Starting phenix.real_space_refine on Fri Mar 6 08:04:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7val_31849/03_2026/7val_31849.cif Found real_map, /net/cci-nas-00/data/ceres_data/7val_31849/03_2026/7val_31849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7val_31849/03_2026/7val_31849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7val_31849/03_2026/7val_31849.map" model { file = "/net/cci-nas-00/data/ceres_data/7val_31849/03_2026/7val_31849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7val_31849/03_2026/7val_31849.cif" } resolution = 3.1 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= 0.007 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 5 residue(s): 0.04s 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: 6.58, per 1000 atoms: 0.22 Number of scatterers: 29558 At special positions: 0 Unit cell: (151.36, 148.72, 178.64, 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.4 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: 149 helices and 24 sheets defined 48.4% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 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: 3.993A 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: 4.016A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 3.721A 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 Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.570A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.541A pdb=" N ARG A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 443 removed outlier: 3.685A pdb=" N ASP A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.997A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.540A 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 550 removed outlier: 3.998A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 removed outlier: 3.557A pdb=" N VAL A 554 " --> pdb=" O ALA A 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 551 through 554' Processing helix chain 'A' and resid 558 through 576 removed outlier: 3.687A 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 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 removed outlier: 3.666A pdb=" N HIS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.955A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.620A 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: 3.835A 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 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: 3.568A 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: 4.106A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 577 removed outlier: 3.539A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (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: 3.893A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 3.553A 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: 3.972A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 4.202A 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 Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.607A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 415 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 removed outlier: 3.511A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 472 removed outlier: 3.930A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 removed outlier: 3.569A pdb=" N LEU C 476 " --> pdb=" O PRO C 473 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.779A 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: 3.530A pdb=" N TYR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN C 571 " --> pdb=" O MET C 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.609A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.516A 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 210 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: 3.755A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 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: 3.597A pdb=" N TYR D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) removed outlier: 3.775A 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 366 removed outlier: 3.794A pdb=" N GLY D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 366 " --> pdb=" O MET D 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 361 through 366' Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.889A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.029A 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: 3.800A 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: 3.694A pdb=" N GLY E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 4.086A 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: 3.975A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.852A 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: 3.932A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.550A 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: 4.174A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.807A 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 445 through 446 No H-bonds generated for 'chain 'E' and resid 445 through 446' Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.539A pdb=" N LEU E 451 " --> pdb=" O GLN E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.820A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) 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: 3.844A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 3.814A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.682A 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: 3.585A 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: 3.550A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.838A 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: 3.684A 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: 3.537A pdb=" N GLU F 469 " --> pdb=" O LYS F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.814A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 3.554A pdb=" N VAL G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.555A pdb=" N ALA G 112 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 208 removed outlier: 3.797A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 5.189A 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 Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.779A pdb=" N LEU H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 64 removed outlier: 6.125A pdb=" N ARG H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 83 removed outlier: 4.037A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 4.032A 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 removed outlier: 4.126A pdb=" N LEU J 67 " --> pdb=" O ALA J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 97 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.569A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 139 removed outlier: 4.357A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.788A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 119 removed outlier: 4.061A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (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 127 through 130 removed outlier: 3.523A pdb=" N HIS L 130 " --> pdb=" O ASP L 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 130' Processing helix chain 'L' and resid 131 through 139 removed outlier: 3.632A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 188 removed outlier: 5.323A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.484A 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: 6.646A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.203A 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: 5.640A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.692A 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: 5.887A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (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: 6.502A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (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: 