6989 (mtm-85) REVERT: A 548 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6763 (tt) REVERT: B 85 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8077 (p0) REVERT: B 92 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: B 156 ARG cc_start: 0.7643 (ttm170) cc_final: 0.7275 (ttp-110) REVERT: B 159 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6841 (mm-30) REVERT: B 165 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7333 (mm-30) REVERT: B 170 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7038 (mm-30) REVERT: B 241 LEU cc_start: 0.8243 (mt) cc_final: 0.7991 (tt) REVERT: B 264 ASP cc_start: 0.7614 (m-30) cc_final: 0.7378 (m-30) REVERT: B 268 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7623 (mt-10) REVERT: B 276 LYS cc_start: 0.6951 (OUTLIER) cc_final: 0.5945 (mmtt) REVERT: B 316 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: B 397 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7799 (mt0) REVERT: B 408 ARG cc_start: 0.7955 (ttm170) cc_final: 0.7697 (tpp80) REVERT: B 525 GLU cc_start: 0.5811 (mt-10) cc_final: 0.5328 (tp30) REVERT: B 541 GLN cc_start: 0.5421 (mp10) cc_final: 0.4602 (mt0) REVERT: B 547 ARG cc_start: 0.5813 (mmm-85) cc_final: 0.5063 (mmt180) REVERT: B 550 ARG cc_start: 0.6110 (tpp-160) cc_final: 0.5857 (tpm170) REVERT: B 553 TYR cc_start: 0.5985 (m-80) cc_final: 0.5543 (m-80) REVERT: C 159 GLU cc_start: 0.7795 (pt0) cc_final: 0.7546 (pp20) REVERT: C 342 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7714 (mm-30) REVERT: C 375 GLU cc_start: 0.7720 (tt0) cc_final: 0.7160 (mt-10) REVERT: C 424 TRP cc_start: 0.7854 (p90) cc_final: 0.7522 (p-90) REVERT: C 456 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7382 (tp30) REVERT: C 480 GLU cc_start: 0.7451 (mp0) cc_final: 0.6826 (mm-30) REVERT: C 530 ILE cc_start: 0.7352 (mt) cc_final: 0.6970 (mt) REVERT: C 565 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6686 (mt-10) REVERT: D 39 THR cc_start: 0.7705 (p) cc_final: 0.7449 (t) REVERT: D 185 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6630 (mm-30) REVERT: D 338 GLN cc_start: 0.8377 (tt0) cc_final: 0.8161 (tp40) REVERT: D 406 GLU cc_start: 0.5959 (mm-30) cc_final: 0.5610 (pm20) REVERT: D 421 PHE cc_start: 0.8205 (m-80) cc_final: 0.7977 (m-80) REVERT: D 452 LYS cc_start: 0.7751 (mmtp) cc_final: 0.7548 (mmtm) REVERT: E 141 MET cc_start: 0.8723 (mtp) cc_final: 0.8440 (mtp) REVERT: E 248 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: E 321 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7714 (ttt-90) REVERT: E 353 ASP cc_start: 0.7907 (t0) cc_final: 0.7638 (t70) REVERT: E 376 LYS cc_start: 0.8156 (tttm) cc_final: 0.7703 (ttpt) REVERT: E 405 THR cc_start: 0.6737 (OUTLIER) cc_final: 0.6337 (p) REVERT: E 420 ARG cc_start: 0.8017 (mtm110) cc_final: 0.7686 (mtm-85) REVERT: E 427 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7276 (mp10) REVERT: E 433 GLU cc_start: 0.7613 (mp0) cc_final: 0.7345 (mp0) REVERT: E 465 GLN cc_start: 0.6599 (tt0) cc_final: 0.6271 (mm110) REVERT: F 7 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7982 (mt-10) REVERT: F 9 THR cc_start: 0.8121 (m) cc_final: 0.7778 (p) REVERT: F 81 ARG cc_start: 0.8732 (mtt-85) cc_final: 0.8421 (mtm180) REVERT: F 162 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: F 437 GLN cc_start: 0.8346 (tt0) cc_final: 0.7749 (mm-40) REVERT: F 452 LYS cc_start: 0.7967 (mmtp) cc_final: 0.7552 (mtmt) REVERT: F 457 ASP cc_start: 0.6901 (OUTLIER) cc_final: 0.6532 (t0) REVERT: G 155 LYS cc_start: 0.6210 (mttt) cc_final: 0.5534 (tptp) REVERT: G 164 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5296 (tp) REVERT: G 197 ILE cc_start: 0.6780 (pt) cc_final: 0.6325 (mm) REVERT: H 1 MET cc_start: 0.3328 (pmm) cc_final: 0.2488 (tmt) REVERT: H 90 MET cc_start: 0.3146 (mmt) cc_final: 0.2742 (tpp) REVERT: J 141 GLU cc_start: 0.4054 (OUTLIER) cc_final: 0.3587 (mt-10) REVERT: J 164 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.4947 (tm-30) REVERT: J 170 ARG cc_start: 0.3454 (mtp85) cc_final: 0.3198 (mtp85) REVERT: L 82 GLU cc_start: 0.2868 (OUTLIER) cc_final: 0.2567 (mp0) outliers start: 103 outliers final: 46 residues processed: 377 average time/residue: 0.8521 time to fit residues: 365.1725 Evaluate side-chains 351 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 287 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 89 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 44 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 chunk 211 optimal weight: 10.0000 chunk 348 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 273 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 overall best weight: 6.