6.606A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR D 54 " --> pdb=" O VAL D 50 " (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: 6.006A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.703A 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: 5.676A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.573A 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: 6.511A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.796A 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: 3.619A pdb=" N GLY A 155 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 7.019A 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: 3.873A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.789A 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 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 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: 6.523A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.927A 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: 3.785A 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: 4.684A 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: 6.628A pdb=" N ARG E 91 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU E 221 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE E 93 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LYS E 223 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET E 194 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 257 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.565A 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: 3.536A 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 removed outlier: 6.593A pdb=" N PHE F 93 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N LYS F 223 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.727A 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 19 through 22 removed outlier: 3.539A pdb=" N ALA H 5 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) 1298 hydrogen bonds defined for protein. 3702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.05 Time building geometry restraints manager: 3.38 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: 9953 1.34 - 1.46: 4219 1.46 - 1.57: 15736 1.57 - 1.69: 12 1.69 - 1.81: 194 Bond restraints: 30114 Sorted by residual: bond pdb=" O3 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.569 1.512 0.057 2.00e-02 2.50e+03 8.01e+00 bond pdb=" O4 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.568 1.513 0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" O2 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.567 1.513 0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" O1 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.565 1.513 0.052 2.00e-02 2.50e+03 6.78e+00 bond pdb=" C MET F 445 " pdb=" N LEU F 446 " ideal model delta sigma weight residual 1.331 1.304 0.027 1.48e-02 4.57e+03 3.34e+00 ... (remaining 30109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 40017 1.61 - 3.21: 673 3.21 - 4.82: 95 4.82 - 6.43: 25 6.43 - 8.03: 3 Bond angle restraints: 40813 Sorted by residual: angle pdb=" C GLU B 347 " pdb=" CA GLU B 347 " pdb=" CB GLU B 347 " ideal model delta sigma weight residual 116.54 110.60 5.94 1.15e+00 7.56e-01 2.67e+01 angle pdb=" N ILE D 470 " pdb=" CA ILE D 470 " pdb=" C ILE D 470 " ideal model delta sigma weight residual 113.53 108.67 4.86 9.80e-01 1.04e+00 2.46e+01 angle pdb=" N ILE F 100 " pdb=" CA ILE F 100 " pdb=" C ILE F 100 " ideal model delta sigma weight residual 113.20 109.51 3.69 9.60e-01 1.09e+00 1.48e+01 angle pdb=" C ASN B 442 " pdb=" N VAL B 443 " pdb=" CA VAL B 443 " ideal model delta sigma weight residual 123.16 119.60 3.56 1.06e+00 8.90e-01 1.13e+01 angle pdb=" N GLY C 142 " pdb=" CA GLY C 142 " pdb=" C GLY C 142 " ideal model delta sigma weight residual 114.67 110.09 4.58 1.41e+00 5.03e-01 1.05e+01 ... (remaining 40808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16973 17.98 - 35.97: 1124 35.97 - 53.95: 192 53.95 - 71.94: 63 71.94 - 89.92: 31 Dihedral angle restraints: 18383 sinusoidal: 7561 harmonic: 10822 Sorted by residual: 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 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA VAL F 21 " pdb=" C VAL F 21 " pdb=" N GLU F 22 " pdb=" CA GLU F 22 " ideal model delta harmonic sigma weight residual -180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PRO G 120 " pdb=" C PRO G 120 " pdb=" N ALA G 121 " pdb=" CA ALA G 121 " ideal model delta harmonic sigma weight residual -180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 18380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3022 0.034 - 0.068: 1005 0.068 - 0.102: 382 0.102 - 0.136: 155 0.136 - 0.170: 8 Chirality restraints: 4572 Sorted by residual: 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 2.47 0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA THR G 119 " pdb=" N THR G 119 " pdb=" C THR G 119 " pdb=" CB THR G 119 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 4569 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO E 324 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 393 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 394 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 323 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO F 324 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 324 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 324 " -0.021 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 39 2.40 - 3.03: 17116 3.03 - 3.65: 43253 3.65 - 4.28: 65932 4.28 - 4.90: 113655 Nonbonded interactions: 239995 Sorted by model distance: nonbonded pdb=" O3B ADP A 601 " pdb=" O2 PO4 A 603 " model vdw 1.776 3.040 nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 1.954 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.959 2.170 nonbonded pdb=" OG SER A 235 " pdb="MG MG A 602 " model vdw 1.980 2.170 nonbonded pdb=" PB ADP A 601 " pdb=" O2 PO4 A 603 " model vdw 2.017 3.400 ... (remaining 239990 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.130 Find NCS groups from input model: 0.640 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30115 Z= 0.157 Angle : 0.549 8.032 40813 Z= 0.308 Chirality : 0.043 0.170 4572 Planarity : 0.004 0.046 5333 Dihedral : 13.213 89.923 11465 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % 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: 1.44 (0.14), residues: 3764 helix: 1.91 (0.14), residues: 1545 sheet: 0.42 (0.22), residues: 563 loop : 0.34 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 95 TYR 0.012 0.001 TYR G 133 PHE 0.018 0.001 PHE G 108 TRP 0.009 0.001 TRP A 119 HIS 0.003 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00337 (30114) covalent geometry : angle 0.54869 (40813) hydrogen bonds : bond 0.15663 ( 1298) hydrogen bonds : angle 5.78055 ( 3702) Misc. bond : bond 0.05579 ( 1) *********************** 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 569 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 569 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8047 (mt0) cc_final: 0.7757 (mt0) REVERT: A 8 LYS cc_start: 0.8361 (tttm) cc_final: 0.8014 (tttm) REVERT: A 20 LEU cc_start: 0.8005 (tp) cc_final: 0.7798 (tp) REVERT: A 114 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7223 (mm-30) REVERT: A 122 MET cc_start: 0.7194 (mtp) cc_final: 0.6890 (mtp) REVERT: A 124 LYS cc_start: 0.7205 (mtmm) cc_final: 0.6876 (mptt) REVERT: A 130 ARG cc_start: 0.7557 (ttm110) cc_final: 0.6633 (ptp90) REVERT: A 134 VAL cc_start: 0.8467 (m) cc_final: 0.8249 (t) REVERT: A 161 LYS cc_start: 0.8131 (mmtm) cc_final: 0.7835 (mmtt) REVERT: A 209 MET cc_start: 0.7308 (mtp) cc_final: 0.6944 (mtt) REVERT: A 220 MET cc_start: 0.7174 (tpt) cc_final: 0.6452 (tpt) REVERT: A 261 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6585 (mt-10) REVERT: A 391 MET cc_start: 0.8102 (mmt) cc_final: 0.7843 (mmt) REVERT: A 456 GLU cc_start: 0.6347 (mt-10) cc_final: 0.5989 (mt-10) REVERT: A 466 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6419 (mp0) REVERT: A 491 ARG cc_start: 0.6498 (mmt180) cc_final: 0.5353 (mtm110) REVERT: A 493 ASP cc_start: 0.7526 (m-30) cc_final: 0.7296 (m-30) REVERT: A 537 ASP cc_start: 0.6489 (t0) cc_final: 0.5783 (m-30) REVERT: A 540 LEU cc_start: 0.6395 (mt) cc_final: 0.6102 (mt) REVERT: A 546 GLU cc_start: 0.5750 (pp20) cc_final: 0.5545 (tm-30) REVERT: B 29 LYS cc_start: 0.7631 (mtpt) cc_final: 0.7137 (mtmm) REVERT: B 114 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7243 (mp0) REVERT: B 122 MET cc_start: 0.8085 (mtm) cc_final: 0.7795 (mtp) REVERT: B 130 ARG cc_start: 0.6730 (mtm110) cc_final: 0.6103 (mtp85) REVERT: B 176 GLU cc_start: 0.7509 (mm-30) cc_final: 0.6644 (pt0) REVERT: B 183 MET cc_start: 0.8786 (mtt) cc_final: 0.8472 (mtt) REVERT: B 197 ARG cc_start: 0.7797 (ttp-110) cc_final: 0.7584 (ttp80) REVERT: B 220 MET cc_start: 0.7283 (ttp) cc_final: 0.6771 (tpp) REVERT: B 248 ASP cc_start: 0.6899 (m-30) cc_final: 0.6653 (m-30) REVERT: B 401 ARG cc_start: 0.7536 (ttm170) cc_final: 0.7293 (mmm-85) REVERT: B 425 ASN cc_start: 0.7291 (m110) cc_final: 0.7056 (m-40) REVERT: B 460 ARG cc_start: 0.5711 (mtp180) cc_final: 0.5505 (mtp-110) REVERT: B 477 GLN cc_start: 0.4426 (pp30) cc_final: 0.3551 (mm110) REVERT: B 485 GLU cc_start: 0.6052 (mm-30) cc_final: 0.4730 (tp30) REVERT: B 558 GLU cc_start: 0.6376 (tt0) cc_final: 0.5960 (mm-30) REVERT: C 1 MET cc_start: 0.5734 (mpp) cc_final: 0.5108 (tpt) REVERT: C 56 SER cc_start: 0.7734 (m) cc_final: 0.7233 (p) REVERT: C 128 GLU cc_start: 0.6674 (tp30) cc_final: 0.6276 (mm-30) REVERT: C 130 ARG cc_start: 0.6973 (ttp-110) cc_final: 0.6617 (mtm-85) REVERT: C 158 LYS cc_start: 0.8165 (ttpp) cc_final: 0.7613 (ttmt) REVERT: C 209 MET cc_start: 0.7674 (mtp) cc_final: 0.7209 (mtm) REVERT: C 220 MET cc_start: 0.7703 (mmt) cc_final: 0.7447 (mmt) REVERT: C 344 MET cc_start: 0.7739 (ttm) cc_final: 0.7010 (ttt) REVERT: C 410 ASP cc_start: 0.7732 (t0) cc_final: 0.7525 (t70) REVERT: C 416 ARG cc_start: 0.7389 (ptm-80) cc_final: 0.6761 (mmt90) REVERT: C 424 TRP cc_start: 0.7406 (p90) cc_final: 0.6668 (p-90) REVERT: C 456 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6087 (tp30) REVERT: C 459 GLN cc_start: 0.7152 (mt0) cc_final: 0.6812 (mt0) REVERT: C 524 LYS cc_start: 0.6587 (ttmm) cc_final: 0.6226 (tppp) REVERT: C 541 GLN cc_start: 0.6705 (mp-120) cc_final: 0.6268 (mt0) REVERT: C 546 GLU cc_start: 0.7165 (tp30) cc_final: 0.6811 (tp30) REVERT: C 550 ARG cc_start: 0.7158 (mmt180) cc_final: 0.6676 (mmt180) REVERT: C 568 LYS cc_start: 0.6367 (mttt) cc_final: 0.5959 (mtpp) REVERT: D 5 LYS cc_start: 0.5758 (mmtt) cc_final: 0.4855 (tttp) REVERT: D 36 LYS cc_start: 0.7654 (ttpp) cc_final: 0.7430 (ttpt) REVERT: D 62 GLU cc_start: 0.7197 (tp30) cc_final: 0.6155 (pm20) REVERT: D 67 ASP cc_start: 0.6931 (p0) cc_final: 0.6465 (p0) REVERT: D 86 LYS cc_start: 0.7781 (mtmm) cc_final: 0.7544 (mtpp) REVERT: D 206 GLN cc_start: 0.6620 (tp40) cc_final: 0.6378 (mm-40) REVERT: D 269 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6575 (mt-10) REVERT: D 274 ARG cc_start: 0.6943 (mtt180) cc_final: 0.6732 (mtt180) REVERT: D 302 GLU cc_start: 0.7443 (tt0) cc_final: 0.7117 (tt0) REVERT: D 410 ARG cc_start: 0.6638 (ttm170) cc_final: 0.6339 (mtt180) REVERT: D 413 GLN cc_start: 0.6555 (mt0) cc_final: 0.6304 (mp10) REVERT: D 456 LYS cc_start: 0.6977 (tppt) cc_final: 0.6606 (mmtm) REVERT: D 461 LYS cc_start: 0.7011 (tttm) cc_final: 0.6530 (ttpt) REVERT: E 6 LYS cc_start: 0.7077 (tttt) cc_final: 0.6754 (tttm) REVERT: E 25 LYS cc_start: 0.7637 (mtmm) cc_final: 0.6994 (mppt) REVERT: E 96 ILE cc_start: 0.7760 (tp) cc_final: 0.7546 (tt) REVERT: E 210 ARG cc_start: 0.7516 (ttp80) cc_final: 0.7141 (ttp-170) REVERT: E 290 ASP cc_start: 0.7767 (t70) cc_final: 0.7468 (t70) REVERT: E 368 LYS cc_start: 0.7376 (mtpt) cc_final: 0.7063 (mptt) REVERT: E 380 ASP cc_start: 0.6780 (m-30) cc_final: 0.6179 (m-30) REVERT: E 409 ARG cc_start: 0.6522 (ttm-80) cc_final: 0.6126 (mtm110) REVERT: E 437 GLN cc_start: 0.7488 (tt0) cc_final: 0.7256 (tt0) REVERT: F 7 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6337 (mm-30) REVERT: F 36 LYS cc_start: 0.7411 (ttpt) cc_final: 0.6916 (ttmt) REVERT: F 54 TYR cc_start: 0.8075 (p90) cc_final: 0.7752 (p90) REVERT: F 81 ARG cc_start: 0.7600 (mtt-85) cc_final: 0.7317 (mtt90) REVERT: F 96 ILE cc_start: 0.7769 (pt) cc_final: 0.7416 (pt) REVERT: F 162 GLU cc_start: 0.7095 (mp0) cc_final: 0.6867 (mt-10) REVERT: F 200 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6406 (mt-10) REVERT: F 206 GLN cc_start: 0.6575 (mt0) cc_final: 0.6185 (mp10) REVERT: F 280 ARG cc_start: 0.7666 (mtt180) cc_final: 0.6512 (mtm110) REVERT: F 302 GLU cc_start: 0.7658 (tt0) cc_final: 0.7448 (tt0) REVERT: F 305 LYS cc_start: 0.7268 (mmtm) cc_final: 0.6887 (mtmt) REVERT: F 318 ASP cc_start: 0.6578 (t0) cc_final: 0.6275 (t70) REVERT: F 401 GLU cc_start: 0.6252 (tt0) cc_final: 0.5738 (tp30) REVERT: F 455 SER cc_start: 0.7693 (t) cc_final: 0.7352 (p) REVERT: F 461 LYS cc_start: 0.7339 (tttp) cc_final: 0.7102 (ttmm) REVERT: F 466 LYS cc_start: 0.6875 (mtmm) cc_final: 0.6161 (ttmm) REVERT: G 14 ARG cc_start: 0.6436 (mmp-170) cc_final: 0.5872 (mmt180) REVERT: G 39 PHE cc_start: 0.5382 (t80) cc_final: 0.5151 (t80) REVERT: G 144 GLU cc_start: 0.4629 (tm-30) cc_final: 0.4404 (tt0) REVERT: G 153 GLU cc_start: 0.4755 (mm-30) cc_final: 0.4472 (tp30) REVERT: G 155 LYS cc_start: 0.6043 (mttt) cc_final: 0.5809 (ttpt) REVERT: G 185 GLN cc_start: 0.6093 (tp40) cc_final: 0.5594 (tp40) REVERT: J 88 ARG cc_start: 0.4232 (ppt170) cc_final: 0.3989 (ttp-170) REVERT: J 99 GLU cc_start: 0.2831 (mp0) cc_final: 0.1629 (tp30) REVERT: J 161 THR cc_start: 0.7016 (p) cc_final: 0.6556 (p) REVERT: L 72 ARG cc_start: 0.5326 (ttp-170) cc_final: 0.5089 (ttt-90) REVERT: L 128 LEU cc_start: 0.4664 (pp) cc_final: 0.4000 (mt) outliers start: 0 outliers final: 0 residues processed: 569 average time/residue: 0.2485 time to fit residues: 206.3261 Evaluate side-chains 391 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS F 23 ASN F 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.134266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.099108 restraints weight = 38415.795| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.47 r_work: 0.2836 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30115 Z= 0.139 Angle : 0.551 10.962 40813 Z= 0.283 Chirality : 0.044 0.167 4572 Planarity : 0.005 0.047 5333 Dihedral : 6.204 89.716 4259 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.75 % Allowed : 6.26 % Favored : 92.99 % 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: 1.30 (0.14), residues: 3764 helix: 1.80 (0.14), residues: 1571 sheet: 0.38 (0.22), residues: 580 loop : 0.21 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 32 TYR 0.012 0.001 TYR G 133 PHE 0.017 0.002 PHE C 230 TRP 0.016 0.001 TRP A 119 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00321 (30114) covalent geometry : angle 0.55056 (40813) hydrogen bonds : bond 0.05123 ( 1298) hydrogen bonds : angle 4.65382 ( 3702) Misc. bond : bond 0.00403 ( 1) *********************** 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 428 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 405 time to evaluate : 1.125 Fit side-chains REVERT: A 3 GLN cc_start: 0.8502 (mt0) cc_final: 0.8291 (mt0) REVERT: A 20 LEU cc_start: 0.8356 (tp) cc_final: 0.7964 (tp) REVERT: A 124 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7490 (mptt) REVERT: A 209 MET cc_start: 0.8393 (mtp) cc_final: 0.8184 (mtt) REVERT: A 393 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6963 (pp20) REVERT: A 456 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7290 (mt-10) REVERT: A 491 ARG cc_start: 0.7518 (mmt180) cc_final: 0.6668 (mtm110) REVERT: A 546 GLU cc_start: 0.6389 (pp20) cc_final: 0.6148 (tm-30) REVERT: A 557 GLU cc_start: 0.7013 (pp20) cc_final: 0.6513 (mp0) REVERT: B 130 ARG cc_start: 0.7592 (mtm110) cc_final: 0.7132 (mtp85) REVERT: B 176 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6808 (pt0) REVERT: B 183 MET cc_start: 0.9031 (mtt) cc_final: 0.8696 (mtt) REVERT: B 240 SER cc_start: 0.7971 (OUTLIER) cc_final: 0.7742 (p) REVERT: B 477 GLN cc_start: 0.4812 (pp30) cc_final: 0.3963 (mm-40) REVERT: B 485 GLU cc_start: 0.6717 (mm-30) cc_final: 0.5178 (tp30) REVERT: B 558 GLU cc_start: 0.6786 (tt0) cc_final: 0.6467 (tp30) REVERT: C 1 MET cc_start: 0.7136 (mpp) cc_final: 0.6304 (tpt) REVERT: C 128 GLU cc_start: 0.7177 (tp30) cc_final: 0.6868 (mm-30) REVERT: C 130 ARG cc_start: 0.7763 (ttp-110) cc_final: 0.7555 (mtm-85) REVERT: C 424 TRP cc_start: 0.8070 (p90) cc_final: 0.7633 (p-90) REVERT: C 456 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7781 (tp30) REVERT: C 541 GLN cc_start: 0.7096 (mp-120) cc_final: 0.6651 (mt0) REVERT: C 546 GLU cc_start: 0.7681 (tp30) cc_final: 0.7407 (tp30) REVERT: C 550 ARG cc_start: 0.8302 (mmt180) cc_final: 0.7951 (mmt180) REVERT: C 568 LYS cc_start: 0.7425 (mttt) cc_final: 0.6894 (mtpp) REVERT: C 569 GLU cc_start: 0.7301 (tt0) cc_final: 0.6995 (mt-10) REVERT: D 62 GLU cc_start: 0.7438 (tp30) cc_final: 0.6823 (pm20) REVERT: D 206 GLN cc_start: 0.7893 (tp40) cc_final: 0.7599 (mm-40) REVERT: D 269 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7483 (mt-10) REVERT: D 274 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7865 (mtt180) REVERT: D 445 MET cc_start: 0.7970 (mtp) cc_final: 0.7503 (mtp) REVERT: D 461 LYS cc_start: 0.7861 (tttm) cc_final: 0.7423 (ttpt) REVERT: E 25 LYS cc_start: 0.7787 (mtmm) cc_final: 0.7327 (mmtt) REVERT: E 210 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7726 (ttp-170) REVERT: E 380 ASP cc_start: 0.8133 (m-30) cc_final: 0.7693 (m-30) REVERT: E 409 ARG cc_start: 0.7008 (ttm-80) cc_final: 0.6582 (mtt-85) REVERT: F 7 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7742 (mm-30) REVERT: F 81 ARG cc_start: 0.8605 (mtt-85) cc_final: 0.8322 (mtt90) REVERT: F 96 ILE cc_start: 0.8282 (pt) cc_final: 0.7984 (pt) REVERT: F 206 GLN cc_start: 0.7960 (mt0) cc_final: 0.7710 (mp10) REVERT: F 280 ARG cc_start: 0.8721 (mtt180) cc_final: 0.7726 (mtm110) REVERT: F 455 SER cc_start: 0.8559 (t) cc_final: 0.8241 (p) REVERT: G 14 ARG cc_start: 0.7876 (mmp-170) cc_final: 0.7274 (mmt180) REVERT: G 23 LYS cc_start: 0.7462 (mtpp) cc_final: 0.6905 (mmmt) REVERT: G 38 GLU cc_start: 0.6339 (tt0) cc_final: 0.5473 (tp30) REVERT: G 39 PHE cc_start: 0.6865 (t80) cc_final: 0.6641 (t80) REVERT: G 45 GLU cc_start: 0.5349 (tp30) cc_final: 0.5149 (tp30) REVERT: G 155 LYS cc_start: 0.6875 (mttt) cc_final: 0.6635 (ttpt) REVERT: G 185 GLN cc_start: 0.7738 (tp40) cc_final: 0.7377 (tp40) REVERT: J 85 ARG cc_start: 0.4697 (mtp180) cc_final: 0.4368 (ptp-170) REVERT: J 88 ARG cc_start: 0.4300 (ppt170) cc_final: 0.4095 (ttp-170) REVERT: J 145 GLU cc_start: 0.4236 (tm-30) cc_final: 0.4002 (tm-30) REVERT: L 72 ARG cc_start: 0.6113 (ttp-170) cc_final: 0.5901 (ttt-90) REVERT: L 78 GLU cc_start: 0.6111 (mt-10) cc_final: 0.5822 (tt0) outliers start: 23 outliers final: 13 residues processed: 416 average time/residue: 0.2464 time to fit residues: 150.4620 Evaluate side-chains 369 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 354 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain J residue 167 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 49 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 270 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 307 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN C 283 HIS ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN F 23 ASN F 323 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.130860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.096097 restraints weight = 38738.740| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.70 r_work: 0.2760 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 30115 Z= 0.258 Angle : 0.677 9.841 40813 Z= 0.350 Chirality : 0.050 0.218 4572 Planarity : 0.006 0.060 5333 Dihedral : 6.594 88.773 4259 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.91 % Allowed : 8.89 % Favored : 89.20 % 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: 0.60 (0.14), residues: 3764 helix: 1.26 (0.13), residues: 1565 sheet: -0.00 (0.22), residues: 579 loop : -0.19 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 105 TYR 0.019 0.002 TYR H 89 PHE 0.021 0.003 PHE C 230 TRP 0.020 0.002 TRP A 119 HIS 0.013 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00640 (30114) covalent geometry : angle 0.67665 (40813) hydrogen bonds : bond 0.06366 ( 1298) hydrogen bonds : angle 4.82718 ( 3702) Misc. bond : bond 0.00018 ( 1) *********************** 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 401 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 342 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6375 (mmt) cc_final: 0.4678 (ptp) REVERT: A 3 GLN cc_start: 0.8631 (mt0) cc_final: 0.8375 (mt0) REVERT: A 20 LEU cc_start: 0.8478 (tp) cc_final: 0.8102 (tp) REVERT: A 124 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7396 (mmtm) REVERT: A 393 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7045 (pp20) REVERT: A 456 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7280 (mt-10) REVERT: A 491 ARG cc_start: 0.7565 (mmt180) cc_final: 0.6998 (ttp-110) REVERT: A 546 GLU cc_start: 0.6457 (pp20) cc_final: 0.6141 (tm-30) REVERT: B 48 PHE cc_start: 0.8500 (m-80) cc_final: 0.8263 (m-80) REVERT: B 130 ARG cc_start: 0.7732 (mtm110) cc_final: 0.7285 (mtp85) REVERT: B 147 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8995 (mp) REVERT: B 154 ARG cc_start: 0.7776 (mtm110) cc_final: 0.7090 (mtt90) REVERT: B 240 SER cc_start: 0.8013 (OUTLIER) cc_final: 0.7809 (p) REVERT: B 329 ARG cc_start: 0.8207 (mmt-90) cc_final: 0.7910 (mmp80) REVERT: B 341 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7848 (mp) REVERT: B 409 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7248 (tp) REVERT: B 477 GLN cc_start: 0.4758 (pp30) cc_final: 0.3842 (mm-40) REVERT: B 485 GLU cc_start: 0.6815 (mm-30) cc_final: 0.5289 (pt0) REVERT: B 509 MET cc_start: 0.7764 (mmp) cc_final: 0.7394 (mmt) REVERT: B 558 GLU cc_start: 0.6688 (tt0) cc_final: 0.6366 (mt-10) REVERT: C 1 MET cc_start: 0.7321 (mpp) cc_final: 0.6338 (mmm) REVERT: C 130 ARG cc_start: 0.7865 (ttp-110) cc_final: 0.7596 (mtm-85) REVERT: C 424 TRP cc_start: 0.8133 (p90) cc_final: 0.7624 (p-90) REVERT: C 456 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7759 (tp30) REVERT: C 541 GLN cc_start: 0.7186 (mp-120) cc_final: 0.6876 (mt0) REVERT: C 546 GLU cc_start: 0.7635 (tp30) cc_final: 0.7344 (tp30) REVERT: C 550 ARG cc_start: 0.8344 (mmt180) cc_final: 0.7907 (mmt180) REVERT: D 206 GLN cc_start: 0.7854 (tp40) cc_final: 0.7187 (pp30) REVERT: D 269 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7644 (mt-10) REVERT: D 461 LYS cc_start: 0.7793 (tttm) cc_final: 0.7299 (ttpt) REVERT: E 25 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7496 (mppt) REVERT: E 380 ASP cc_start: 0.8229 (m-30) cc_final: 0.7816 (m-30) REVERT: F 7 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7634 (mm-30) REVERT: F 96 ILE cc_start: 0.8202 (pt) cc_final: 0.7916 (pt) REVERT: F 206 GLN cc_start: 0.7937 (mt0) cc_final: 0.7648 (mp10) REVERT: F 280 ARG cc_start: 0.8726 (mtt180) cc_final: 0.7632 (mtm110) REVERT: F 455 SER cc_start: 0.8684 (t) cc_final: 0.8418 (m) REVERT: G 9 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7024 (mtp) REVERT: G 14 ARG cc_start: 0.7909 (mmp-170) cc_final: 0.7248 (mmt180) REVERT: G 39 PHE cc_start: 0.6912 (t80) cc_final: 0.6682 (t80) REVERT: G 45 GLU cc_start: 0.5368 (tp30) cc_final: 0.5051 (tp30) REVERT: G 155 LYS cc_start: 0.6819 (mttt) cc_final: 0.6489 (ttpt) REVERT: G 185 GLN cc_start: 0.7844 (tp40) cc_final: 0.7464 (tp40) REVERT: H 103 LYS cc_start: 0.4493 (tttm) cc_final: 0.3700 (pttp) REVERT: J 85 ARG cc_start: 0.4636 (mtp180) cc_final: 0.4265 (ptp-170) REVERT: J 88 ARG cc_start: 0.4359 (ppt170) cc_final: 0.4155 (ttp-110) REVERT: L 72 ARG cc_start: 0.6113 (ttp-170) cc_final: 0.5878 (ttt-90) outliers start: 59 outliers final: 39 residues processed: 380 average time/residue: 0.2414 time to fit residues: 134.9151 Evaluate side-chains 374 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 329 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 28 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 167 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 260 optimal weight: 8.9990 chunk 206 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 293 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 311 optimal weight: 0.0060 chunk 86 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 342 optimal weight: 7.9990 chunk 239 optimal weight: 4.