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN F 425 GLN ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108749 restraints weight = 38393.775| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.79 r_work: 0.2985 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 30114 Z= 0.269 Angle : 0.710 9.266 40813 Z= 0.368 Chirality : 0.050 0.197 4572 Planarity : 0.006 0.056 5333 Dihedral : 6.862 129.024 4261 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.09 % Allowed : 13.53 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.15 (0.13), residues: 3764 helix: 0.99 (0.13), residues: 1550 sheet: -0.19 (0.22), residues: 554 loop : -0.57 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 532 TYR 0.022 0.002 TYR B 25 PHE 0.026 0.003 PHE C 230 TRP 0.015 0.002 TRP C 119 HIS 0.019 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00656 (30114) covalent geometry : angle 0.71011 (40813) hydrogen bonds : bond 0.06416 ( 1274) hydrogen bonds : angle 5.03916 ( 3651) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 300 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7939 (mt0) cc_final: 0.7473 (mt0) REVERT: A 38 GLU cc_start: 0.8536 (tt0) cc_final: 0.8192 (tt0) REVERT: A 54 ASP cc_start: 0.8299 (t0) cc_final: 0.8031 (t0) REVERT: A 93 ARG cc_start: 0.8505 (mmm160) cc_final: 0.8285 (mmp80) REVERT: A 209 MET cc_start: 0.8418 (mtp) cc_final: 0.8105 (mtt) REVERT: A 344 MET cc_start: 0.7778 (tpt) cc_final: 0.7190 (tmm) REVERT: A 348 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: A 461 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: A 466 GLU cc_start: 0.6405 (mt-10) cc_final: 0.6041 (tt0) REVERT: A 491 ARG cc_start: 0.7824 (mmt180) cc_final: 0.7045 (mtm-85) REVERT: A 548 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6838 (tt) REVERT: B 85 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8068 (p0) REVERT: B 92 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: B 156 ARG cc_start: 0.7603 (ttm170) cc_final: 0.7202 (ttp-110) REVERT: B 159 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6703 (mm-30) REVERT: B 165 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7390 (mm-30) REVERT: B 241 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8045 (tt) REVERT: B 264 ASP cc_start: 0.7628 (m-30) cc_final: 0.7423 (m-30) REVERT: B 276 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6045 (mmtt) REVERT: B 397 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7830 (mt0) REVERT: B 408 ARG cc_start: 0.7923 (ttm170) cc_final: 0.7653 (tpp80) REVERT: B 541 GLN cc_start: 0.5344 (mp10) cc_final: 0.4599 (mt0) REVERT: B 547 ARG cc_start: 0.5814 (mmm-85) cc_final: 0.5061 (mmt180) REVERT: B 553 TYR cc_start: 0.6043 (m-80) cc_final: 0.5805 (m-80) REVERT: C 159 GLU cc_start: 0.7790 (pt0) cc_final: 0.7585 (pp20) REVERT: C 342 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7921 (mm-30) REVERT: C 375 GLU cc_start: 0.7780 (tt0) cc_final: 0.7213 (mt-10) REVERT: C 456 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7518 (tp30) REVERT: C 480 GLU cc_start: 0.7398 (mp0) cc_final: 0.6844 (mm-30) REVERT: C 530 ILE cc_start: 0.7445 (mt) cc_final: 0.7041 (mt) REVERT: C 532 ARG cc_start: 0.6727 (mtm180) cc_final: 0.6368 (mtm180) REVERT: C 565 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6721 (mt-10) REVERT: D 185 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6712 (mm-30) REVERT: D 280 ARG cc_start: 0.7693 (mtm180) cc_final: 0.7411 (mtm180) REVERT: D 287 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8548 (ttm) REVERT: D 406 GLU cc_start: 0.6027 (mm-30) cc_final: 0.5647 (pm20) REVERT: D 452 LYS cc_start: 0.7888 (mmtp) cc_final: 0.7628 (mmtp) REVERT: D 457 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: E 141 MET cc_start: 0.8746 (mtp) cc_final: 0.8424 (mtp) REVERT: E 248 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: E 276 GLU cc_start: 0.6040 (OUTLIER) cc_final: 0.5065 (mp0) REVERT: E 321 ARG cc_start: 0.8031 (ttm110) cc_final: 0.7731 (ttm-80) REVERT: E 353 ASP cc_start: 0.7946 (t0) cc_final: 0.7701 (t70) REVERT: E 376 LYS cc_start: 0.8321 (tttm) cc_final: 0.8064 (tttp) REVERT: E 398 ILE cc_start: 0.5768 (mm) cc_final: 0.5512 (pt) REVERT: E 405 THR cc_start: 0.6626 (OUTLIER) cc_final: 0.6163 (p) REVERT: E 420 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7851 (mtm-85) REVERT: E 427 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7272 (mp10) REVERT: E 433 GLU cc_start: 0.7661 (mp0) cc_final: 0.7379 (mp0) REVERT: E 465 GLN cc_start: 0.6888 (tt0) cc_final: 0.6302 (mm110) REVERT: F 7 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8084 (mt-10) REVERT: F 9 THR cc_start: 0.8310 (m) cc_final: 0.7955 (p) REVERT: F 81 ARG cc_start: 0.8754 (mtt-85) cc_final: 0.8403 (mtm180) REVERT: F 87 GLU cc_start: 0.7365 (pt0) cc_final: 0.7102 (pt0) REVERT: F 207 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7636 (mm-30) REVERT: F 210 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7850 (ttp-110) REVERT: F 437 GLN cc_start: 0.8314 (tt0) cc_final: 0.7776 (mm-40) REVERT: F 452 LYS cc_start: 0.8070 (mmtp) cc_final: 0.7579 (mtmt) REVERT: G 155 LYS cc_start: 0.6222 (mttt) cc_final: 0.5614 (tptp) REVERT: G 164 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5411 (tp) REVERT: H 1 MET cc_start: 0.2929 (pmm) cc_final: 0.2369 (tmt) REVERT: H 63 MET cc_start: 0.1922 (OUTLIER) cc_final: 0.1521 (mpt) REVERT: H 93 LEU cc_start: 0.3715 (OUTLIER) cc_final: 0.3453 (pp) REVERT: J 141 GLU cc_start: 0.3967 (OUTLIER) cc_final: 0.3493 (mt-10) REVERT: J 158 GLU cc_start: 0.5059 (tp30) cc_final: 0.4801 (mm-30) REVERT: J 164 GLU cc_start: 0.5992 (OUTLIER) cc_final: 0.5018 (tm-30) REVERT: L 82 GLU cc_start: 0.2729 (OUTLIER) cc_final: 0.2433 (mp0) outliers start: 126 outliers final: 56 residues processed: 399 average time/residue: 0.8472 time to fit residues: 383.9993 Evaluate side-chains 358 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 281 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 89 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 158 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 253 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 296 optimal weight: 0.7980 chunk 242 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 361 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN E 310 GLN F 465 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112704 restraints weight = 38193.817| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.67 r_work: 0.3052 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 30114 Z= 0.106 Angle : 0.499 11.082 40813 Z= 0.256 Chirality : 0.042 0.185 4572 Planarity : 0.004 0.049 5333 Dihedral : 6.047 111.241 4261 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.01 % Allowed : 15.86 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.79 (0.14), residues: 3764 helix: 1.60 (0.13), residues: 1578 sheet: -0.02 (0.23), residues: 554 loop : -0.26 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 460 TYR 0.012 0.001 TYR H 89 PHE 0.018 0.001 PHE A 230 TRP 0.015 0.001 TRP J 100 HIS 0.003 0.001 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00224 (30114) covalent geometry : angle 0.49915 (40813) hydrogen bonds : bond 0.03880 ( 1274) hydrogen bonds : angle 4.47831 ( 3651) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 316 time to evaluate : 1.127 Fit side-chains REVERT: A 3 GLN cc_start: 0.7855 (mt0) cc_final: 0.7430 (mt0) REVERT: A 38 GLU cc_start: 0.8412 (tt0) cc_final: 0.8051 (tt0) REVERT: A 93 ARG cc_start: 0.8496 (mmm160) cc_final: 0.8237 (mmp80) REVERT: A 209 MET cc_start: 0.8336 (mtp) cc_final: 0.8053 (mtt) REVERT: A 343 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7514 (mt-10) REVERT: A 344 MET cc_start: 0.7682 (tpt) cc_final: 0.7479 (tpt) REVERT: A 348 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: A 466 GLU cc_start: 0.6254 (mt-10) cc_final: 0.5938 (tt0) REVERT: B 85 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8004 (p0) REVERT: B 92 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: B 156 ARG cc_start: 0.7481 (ttm170) cc_final: 0.7103 (ttp-110) REVERT: B 159 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6609 (mm-30) REVERT: B 165 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7210 (mm-30) REVERT: B 276 LYS cc_start: 0.7051 (mttp) cc_final: 0.6141 (ttpp) REVERT: B 294 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8309 (mtt) REVERT: B 397 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7733 (mt0) REVERT: B 408 ARG cc_start: 0.7861 (ttm170) cc_final: 0.7581 (tpp80) REVERT: B 460 ARG cc_start: 0.6684 (mtp180) cc_final: 0.6463 (mtp180) REVERT: B 525 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5606 (tp30) REVERT: B 541 GLN cc_start: 0.5454 (mp10) cc_final: 0.4704 (mt0) REVERT: B 547 ARG cc_start: 0.5733 (mmm-85) cc_final: 0.4962 (mmt180) REVERT: B 553 TYR cc_start: 0.6115 (m-80) cc_final: 0.5767 (m-80) REVERT: C 342 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7669 (mm-30) REVERT: C 375 GLU cc_start: 0.7675 (tt0) cc_final: 0.7113 (mt-10) REVERT: C 424 TRP cc_start: 0.7783 (p90) cc_final: 0.7451 (p-90) REVERT: C 480 GLU cc_start: 0.7394 (mp0) cc_final: 0.6750 (mm-30) REVERT: C 530 ILE cc_start: 0.7389 (mt) cc_final: 0.7092 (mt) REVERT: C 565 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6606 (mt-10) REVERT: D 406 GLU cc_start: 0.5855 (mm-30) cc_final: 0.5540 (pm20) REVERT: D 452 LYS cc_start: 0.7864 (mmtp) cc_final: 0.7604 (mmtp) REVERT: D 465 GLN cc_start: 0.7076 (pt0) cc_final: 0.6461 (mm-40) REVERT: E 248 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: E 321 ARG cc_start: 0.7972 (ttm110) cc_final: 0.7724 (ttm-80) REVERT: E 353 ASP cc_start: 0.7885 (t0) cc_final: 0.7632 (t70) REVERT: E 376 LYS cc_start: 0.8143 (tttm) cc_final: 0.7826 (tttp) REVERT: E 380 ASP cc_start: 0.7781 (m-30) cc_final: 0.7516 (m-30) REVERT: E 420 ARG cc_start: 0.8060 (mtm110) cc_final: 0.7758 (mtm-85) REVERT: E 427 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7216 (mp10) REVERT: E 465 GLN cc_start: 0.6719 (tt0) cc_final: 0.6210 (mm110) REVERT: F 7 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7919 (mm-30) REVERT: F 9 THR cc_start: 0.7954 (m) cc_final: 0.7574 (p) REVERT: F 81 ARG cc_start: 0.8684 (mtt-85) cc_final: 0.8431 (mtm180) REVERT: F 437 GLN cc_start: 0.8405 (tt0) cc_final: 0.7834 (mm-40) REVERT: F 452 LYS cc_start: 0.8033 (mmtp) cc_final: 0.7551 (mtmt) REVERT: F 457 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6547 (t0) REVERT: G 22 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6740 (tt0) REVERT: G 155 LYS cc_start: 0.6196 (mttt) cc_final: 0.5583 (tptp) REVERT: H 1 MET cc_start: 0.2974 (pmm) cc_final: 0.2465 (tmt) REVERT: H 90 MET cc_start: 0.3039 (mmt) cc_final: 0.2725 (tpp) REVERT: J 141 GLU cc_start: 0.3983 (OUTLIER) cc_final: 0.3668 (mt-10) REVERT: J 158 GLU cc_start: 0.4824 (tp30) cc_final: 0.4624 (mm-30) REVERT: J 164 GLU cc_start: 0.5742 (OUTLIER) cc_final: 0.4734 (tm-30) outliers start: 62 outliers final: 26 residues processed: 358 average time/residue: 0.8754 time to fit residues: 354.4355 Evaluate side-chains 324 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 303 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 223 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 371 optimal weight: 20.0000 chunk 324 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN E 310 GLN F 142 ASN F 388 ASN F 465 GLN ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.147020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109041 restraints weight = 38242.103| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.67 r_work: 0.2972 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 30114 Z= 0.299 Angle : 0.710 8.675 40813 Z= 0.368 Chirality : 0.051 0.235 4572 Planarity : 0.006 0.056 5333 Dihedral : 6.640 114.613 4261 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.83 % Allowed : 14.86 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.14 (0.13), residues: 3764 helix: 0.99 (0.13), residues: 1567 sheet: -0.19 (0.22), residues: 555 loop : -0.60 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 550 TYR 0.024 0.002 TYR B 25 PHE 0.028 0.003 PHE C 230 TRP 0.014 0.002 TRP C 119 HIS 0.018 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00736 (30114) covalent geometry : angle 0.71023 (40813) hydrogen bonds : bond 0.06228 ( 1274) hydrogen bonds : angle 4.96870 ( 3651) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 284 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7948 (mt0) cc_final: 0.7458 (mt0) REVERT: A 38 GLU cc_start: 0.8583 (tt0) cc_final: 0.8261 (tt0) REVERT: A 93 ARG cc_start: 0.8527 (mmm160) cc_final: 0.8282 (mmp80) REVERT: A 344 MET cc_start: 0.7821 (tpt) cc_final: 0.7197 (tmm) REVERT: A 348 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: A 491 ARG cc_start: 0.7847 (mmt180) cc_final: 0.7046 (mtm-85) REVERT: A 548 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6789 (tt) REVERT: A 569 GLU cc_start: 0.6111 (tt0) cc_final: 0.5866 (mt-10) REVERT: A 570 ILE cc_start: 0.6455 (OUTLIER) cc_final: 0.5961 (mp) REVERT: B 85 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8045 (p0) REVERT: B 92 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: B 156 ARG cc_start: 0.7518 (ttm170) cc_final: 0.7138 (ttp-110) REVERT: B 159 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6783 (mm-30) REVERT: B 165 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7483 (mm-30) REVERT: B 220 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7690 (tpp) REVERT: B 276 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6042 (mmtt) REVERT: B 397 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7836 (mt0) REVERT: B 408 ARG cc_start: 0.7954 (ttm170) cc_final: 0.7689 (tpp80) REVERT: B 525 GLU cc_start: 0.6187 (mt-10) cc_final: 0.5597 (tp30) REVERT: B 547 ARG cc_start: 0.5729 (mmm-85) cc_final: 0.4938 (mmt180) REVERT: C 342 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7948 (mm-30) REVERT: C 375 GLU cc_start: 0.7818 (tt0) cc_final: 0.7271 (mt-10) REVERT: C 456 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7532 (tp30) REVERT: C 480 GLU cc_start: 0.7410 (mp0) cc_final: 