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 397 GLN A 541 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.134954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.100398 restraints weight = 38110.500| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.40 r_work: 0.2838 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30115 Z= 0.112 Angle : 0.500 10.210 40813 Z= 0.258 Chirality : 0.043 0.162 4572 Planarity : 0.004 0.048 5333 Dihedral : 6.003 84.682 4259 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.27 % Allowed : 9.96 % Favored : 88.78 % 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: 1.04 (0.14), residues: 3764 helix: 1.69 (0.14), residues: 1564 sheet: 0.21 (0.22), residues: 580 loop : -0.04 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 547 TYR 0.013 0.001 TYR G 133 PHE 0.015 0.001 PHE A 230 TRP 0.011 0.001 TRP C 119 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00249 (30114) covalent geometry : angle 0.49974 (40813) hydrogen bonds : bond 0.04318 ( 1298) hydrogen bonds : angle 4.39872 ( 3702) Misc. bond : bond 0.00004 ( 1) *********************** 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 396 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 357 time to evaluate : 1.080 Fit side-chains REVERT: A 1 MET cc_start: 0.6301 (mmt) cc_final: 0.4767 (ptp) REVERT: A 3 GLN cc_start: 0.8453 (mt0) cc_final: 0.8229 (mt0) REVERT: A 20 LEU cc_start: 0.8484 (tp) cc_final: 0.8110 (tp) REVERT: A 28 CYS cc_start: 0.8600 (m) cc_final: 0.8389 (m) REVERT: A 124 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7396 (mmtm) REVERT: A 183 MET cc_start: 0.9063 (mtt) cc_final: 0.8561 (mtt) REVERT: A 393 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6891 (pp20) REVERT: A 456 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7271 (mt-10) REVERT: A 491 ARG cc_start: 0.7533 (mmt180) cc_final: 0.7025 (ttp-110) REVERT: A 537 ASP cc_start: 0.6763 (t70) cc_final: 0.6382 (m-30) REVERT: A 546 GLU cc_start: 0.6377 (pp20) cc_final: 0.6105 (tm-30) REVERT: B 48 PHE cc_start: 0.8479 (m-80) cc_final: 0.8167 (m-80) REVERT: B 108 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8180 (t) REVERT: B 130 ARG cc_start: 0.7642 (mtm110) cc_final: 0.7223 (mtp85) REVERT: B 154 ARG cc_start: 0.7601 (mtm110) cc_final: 0.6966 (mtt90) REVERT: B 329 ARG cc_start: 0.7976 (mmt-90) cc_final: 0.7679 (mmp80) REVERT: B 341 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7732 (mp) REVERT: B 465 GLN cc_start: 0.6349 (mm-40) cc_final: 0.5523 (mm-40) REVERT: B 477 GLN cc_start: 0.4775 (pp30) cc_final: 0.3932 (mm-40) REVERT: B 481 ARG cc_start: 0.6483 (mtp180) cc_final: 0.6010 (mtp-110) REVERT: B 485 GLU cc_start: 0.6711 (mm-30) cc_final: 0.5162 (tp30) REVERT: B 509 MET cc_start: 0.7669 (mmp) cc_final: 0.7370 (mmt) REVERT: B 558 GLU cc_start: 0.6606 (tt0) cc_final: 0.6324 (mt-10) REVERT: C 1 MET cc_start: 0.7307 (mpp) cc_final: 0.6356 (mmm) REVERT: C 424 TRP cc_start: 0.8097 (p90) cc_final: 0.7621 (p-90) REVERT: C 456 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7770 (tp30) REVERT: C 541 GLN cc_start: 0.6979 (mp-120) cc_final: 0.6773 (mt0) REVERT: C 546 GLU cc_start: 0.7561 (tp30) cc_final: 0.7318 (tp30) REVERT: C 550 ARG cc_start: 0.8297 (mmt180) cc_final: 0.7966 (mmt180) REVERT: C 568 LYS cc_start: 0.7431 (mttt) cc_final: 0.6994 (mtpp) REVERT: D 206 GLN cc_start: 0.7874 (tp40) cc_final: 0.7498 (mm-40) REVERT: D 269 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7526 (mt-10) REVERT: D 461 LYS cc_start: 0.7839 (tttm) cc_final: 0.7379 (ttpt) REVERT: E 25 LYS cc_start: 0.7760 (mtmm) cc_final: 0.7398 (mppt) REVERT: E 334 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: E 380 ASP cc_start: 0.8067 (m-30) cc_final: 0.7612 (m-30) REVERT: E 409 ARG cc_start: 0.7049 (ttm-80) cc_final: 0.6570 (mtt-85) REVERT: F 7 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7616 (mm-30) REVERT: F 206 GLN cc_start: 0.7904 (mt0) cc_final: 0.7642 (mp10) REVERT: F 280 ARG cc_start: 0.8739 (mtt180) cc_final: 0.7588 (mtm110) REVERT: F 455 SER cc_start: 0.8609 (t) cc_final: 0.8222 (p) REVERT: G 14 ARG cc_start: 0.7853 (mmp-170) cc_final: 0.7253 (mmt180) REVERT: G 45 GLU cc_start: 0.5332 (tp30) cc_final: 0.5067 (tp30) REVERT: G 155 LYS cc_start: 0.6776 (mttt) cc_final: 0.6541 (ttpt) REVERT: G 177 ARG cc_start: 0.7494 (ttp80) cc_final: 0.6820 (mtm-85) REVERT: G 185 GLN cc_start: 0.7692 (tp40) cc_final: 0.7323 (tp40) REVERT: G 190 ASP cc_start: 0.7911 (m-30) cc_final: 0.7596 (m-30) REVERT: H 103 LYS cc_start: 0.4692 (tttm) cc_final: 0.3726 (pttp) REVERT: J 85 ARG cc_start: 0.4720 (mtp180) cc_final: 0.4352 (ptp-170) REVERT: J 145 GLU cc_start: 0.3913 (tm-30) cc_final: 0.3709 (tm-30) outliers start: 39 outliers final: 24 residues processed: 383 average time/residue: 0.2311 time to fit residues: 131.7948 Evaluate side-chains 354 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 326 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain I residue 115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 44 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 348 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 273 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN L 130 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.097330 restraints weight = 38574.549| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.48 r_work: 0.2790 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 30115 Z= 0.224 Angle : 0.622 9.288 40813 Z= 0.320 Chirality : 0.048 0.206 4572 Planarity : 0.006 0.050 5333 Dihedral : 6.311 87.483 4259 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.11 % Allowed : 10.31 % Favored : 87.58 % 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: 0.62 (0.14), residues: 3764 helix: 1.38 (0.13), residues: 1565 sheet: -0.08 (0.22), residues: 575 loop : -0.27 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 410 TYR 0.019 0.002 TYR E 13 PHE 0.021 0.002 PHE C 230 TRP 0.014 0.002 TRP A 119 HIS 0.011 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00554 (30114) covalent geometry : angle 0.62220 (40813) hydrogen bonds : bond 0.05704 ( 1298) hydrogen bonds : angle 4.63423 ( 3702) Misc. bond : bond 0.00024 ( 1) *********************** 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 393 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 328 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6411 (mmt) cc_final: 0.4638 (ptp) REVERT: A 3 GLN cc_start: 0.8551 (mt0) cc_final: 0.8293 (mt0) REVERT: A 20 LEU cc_start: 0.8477 (tp) cc_final: 0.8143 (tp) REVERT: A 28 CYS cc_start: 0.8709 (m) cc_final: 0.8442 (m) REVERT: A 124 LYS cc_start: 0.7977 (mtmm) cc_final: 0.7407 (mmtm) REVERT: A 183 MET cc_start: 0.9066 (mtt) cc_final: 0.8584 (mtt) REVERT: A 393 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7076 (pp20) REVERT: A 456 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7309 (mt-10) REVERT: A 491 ARG cc_start: 0.7540 (mmt180) cc_final: 0.7037 (ttp-110) REVERT: A 546 GLU cc_start: 0.6395 (pp20) cc_final: 0.6108 (tm-30) REVERT: B 48 PHE cc_start: 0.8451 (m-80) cc_final: 0.8110 (m-80) REVERT: B 130 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7278 (mtp85) REVERT: B 154 ARG cc_start: 0.7763 (mtm110) cc_final: 0.7044 (mtt90) REVERT: B 329 ARG cc_start: 0.8179 (mmt-90) cc_final: 0.7865 (mmp80) REVERT: B 341 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7880 (mp) REVERT: B 477 GLN cc_start: 0.4870 (pp30) cc_final: 0.3954 (mm-40) REVERT: B 481 ARG cc_start: 0.6457 (mtp180) cc_final: 0.5891 (mtp-110) REVERT: B 485 GLU cc_start: 0.6842 (mm-30) cc_final: 0.5228 (pt0) REVERT: B 509 MET cc_start: 0.7751 (mmp) cc_final: 0.7417 (mmt) REVERT: B 558 GLU cc_start: 0.6714 (tt0) cc_final: 0.6384 (mt-10) REVERT: C 1 MET cc_start: 0.7311 (mpp) cc_final: 0.6376 (mmm) REVERT: C 292 SER cc_start: 0.8797 (OUTLIER) cc_final: 0.8466 (p) REVERT: C 424 TRP cc_start: 0.8123 (p90) cc_final: 0.7624 (p-90) REVERT: C 456 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7749 (tp30) REVERT: C 541 GLN cc_start: 0.7156 (mp-120) cc_final: 0.6802 (mt0) REVERT: C 546 GLU cc_start: 0.7649 (tp30) cc_final: 0.7351 (tp30) REVERT: C 550 ARG cc_start: 0.8339 (mmt180) cc_final: 0.7981 (mmt180) REVERT: D 206 GLN cc_start: 0.7924 (tp40) cc_final: 0.7587 (mm-40) REVERT: D 269 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7591 (mt-10) REVERT: D 461 LYS cc_start: 0.7794 (tttm) cc_final: 0.7329 (ttpt) REVERT: E 334 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: E 380 ASP cc_start: 0.8180 (m-30) cc_final: 0.7732 (m-30) REVERT: E 409 ARG cc_start: 0.7231 (ttm-80) cc_final: 0.6748 (mtt-85) REVERT: E 468 GLU cc_start: 0.3461 (OUTLIER) cc_final: 0.3225 (pm20) REVERT: F 7 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7610 (mm-30) REVERT: F 206 GLN cc_start: 0.7964 (mt0) cc_final: 0.7694 (mp10) REVERT: F 280 ARG cc_start: 0.8738 (mtt180) cc_final: 0.7580 (mtm110) REVERT: F 455 SER cc_start: 0.8727 (t) cc_final: 0.8409 (m) REVERT: G 14 ARG cc_start: 0.7896 (mmp-170) cc_final: 0.7246 (mmt180) REVERT: G 45 GLU cc_start: 0.5451 (tp30) cc_final: 0.5170 (tp30) REVERT: G 148 LYS cc_start: 0.6275 (pttt) cc_final: 0.5604 (mttt) REVERT: G 155 LYS cc_start: 0.6777 (mttt) cc_final: 0.6432 (ttpt) REVERT: G 160 ARG cc_start: 0.5978 (mmm-85) cc_final: 0.5627 (tpt-90) REVERT: G 177 ARG cc_start: 0.7616 (ttp80) cc_final: 0.7212 (ttp-110) REVERT: G 184 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: G 185 GLN cc_start: 0.7799 (tp40) cc_final: 0.7402 (tp40) REVERT: H 93 LEU cc_start: 0.5179 (mt) cc_final: 0.4699 (mp) REVERT: J 85 ARG cc_start: 0.4617 (mtp180) cc_final: 0.4413 (ptp-170) REVERT: L 94 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5570 (mm) outliers start: 65 outliers final: 52 residues processed: 376 average time/residue: 0.2206 time to fit residues: 124.1980 Evaluate side-chains 378 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 320 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 158 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 296 optimal weight: 0.9990 chunk 242 optimal weight: 7.9990 chunk 240 optimal weight: 0.0170 chunk 257 optimal weight: 7.9990 chunk 361 optimal weight: 7.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN F 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.101064 restraints weight = 38203.478| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.41 r_work: 0.2845 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30115 Z= 0.105 Angle : 0.490 9.737 40813 Z= 0.252 Chirality : 0.042 0.162 4572 Planarity : 0.004 0.049 5333 Dihedral : 5.820 83.923 4259 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.65 % Allowed : 11.29 % Favored : 87.06 % 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: 1.01 (0.14), residues: 3764 helix: 1.73 (0.14), residues: 1573 sheet: 0.19 (0.22), residues: 569 loop : -0.13 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 410 TYR 0.017 0.001 TYR E 13 PHE 0.013 0.001 PHE A 230 TRP 0.012 0.001 TRP D 471 HIS 0.004 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00230 (30114) covalent geometry : angle 0.48967 (40813) hydrogen bonds : bond 0.04116 ( 1298) hydrogen bonds : angle 4.32143 ( 3702) Misc. bond : bond 0.00009 ( 1) *********************** 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 395 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 344 time to evaluate : 1.200 Fit side-chains REVERT: A 1 MET cc_start: 0.6390 (mmt) cc_final: 0.4683 (ptp) REVERT: A 3 GLN cc_start: 0.8453 (mt0) cc_final: 0.8212 (mt0) REVERT: A 20 LEU cc_start: 0.8464 (tp) cc_final: 0.8104 (tp) REVERT: A 28 CYS cc_start: 0.8610 (m) cc_final: 0.8397 (m) REVERT: A 124 LYS cc_start: 0.7948 (mtmm) cc_final: 0.7435 (mmtm) REVERT: A 183 MET cc_start: 0.9033 (mtt) cc_final: 0.8571 (mtt) REVERT: A 393 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7032 (pp20) REVERT: A 456 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7279 (mt-10) REVERT: A 491 ARG cc_start: 0.7527 (mmt180) cc_final: 0.7023 (ttp-110) REVERT: A 530 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7637 (mt) REVERT: A 537 ASP cc_start: 0.6789 (t70) cc_final: 0.6392 (m-30) REVERT: A 546 GLU cc_start: 0.6320 (pp20) cc_final: 0.5905 (tm-30) REVERT: B 48 PHE cc_start: 0.8443 (m-80) cc_final: 0.8085 (m-80) REVERT: B 108 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.8127 (t) REVERT: B 130 ARG cc_start: 0.7664 (mtm110) cc_final: 0.7296 (mtp85) REVERT: B 154 ARG cc_start: 0.7616 (mtm110) cc_final: 0.7003 (mtt90) REVERT: B 220 MET cc_start: 0.8349 (ttp) cc_final: 0.8122 (tpp) REVERT: B 329 ARG cc_start: 0.7974 (mmt-90) cc_final: 0.7663 (mmp80) REVERT: B 341 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7756 (mp) REVERT: B 342 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7639 (mt-10) REVERT: B 477 GLN cc_start: 0.4829 (pp30) cc_final: 0.4042 (mm-40) REVERT: B 481 ARG cc_start: 0.6384 (mtp180) cc_final: 0.6075 (mtp-110) REVERT: B 485 GLU cc_start: 0.6747 (mm-30) cc_final: 0.5172 (tp30) REVERT: B 509 MET cc_start: 0.7629 (mmp) cc_final: 0.7391 (mmt) REVERT: B 558 GLU cc_start: 0.6684 (tt0) cc_final: 0.6360 (mt-10) REVERT: C 1 MET cc_start: 0.7253 (mpp) cc_final: 0.6321 (mmm) REVERT: C 424 TRP cc_start: 0.8078 (p90) cc_final: 0.7580 (p-90) REVERT: C 456 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7770 (tp30) REVERT: C 541 GLN cc_start: 0.7030 (mp-120) cc_final: 0.6763 (mt0) REVERT: C 546 GLU cc_start: 0.7562 (tp30) cc_final: 0.7287 (tp30) REVERT: C 550 ARG cc_start: 0.8279 (mmt180) cc_final: 0.7910 (mmt180) REVERT: D 37 ASP cc_start: 0.8162 (p0) cc_final: 0.7950 (p0) REVERT: D 206 GLN cc_start: 0.7904 (tp40) cc_final: 0.7506 (mm-40) REVERT: D 269 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7517 (mt-10) REVERT: D 461 LYS cc_start: 0.7781 (tttm) cc_final: 0.7300 (ttpt) REVERT: E 380 ASP cc_start: 0.8045 (m-30) cc_final: 0.7595 (m-30) REVERT: E 409 ARG cc_start: 0.7053 (ttm-80) cc_final: 0.6581 (mtt-85) REVERT: E 468 GLU cc_start: 0.3445 (OUTLIER) cc_final: 0.3190 (pm20) REVERT: F 7 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7573 (mm-30) REVERT: F 206 GLN cc_start: 0.7937 (mt0) cc_final: 0.7656 (mp10) REVERT: F 280 ARG cc_start: 0.8737 (mtt180) cc_final: 0.7607 (mtm110) REVERT: F 455 SER cc_start: 0.8615 (t) cc_final: 0.8205 (p) REVERT: G 45 GLU cc_start: 0.5359 (tp30) cc_final: 0.5158 (tp30) REVERT: G 146 ARG cc_start: 0.5552 (mtm180) cc_final: 0.5349 (mtp180) REVERT: G 148 LYS cc_start: 0.6175 (pttt) cc_final: 0.5516 (mttt) REVERT: G 155 LYS cc_start: 0.6780 (mttt) cc_final: 0.6532 (ttpt) REVERT: G 160 ARG cc_start: 0.5981 (mmm-85) cc_final: 0.5776 (tpt-90) REVERT: G 177 ARG cc_start: 0.7490 (ttp80) cc_final: 0.6823 (mtm-85) REVERT: G 185 GLN cc_start: 0.7684 (tp40) cc_final: 0.7322 (tp40) REVERT: G 190 ASP cc_start: 0.7890 (m-30) cc_final: 0.7577 (m-30) REVERT: H 93 LEU cc_start: 0.4945 (mt) cc_final: 0.4524 (mp) REVERT: J 85 ARG cc_start: 0.4556 (mtp180) cc_final: 0.4300 (ptp-170) REVERT: L 74 GLN cc_start: 0.6364 (tt0) cc_final: 0.5955 (mt0) REVERT: L 94 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5584 (mm) outliers start: 51 outliers final: 37 residues processed: 379 average time/residue: 0.2219 time to fit residues: 127.0463 Evaluate side-chains 370 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 328 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 303 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 223 optimal weight: 0.8980 chunk 272 optimal weight: 0.0020 chunk 208 optimal weight: 4.9990 chunk 371 optimal weight: 10.0000 chunk 324 optimal weight: 20.0000 chunk 313 optimal weight: 8.9990 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.101364 restraints weight = 38095.467| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.42 r_work: 0.2852 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30115 Z= 0.106 Angle : 0.491 12.179 40813 Z= 0.250 Chirality : 0.043 0.164 4572 Planarity : 0.004 0.048 5333 Dihedral : 5.656 83.863 4259 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.95 % Allowed : 11.58 % Favored : 86.47 % 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: 1.15 (0.14), residues: 3764 helix: 1.86 (0.14), residues: 1581 sheet: 0.24 (0.22), residues: 569 loop : -0.06 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 460 TYR 0.018 0.001 TYR E 13 PHE 0.012 0.001 PHE B 559 TRP 0.011 0.001 TRP C 119 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00241 (30114) covalent geometry : angle 0.49065 (40813) hydrogen bonds : bond 0.03980 ( 1298) hydrogen bonds : angle 4.23715 ( 3702) Misc. bond : bond 0.00022 ( 1) *********************** 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 388 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 328 time to evaluate : 1.181 Fit side-chains REVERT: A 1 MET cc_start: 0.6396 (mmt) cc_final: 0.4679 (ptp) REVERT: A 3 GLN cc_start: 0.8473 (mt0) cc_final: 0.8242 (mt0) REVERT: A 20 LEU cc_start: 0.8500 (tp) cc_final: 0.8098 (tp) REVERT: A 28 CYS cc_start: 0.8595 (m) cc_final: 0.8382 (m) REVERT: A 124 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7453 (mmtm) REVERT: A 183 MET cc_start: 0.9008 (mtt) cc_final: 0.8551 (mtt) REVERT: A 393 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6945 (pp20) REVERT: A 456 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7289 (mt-10) REVERT: A 491 ARG cc_start: 0.7504 (mmt180) cc_final: 0.7021 (ttp-110) REVERT: A 530 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7670 (mt) REVERT: A 537 ASP cc_start: 0.6794 (t70) cc_final: 0.6384 (m-30) REVERT: A 546 GLU cc_start: 0.6296 (pp20) cc_final: 0.5901 (tm-30) REVERT: B 48 PHE cc_start: 0.8453 (m-80) cc_final: 0.8088 (m-80) REVERT: B 108 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8109 (t) REVERT: B 130 ARG cc_start: 0.7649 (mtm110) cc_final: 0.7275 (mtp85) REVERT: B 154 ARG cc_start: 0.7625 (mtm110) cc_final: 0.6978 (mtt90) REVERT: B 220 MET cc_start: 0.8346 (ttp) cc_final: 0.8142 (tpp) REVERT: B 329 ARG cc_start: 0.8025 (mmt-90) cc_final: 0.7715 (mmp80) REVERT: B 341 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7742 (mp) REVERT: B 342 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7669 (mt-10) REVERT: B 409 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7034 (tp) REVERT: B 477 GLN cc_start: 0.4810 (pp30) cc_final: 0.3985 (mm-40) REVERT: B 481 ARG cc_start: 0.6437 (mtp180) cc_final: 0.6116 (mtp-110) REVERT: B 485 GLU cc_start: 0.6816 (mm-30) cc_final: 0.5407 (tm-30) REVERT: B 509 MET cc_start: 0.7594 (mmp) cc_final: 0.7364 (mmt) REVERT: B 558 GLU cc_start: 0.6689 (tt0) cc_final: 0.6426 (mt-10) REVERT: C 1 MET cc_start: 0.7229 (mpp) cc_final: 0.6353 (mmm) REVERT: C 292 SER cc_start: 0.8795 (OUTLIER) cc_final: 0.8382 (p) REVERT: C 424 TRP cc_start: 0.8052 (p90) cc_final: 0.7573 (p-90) REVERT: C 456 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7759 (tp30) REVERT: C 541 GLN cc_start: 0.6912 (mp-120) cc_final: 0.6608 (mt0) REVERT: C 546 GLU cc_start: 0.7580 (tp30) cc_final: 0.7293 (tp30) REVERT: C 550 ARG cc_start: 0.8319 (mmt180) cc_final: 0.7930 (mmt180) REVERT: D 206 GLN cc_start: 0.7896 (tp40) cc_final: 0.7535 (mm-40) REVERT: D 269 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7548 (mt-10) REVERT: D 461 LYS cc_start: 0.7782 (tttm) cc_final: 0.7308 (ttpt) REVERT: E 380 ASP cc_start: 0.8047 (m-30) cc_final: 0.7599 (m-30) REVERT: E 409 ARG cc_start: 0.7057 (ttm-80) cc_final: 0.6625 (mtt-85) REVERT: E 468 GLU cc_start: 0.3415 (OUTLIER) cc_final: 0.3158 (pm20) REVERT: F 7 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7596 (mm-30) REVERT: F 200 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7635 (mp0) REVERT: F 206 GLN cc_start: 0.7963 (mt0) cc_final: 0.7691 (mp10) REVERT: F 280 ARG cc_start: 0.8739 (mtt180) cc_final: 0.7542 (mtm110) REVERT: F 455 SER cc_start: 0.8647 (t) cc_final: 0.8231 (p) REVERT: G 45 GLU cc_start: 0.5469 (tp30) cc_final: 0.5259 (tp30) REVERT: G 148 LYS cc_start: 0.6026 (pttt) cc_final: 0.5384 (mttt) REVERT: G 155 LYS cc_start: 0.6770 (mttt) cc_final: 0.6540 (ttpt) REVERT: G 177 ARG cc_start: 0.7442 (ttp80) cc_final: 0.6774 (mtm-85) REVERT: G 185 GLN cc_start: 0.7679 (tp40) cc_final: 0.7309 (tp40) REVERT: J 85 ARG cc_start: 0.4539 (mtp180) cc_final: 0.4228 (ptp-170) REVERT: J 164 GLU cc_start: 0.6924 (tp30) cc_final: 0.6339 (tp30) REVERT: L 74 GLN cc_start: 0.6457 (tt0) cc_final: 0.5989 (mt0) REVERT: L 94 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5588 (mm) outliers start: 60 outliers final: 40 residues processed: 372 average time/residue: 0.2277 time to fit residues: 128.0208 Evaluate side-chains 368 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 321 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 316 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 327 optimal weight: 0.9990 chunk 310 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 330 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 347 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.133623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.098717 restraints weight = 38514.520| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.66 r_work: 0.2801 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30115 Z= 0.146 Angle : 0.542 16.947 40813 Z= 0.276 Chirality : 0.044 0.165 4572 Planarity : 0.005 0.048 5333 Dihedral : 5.827 85.551 4259 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.27 % Allowed : 11.61 % Favored : 86.12 % 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: 1.75 (0.13), residues: 1572 sheet: 0.02 (0.21), residues: 602 loop : -0.12 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 44 TYR 0.019 0.001 TYR E 13 PHE 0.018 0.002 PHE C 230 TRP 0.011 0.001 TRP A 119 HIS 0.007 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00350 (30114) covalent geometry : angle 0.54221 (40813) hydrogen bonds : bond 0.04624 ( 1298) hydrogen bonds : angle 4.36741 ( 3702) Misc. bond : bond 0.00027 ( 1) *********************** 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 394 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 324 time to evaluate : 1.081 Fit side-chains REVERT: A 1 MET cc_start: 0.6380 (mmt) cc_final: 0.4988 (pmm) REVERT: A 20 LEU cc_start: 0.8480 (tp) cc_final: 0.8265 (tp) REVERT: A 28 CYS cc_start: 0.8717 (m) cc_final: 0.8497 (m) REVERT: A 124 LYS cc_start: 0.7946 (mtmm) cc_final: 0.7391 (mmtp) REVERT: A 183 MET cc_start: 0.9067 (mtt) cc_final: 0.8626 (mtt) REVERT: A 393 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7043 (pp20) REVERT: A 456 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7345 (mt-10) REVERT: A 491 ARG cc_start: 0.7521 (mmt180) cc_final: 0.6986 (ttp-110) REVERT: A 530 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7614 (mt) REVERT: A 537 ASP cc_start: 0.6830 (t70) cc_final: 0.6372 (m-30) REVERT: A 542 LEU