0.6984 (mp0) REVERT: C 530 ILE cc_start: 0.7600 (mt) cc_final: 0.7275 (mt) REVERT: D 34 ASP cc_start: 0.7745 (p0) cc_final: 0.7474 (p0) REVERT: D 280 ARG cc_start: 0.7693 (mtm180) cc_final: 0.7445 (mtm180) REVERT: D 287 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8524 (ttm) REVERT: D 406 GLU cc_start: 0.6006 (mm-30) cc_final: 0.5630 (pm20) REVERT: D 452 LYS cc_start: 0.7917 (mmtp) cc_final: 0.7654 (mmtp) REVERT: D 457 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: E 248 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: E 321 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7707 (ttt-90) REVERT: E 353 ASP cc_start: 0.7977 (t0) cc_final: 0.7716 (t70) REVERT: E 376 LYS cc_start: 0.8332 (tttm) cc_final: 0.8077 (tttp) REVERT: E 398 ILE cc_start: 0.5897 (mm) cc_final: 0.5630 (pt) REVERT: E 405 THR cc_start: 0.6611 (OUTLIER) cc_final: 0.6161 (p) REVERT: E 420 ARG cc_start: 0.8168 (mtm110) cc_final: 0.7868 (mtm-85) REVERT: E 427 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: E 433 GLU cc_start: 0.7535 (mp0) cc_final: 0.7294 (mp0) REVERT: E 465 GLN cc_start: 0.6852 (tt0) cc_final: 0.6311 (mm110) REVERT: F 7 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8176 (mt-10) REVERT: F 9 THR cc_start: 0.8316 (m) cc_final: 0.7950 (p) REVERT: F 81 ARG cc_start: 0.8785 (mtt-85) cc_final: 0.8509 (mtm180) REVERT: F 437 GLN cc_start: 0.8420 (tt0) cc_final: 0.7851 (mm-40) REVERT: G 155 LYS cc_start: 0.6127 (mttt) cc_final: 0.5498 (tptp) REVERT: G 164 LEU cc_start: 0.5852 (OUTLIER) cc_final: 0.5261 (tp) REVERT: H 1 MET cc_start: 0.3198 (pmm) cc_final: 0.2705 (tmt) REVERT: H 90 MET cc_start: 0.2999 (mmt) cc_final: 0.2138 (mmt) REVERT: J 81 GLU cc_start: 0.2395 (OUTLIER) cc_final: 0.2058 (pt0) REVERT: J 141 GLU cc_start: 0.4137 (OUTLIER) cc_final: 0.3676 (mt-10) REVERT: J 158 GLU cc_start: 0.4799 (tp30) cc_final: 0.4474 (mm-30) REVERT: J 164 GLU cc_start: 0.5890 (OUTLIER) cc_final: 0.4866 (tm-30) outliers start: 118 outliers final: 54 residues processed: 376 average time/residue: 0.8416 time to fit residues: 359.3836 Evaluate side-chains 352 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 281 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 316 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 327 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 330 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 347 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN D 465 GLN E 310 GLN F 465 GLN L 130 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111660 restraints weight = 38383.863| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.79 r_work: 0.3044 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30114 Z= 0.110 Angle : 0.521 14.670 40813 Z= 0.266 Chirality : 0.043 0.197 4572 Planarity : 0.005 0.052 5333 Dihedral : 6.066 104.504 4261 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.04 % Allowed : 17.06 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.63 (0.14), residues: 3764 helix: 1.45 (0.13), residues: 1593 sheet: -0.06 (0.22), residues: 555 loop : -0.37 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 460 TYR 0.011 0.001 TYR H 89 PHE 0.017 0.001 PHE A 230 TRP 0.016 0.001 TRP J 100 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00241 (30114) covalent geometry : angle 0.52143 (40813) hydrogen bonds : bond 0.04112 ( 1274) hydrogen bonds : angle 4.52462 ( 3651) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 289 time to evaluate : 1.095 Fit side-chains REVERT: A 3 GLN cc_start: 0.7862 (mt0) cc_final: 0.7403 (mt0) REVERT: A 38 GLU cc_start: 0.8399 (tt0) cc_final: 0.7996 (tt0) REVERT: A 93 ARG cc_start: 0.8495 (mmm160) cc_final: 0.8215 (mmp80) REVERT: A 343 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7420 (mt-10) REVERT: A 344 MET cc_start: 0.7683 (tpt) cc_final: 0.7466 (tpt) REVERT: A 348 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: A 461 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: A 518 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7763 (ttp) REVERT: B 85 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.7994 (p0) REVERT: B 92 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: B 156 ARG cc_start: 0.7398 (ttm170) cc_final: 0.7016 (ttp-110) REVERT: B 159 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6693 (mm-30) REVERT: B 165 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7192 (mm-30) REVERT: B 170 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6941 (mm-30) REVERT: B 397 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7737 (mt0) REVERT: B 408 ARG cc_start: 0.7883 (ttm170) cc_final: 0.7569 (tpp80) REVERT: B 525 GLU cc_start: 0.6141 (mt-10) cc_final: 0.5787 (tp30) REVERT: B 547 ARG cc_start: 0.5773 (mmm-85) cc_final: 0.4945 (mmt180) REVERT: B 553 TYR cc_start: 0.5693 (m-80) cc_final: 0.5410 (m-80) REVERT: C 342 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7721 (mm-30) REVERT: C 375 GLU cc_start: 0.7685 (tt0) cc_final: 0.7122 (mt-10) REVERT: C 424 TRP cc_start: 0.7770 (p90) cc_final: 0.7477 (p-90) REVERT: C 480 GLU cc_start: 0.7330 (mp0) cc_final: 0.7021 (mp0) REVERT: C 530 ILE cc_start: 0.7481 (mt) cc_final: 0.7198 (mt) REVERT: D 34 ASP cc_start: 0.7626 (p0) cc_final: 0.7397 (p0) REVERT: D 406 GLU cc_start: 0.5833 (mm-30) cc_final: 0.5544 (pm20) REVERT: D 452 LYS cc_start: 0.7889 (mmtp) cc_final: 0.7611 (mmtp) REVERT: E 128 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: E 248 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: E 321 ARG cc_start: 0.7973 (ttm110) cc_final: 0.7712 (ttm-80) REVERT: E 353 ASP cc_start: 0.7903 (t0) cc_final: 0.7637 (t70) REVERT: E 376 LYS cc_start: 0.8143 (tttm) cc_final: 0.7821 (tttp) REVERT: E 380 ASP cc_start: 0.7741 (m-30) cc_final: 0.7426 (m-30) REVERT: E 405 THR cc_start: 0.6889 (OUTLIER) cc_final: 0.6502 (p) REVERT: E 420 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7777 (mtm-85) REVERT: E 427 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: F 7 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7930 (mm-30) REVERT: F 9 THR cc_start: 0.8006 (m) cc_final: 0.7649 (p) REVERT: F 25 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7533 (pttp) REVERT: F 81 ARG cc_start: 0.8678 (mtt-85) cc_final: 0.8442 (mtm180) REVERT: F 87 GLU cc_start: 0.7298 (pt0) cc_final: 0.7074 (pt0) REVERT: F 437 GLN cc_start: 0.8399 (tt0) cc_final: 0.7797 (mm-40) REVERT: G 155 LYS cc_start: 0.6154 (mttt) cc_final: 0.5537 (tptp) REVERT: G 164 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.5250 (tp) REVERT: H 1 MET cc_start: 0.3167 (pmm) cc_final: 0.2698 (tmt) REVERT: J 141 GLU cc_start: 0.3906 (OUTLIER) cc_final: 0.3626 (mt-10) REVERT: J 158 GLU cc_start: 0.4812 (tp30) cc_final: 0.4563 (mm-30) REVERT: J 164 GLU cc_start: 0.5700 (OUTLIER) cc_final: 0.4695 (tm-30) outliers start: 63 outliers final: 34 residues processed: 336 average time/residue: 0.8501 time to fit residues: 324.2721 Evaluate side-chains 331 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 283 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 371 optimal weight: 0.0000 chunk 370 optimal weight: 8.9990 chunk 203 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 141 optimal weight: 0.0370 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 294 optimal weight: 8.9990 chunk 289 optimal weight: 3.9990 chunk 16 optimal weight: 0.0770 overall best weight: 0.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN B 260 ASN B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN F 170 GLN F 407 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113976 restraints weight = 38328.763| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.78 r_work: 0.3093 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 30114 Z= 0.093 Angle : 0.481 10.156 40813 Z= 0.244 Chirality : 0.042 0.188 4572 Planarity : 0.004 0.052 5333 Dihedral : 5.591 83.638 4261 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.75 % Allowed : 17.45 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.09 (0.14), residues: 3764 helix: 1.83 (0.13), residues: 1594 sheet: 0.14 (0.23), residues: 568 loop : -0.11 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 550 TYR 0.009 0.001 TYR D 13 PHE 0.016 0.001 PHE A 230 TRP 0.015 0.001 TRP C 119 HIS 0.004 0.001 HIS E 458 Details of bonding type rmsd covalent geometry : bond 0.00203 (30114) covalent geometry : angle 0.48079 (40813) hydrogen bonds : bond 0.03251 ( 1274) hydrogen bonds : angle 4.22851 ( 3651) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 306 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7849 (mt0) cc_final: 0.7397 (mt0) REVERT: A 38 GLU cc_start: 0.8309 (tt0) cc_final: 0.7937 (tt0) REVERT: A 122 MET cc_start: 0.7920 (mmm) cc_final: 0.7386 (mmm) REVERT: A 343 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7321 (mt-10) REVERT: A 344 MET cc_start: 0.7623 (tpt) cc_final: 0.7377 (tpt) REVERT: A 348 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: A 461 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: A 570 ILE cc_start: 0.6009 (OUTLIER) cc_final: 0.5791 (mt) REVERT: B 85 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7937 (p0) REVERT: B 92 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: B 156 ARG cc_start: 0.7359 (ttm170) cc_final: 0.6944 (ttp-110) REVERT: B 159 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6672 (mm-30) REVERT: B 165 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7248 (mm-30) REVERT: B 276 LYS cc_start: 0.7039 (mttp) cc_final: 0.6154 (ttpp) REVERT: B 393 GLU cc_start: 0.7232 (pt0) cc_final: 0.6916 (pp20) REVERT: B 397 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7694 (mt0) REVERT: B 408 ARG cc_start: 0.7845 (ttm170) cc_final: 0.7532 (tpp80) REVERT: B 460 ARG cc_start: 0.6662 (mtp180) cc_final: 0.6372 (mtp180) REVERT: B 525 GLU cc_start: 0.6061 (mt-10) cc_final: 0.5670 (tp30) REVERT: B 547 ARG cc_start: 0.5663 (mmm-85) cc_final: 0.4845 (mmt180) REVERT: C 342 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7540 (mm-30) REVERT: C 343 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7773 (mt-10) REVERT: C 375 GLU cc_start: 0.7630 (tt0) cc_final: 0.7053 (mt-10) REVERT: C 410 ASP cc_start: 0.8418 (t0) cc_final: 0.8183 (t70) REVERT: C 424 TRP cc_start: 0.7645 (p90) cc_final: 0.7399 (p-90) REVERT: C 480 GLU cc_start: 0.7343 (mp0) cc_final: 0.7115 (mp0) REVERT: C 530 ILE cc_start: 0.7481 (mt) cc_final: 0.7169 (mt) REVERT: C 532 ARG cc_start: 0.6699 (ptp90) cc_final: 0.5898 (tmm-80) REVERT: D 280 ARG cc_start: 0.7563 (mtm180) cc_final: 0.7236 (mtm180) REVERT: D 316 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.6992 (mtp) REVERT: D 406 GLU cc_start: 0.5828 (mm-30) cc_final: 0.5599 (pm20) REVERT: D 452 LYS cc_start: 0.7864 (mmtp) cc_final: 0.7537 (mttp) REVERT: E 248 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: E 321 ARG cc_start: 0.7915 (ttm110) cc_final: 0.7635 (ttm170) REVERT: E 353 ASP cc_start: 0.7798 (t0) cc_final: 0.7548 (t70) REVERT: E 376 LYS cc_start: 0.8047 (tttm) cc_final: 0.7778 (tttt) REVERT: E 380 ASP cc_start: 0.7598 (m-30) cc_final: 0.7308 (m-30) REVERT: E 405 THR cc_start: 0.6837 (OUTLIER) cc_final: 0.6470 (p) REVERT: E 420 ARG cc_start: 0.7952 (mtm110) cc_final: 0.7749 (mtm-85) REVERT: E 427 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7239 (mp10) REVERT: F 7 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7869 (mm-30) REVERT: F 9 THR cc_start: 0.7832 (m) cc_final: 0.7436 (p) REVERT: F 25 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7495 (pttp) REVERT: F 81 ARG cc_start: 0.8615 (mtt-85) cc_final: 0.8311 (mtm180) REVERT: F 87 GLU cc_start: 0.7127 (pt0) cc_final: 0.6915 (pt0) REVERT: F 437 GLN cc_start: 0.8379 (tt0) cc_final: 0.7769 (mm-40) REVERT: F 457 ASP cc_start: 0.6815 (OUTLIER) cc_final: 0.6428 (t0) REVERT: G 10 ASN cc_start: 0.7508 (m-40) cc_final: 0.7170 (m110) REVERT: G 148 LYS cc_start: 0.3903 (mtmm) cc_final: 0.3299 (pttp) REVERT: G 155 LYS cc_start: 0.6089 (mttt) cc_final: 0.5460 (tptp) REVERT: H 1 MET cc_start: 0.3036 (pmm) cc_final: 0.2582 (tmt) REVERT: J 141 GLU cc_start: 0.4173 (OUTLIER) cc_final: 0.3900 (mt-10) REVERT: J 158 GLU cc_start: 0.4848 (tp30) cc_final: 0.4572 (mm-30) REVERT: L 141 GLU cc_start: 0.3305 (tp30) cc_final: 0.2616 (tt0) outliers start: 54 outliers final: 23 residues processed: 348 average time/residue: 0.8669 time to fit residues: 340.6122 Evaluate side-chains 324 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 289 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 295 optimal weight: 10.0000 chunk 339 optimal weight: 20.0000 chunk 288 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 chunk 325 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 284 optimal weight: 9.9990 chunk 272 optimal weight: 7.9990 chunk 286 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 219 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111525 restraints weight = 38237.822| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.81 r_work: 0.3047 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30114 Z= 0.133 Angle : 0.541 9.413 40813 Z= 0.274 Chirality : 0.044 0.192 4572 Planarity : 0.005 0.053 5333 Dihedral : 5.821 86.798 4261 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.46 % Allowed : 18.07 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.98 (0.14), residues: 3764 helix: 1.74 (0.13), residues: 1585 sheet: 0.13 (0.23), residues: 561 loop : -0.18 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 550 TYR 0.012 0.001 TYR B 25 PHE 0.019 0.001 PHE C 230 TRP 0.014 0.001 TRP J 100 HIS 0.008 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00313 (30114) covalent geometry : angle 0.54059 (40813) hydrogen bonds : bond 0.04172 ( 1274) hydrogen bonds : angle 4.36500 ( 3651) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 285 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6310 (mpp) cc_final: 0.5991 (mpp) REVERT: A 3 GLN cc_start: 0.7864 (mt0) cc_final: 0.7409 (mt0) REVERT: A 38 GLU cc_start: 0.8418 (tt0) cc_final: 0.8038 (tt0) REVERT: A 122 MET cc_start: 0.7992 (mmm) cc_final: 0.7458 (mmm) REVERT: A 343 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7371 (mt-10) REVERT: A 344 MET cc_start: 0.7700 (tpt) cc_final: 0.7101 (tmm) REVERT: A 348 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: A 461 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: A 491 ARG cc_start: 0.7714 (mmt180) cc_final: 0.6959 (mtm-85) REVERT: B 85 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7966 (p0) REVERT: B 92 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: B 156 ARG cc_start: 0.7391 (ttm170) cc_final: 0.6972 (ttp-110) REVERT: B 159 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6678 (mm-30) REVERT: B 165 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7226 (mm-30) REVERT: B 393 GLU cc_start: 0.7253 (pt0) cc_final: 0.6887 (pp20) REVERT: B 397 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7753 (mt0) REVERT: B 525 GLU cc_start: 0.6132 (mt-10) cc_final: 0.5735 (tp30) REVERT: B 547 ARG cc_start: 0.5686 (mmm-85) cc_final: 0.4952 (mmt180) REVERT: B 553 TYR cc_start: 0.5687 (m-80) cc_final: 0.5350 (m-80) REVERT: C 342 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7705 (mm-30) REVERT: C 375 GLU cc_start: 0.7678 (tt0) cc_final: 0.7133 (mt-10) REVERT: C 424 TRP cc_start: 0.7714 (p90) cc_final: 0.7472 (p-90) REVERT: C 480 GLU cc_start: 0.7324 (mp0) cc_final: 0.7041 (mp0) REVERT: C 532 ARG cc_start: 0.6717 (ptp90) cc_final: 0.5930 (tmm-80) REVERT: D 280 ARG cc_start: 0.7580 (mtm180) cc_final: 0.7322 (mtm180) REVERT: D 316 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7086 (mtp) REVERT: D 406 GLU cc_start: 0.5834 (mm-30) cc_final: 0.5552 (pm20) REVERT: D 452 LYS cc_start: 0.7851 (mmtp) cc_final: 0.7598 (mmtp) REVERT: E 248 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: E 321 ARG cc_start: 0.7976 (ttm110) cc_final: 0.7664 (ttt-90) REVERT: E 353 ASP cc_start: 0.7876 (t0) cc_final: 0.7626 (t70) REVERT: E 376 LYS cc_start: 0.8177 (tttm) cc_final: 0.7866 (tttp) REVERT: E 380 ASP cc_start: 0.7729 (m-30) cc_final: 0.7408 (m-30) REVERT: E 405 THR cc_start: 0.6808 (OUTLIER) cc_final: 0.6398 (p) REVERT: E 420 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7794 (mtm-85) REVERT: E 427 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7267 (mp10) REVERT: F 7 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7981 (mt-10) REVERT: F 9 THR cc_start: 0.8032 (m) cc_final: 0.7660 (p) REVERT: F 81 ARG cc_start: 0.8658 (mtt-85) cc_final: 0.8424 (mtm180) REVERT: F 437 GLN cc_start: 0.8379 (tt0) cc_final: 0.7768 (mm-40) REVERT: F 457 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6493 (t0) REVERT: G 10 ASN cc_start: 0.7573 (m-40) cc_final: 0.7329 (m-40) REVERT: G 148 LYS cc_start: 0.3930 (mtmm) cc_final: 0.3253 (pttp) REVERT: G 155 LYS cc_start: 0.6055 (mttt) cc_final: 0.5437 (tptp) REVERT: H 1 MET cc_start: 0.3121 (pmm) cc_final: 0.2672 (tmt) REVERT: H 90 MET cc_start: 0.2280 (tpp) cc_final: 0.1976 (tpp) REVERT: J 141 GLU cc_start: 0.4177 (OUTLIER) cc_final: 0.3959 (mt-10) REVERT: J 158 GLU cc_start: 0.4774 (tp30) cc_final: 0.4491 (mm-30) REVERT: L 141 GLU cc_start: 0.3084 (tp30) cc_final: 0.2385 (tt0) outliers start: 45 outliers final: 25 residues processed: 320 average time/residue: 0.8520 time to fit residues: 309.1188 Evaluate side-chains 322 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain J residue 103 VAL Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 31 optimal weight: 6.9990 chunk 361 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 367 optimal weight: 8.9990 chunk 210 optimal weight: 0.0470 chunk 254 optimal weight: 4.9990 chunk 181 optimal weight: 0.4980 chunk 226 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 overall best weight: 2.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111970 restraints weight = 38194.775| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.86 r_work: 0.3049 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30114 Z= 0.115 Angle : 0.513 9.646 40813 Z= 0.261 Chirality : 0.043 0.192 4572 Planarity : 0.004 0.052 5333 Dihedral : 5.783 86.411 4261 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.72 % Allowed : 17.97 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.00 (0.14), residues: 3764 helix: 1.76 (0.13), residues: 1587 sheet: 0.14 (0.23), residues: 561 loop : -0.18 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 550 TYR 0.009 0.001 TYR E 13 PHE 0.015 0.001 PHE C 574 TRP 0.015 0.001 TRP J 100 HIS 0.006 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00267 (30114) covalent geometry : angle 0.51328 (40813) hydrogen bonds : bond 0.03933 ( 1274) hydrogen bonds : angle 4.32120 ( 3651) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10877.98 seconds wall clock time: 185 minutes 4.93 seconds (11104.93 seconds total)