cc_start: 0.6452 (mt) cc_final: 0.6238 (mt) REVERT: A 546 GLU cc_start: 0.6345 (pp20) cc_final: 0.5923 (tm-30) REVERT: B 108 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.8108 (t) REVERT: B 130 ARG cc_start: 0.7580 (mtm110) cc_final: 0.7153 (mtp85) REVERT: B 154 ARG cc_start: 0.7690 (mtm110) cc_final: 0.6988 (mtt90) REVERT: B 220 MET cc_start: 0.8370 (ttp) cc_final: 0.8133 (tpp) REVERT: B 329 ARG cc_start: 0.8104 (mmt-90) cc_final: 0.7807 (mmp80) REVERT: B 341 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7847 (mp) REVERT: B 342 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7721 (mt-10) REVERT: B 409 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7175 (tp) REVERT: B 477 GLN cc_start: 0.4781 (pp30) cc_final: 0.4120 (mm-40) REVERT: B 481 ARG cc_start: 0.6348 (mtp180) cc_final: 0.5977 (mtp-110) REVERT: B 485 GLU cc_start: 0.6820 (mm-30) cc_final: 0.5192 (pt0) REVERT: B 509 MET cc_start: 0.7609 (mmp) cc_final: 0.7366 (mmt) REVERT: B 558 GLU cc_start: 0.6673 (tt0) cc_final: 0.6302 (mt-10) REVERT: C 1 MET cc_start: 0.7290 (mpp) cc_final: 0.6348 (mmm) REVERT: C 292 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8459 (p) REVERT: C 424 TRP cc_start: 0.8123 (p90) cc_final: 0.7583 (p-90) REVERT: C 456 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7733 (tp30) REVERT: C 541 GLN cc_start: 0.7050 (mp-120) cc_final: 0.6699 (mt0) REVERT: C 546 GLU cc_start: 0.7611 (tp30) cc_final: 0.7286 (tp30) REVERT: C 550 ARG cc_start: 0.8342 (mmt180) cc_final: 0.7926 (mmt180) REVERT: D 206 GLN cc_start: 0.7858 (tp40) cc_final: 0.7501 (mm-40) REVERT: D 269 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7620 (mt-10) REVERT: D 461 LYS cc_start: 0.7751 (tttm) cc_final: 0.7245 (ttpt) REVERT: E 380 ASP cc_start: 0.8112 (m-30) cc_final: 0.7667 (m-30) REVERT: E 409 ARG cc_start: 0.7133 (ttm-80) cc_final: 0.6630 (mtt-85) REVERT: E 468 GLU cc_start: 0.3342 (OUTLIER) cc_final: 0.3080 (pm20) REVERT: F 7 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7598 (mm-30) REVERT: F 200 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7641 (mp0) REVERT: F 206 GLN cc_start: 0.7931 (mt0) cc_final: 0.7606 (mp10) REVERT: F 280 ARG cc_start: 0.8774 (mtt180) cc_final: 0.7637 (mtm110) REVERT: F 455 SER cc_start: 0.8661 (t) cc_final: 0.8212 (p) REVERT: G 148 LYS cc_start: 0.6029 (pttt) cc_final: 0.5389 (mttt) REVERT: G 155 LYS cc_start: 0.6807 (mttt) cc_final: 0.6562 (ttpt) REVERT: G 177 ARG cc_start: 0.7489 (ttp80) cc_final: 0.6806 (mtm-85) REVERT: G 185 GLN cc_start: 0.7715 (tp40) cc_final: 0.7325 (tp40) REVERT: G 207 GLU cc_start: 0.2979 (OUTLIER) cc_final: 0.2287 (tm-30) REVERT: J 85 ARG cc_start: 0.4588 (mtp180) cc_final: 0.4274 (ptp-170) REVERT: J 164 GLU cc_start: 0.6955 (tp30) cc_final: 0.6359 (tp30) REVERT: L 74 GLN cc_start: 0.6281 (tt0) cc_final: 0.5795 (mt0) REVERT: L 94 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5553 (mm) REVERT: L 150 LEU cc_start: 0.5301 (OUTLIER) cc_final: 0.5033 (pp) outliers start: 70 outliers final: 49 residues processed: 380 average time/residue: 0.2190 time to fit residues: 126.1510 Evaluate side-chains 378 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 320 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 150 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 371 optimal weight: 9.9990 chunk 370 optimal weight: 0.4980 chunk 203 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 294 optimal weight: 9.9990 chunk 289 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.132202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.096993 restraints weight = 38433.265| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.70 r_work: 0.2783 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30115 Z= 0.181 Angle : 0.575 9.211 40813 Z= 0.296 Chirality : 0.046 0.186 4572 Planarity : 0.005 0.049 5333 Dihedral : 6.024 86.496 4259 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.24 % Allowed : 11.61 % Favored : 86.15 % 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: 0.72 (0.14), residues: 3764 helix: 1.53 (0.13), residues: 1569 sheet: -0.08 (0.22), residues: 575 loop : -0.28 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 321 TYR 0.020 0.002 TYR E 13 PHE 0.020 0.002 PHE C 415 TRP 0.012 0.002 TRP A 119 HIS 0.008 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00443 (30114) covalent geometry : angle 0.57546 (40813) hydrogen bonds : bond 0.05133 ( 1298) hydrogen bonds : angle 4.49771 ( 3702) Misc. bond : bond 0.00005 ( 1) *********************** 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 399 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 330 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6337 (mmt) cc_final: 0.6029 (mmt) REVERT: A 20 LEU cc_start: 0.8492 (tp) cc_final: 0.8170 (tp) REVERT: A 28 CYS cc_start: 0.8760 (m) cc_final: 0.8504 (m) REVERT: A 124 LYS cc_start: 0.7984 (mtmm) cc_final: 0.7328 (mptt) REVERT: A 183 MET cc_start: 0.9074 (mtt) cc_final: 0.8604 (mtt) REVERT: A 456 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7402 (mt-10) REVERT: A 491 ARG cc_start: 0.7533 (mmt180) cc_final: 0.6991 (ttp-110) REVERT: A 537 ASP cc_start: 0.6833 (t70) cc_final: 0.6346 (m-30) REVERT: A 546 GLU cc_start: 0.6334 (pp20) cc_final: 0.5901 (tm-30) REVERT: B 108 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8140 (t) REVERT: B 130 ARG cc_start: 0.7601 (mtm110) cc_final: 0.7184 (mtp85) REVERT: B 154 ARG cc_start: 0.7759 (mtm110) cc_final: 0.7046 (mtt90) REVERT: B 329 ARG cc_start: 0.8146 (mmt-90) cc_final: 0.7851 (mmp80) REVERT: B 341 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7855 (mp) REVERT: B 342 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7707 (mt-10) REVERT: B 409 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7182 (tp) REVERT: B 477 GLN cc_start: 0.4886 (pp30) cc_final: 0.4033 (mm-40) REVERT: B 481 ARG cc_start: 0.6369 (mtp180) cc_final: 0.6007 (mtp-110) REVERT: B 485 GLU cc_start: 0.6840 (mm-30) cc_final: 0.5170 (pt0) REVERT: B 509 MET cc_start: 0.7583 (mmp) cc_final: 0.7296 (mmt) REVERT: B 558 GLU cc_start: 0.6741 (tt0) cc_final: 0.6319 (mt-10) REVERT: C 1 MET cc_start: 0.7300 (mpp) cc_final: 0.6359 (mmm) REVERT: C 209 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8335 (mtm) REVERT: C 292 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8457 (p) REVERT: C 424 TRP cc_start: 0.8150 (p90) cc_final: 0.7615 (p-90) REVERT: C 541 GLN cc_start: 0.7179 (mp-120) cc_final: 0.6819 (mt0) REVERT: C 546 GLU cc_start: 0.7634 (tp30) cc_final: 0.7311 (tp30) REVERT: C 550 ARG cc_start: 0.8349 (mmt180) cc_final: 0.7928 (mmt180) REVERT: D 206 GLN cc_start: 0.7898 (tp40) cc_final: 0.7532 (mm-40) REVERT: D 269 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7641 (mt-10) REVERT: D 461 LYS cc_start: 0.7702 (tttm) cc_final: 0.7173 (ttpt) REVERT: E 380 ASP cc_start: 0.8125 (m-30) cc_final: 0.7682 (m-30) REVERT: E 409 ARG cc_start: 0.7106 (ttm-80) cc_final: 0.6611 (mtt-85) REVERT: E 468 GLU cc_start: 0.3413 (OUTLIER) cc_final: 0.3167 (pm20) REVERT: F 7 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7561 (mm-30) REVERT: F 162 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: F 200 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7656 (mp0) REVERT: F 206 GLN cc_start: 0.7922 (mt0) cc_final: 0.7581 (mp10) REVERT: F 280 ARG cc_start: 0.8784 (mtt180) cc_final: 0.7639 (mtm110) REVERT: F 409 ARG cc_start: 0.7781 (ttm110) cc_final: 0.7482 (mtt90) REVERT: F 455 SER cc_start: 0.8689 (t) cc_final: 0.8374 (m) REVERT: G 148 LYS cc_start: 0.6006 (pttt) cc_final: 0.5372 (mttt) REVERT: G 155 LYS cc_start: 0.6823 (mttt) cc_final: 0.6525 (ttpt) REVERT: G 177 ARG cc_start: 0.7566 (ttp80) cc_final: 0.6860 (mtm-85) REVERT: G 185 GLN cc_start: 0.7739 (tp40) cc_final: 0.7348 (tp40) REVERT: G 207 GLU cc_start: 0.2883 (OUTLIER) cc_final: 0.2299 (tm-30) REVERT: J 85 ARG cc_start: 0.4631 (mtp180) cc_final: 0.4389 (ptp-170) REVERT: L 74 GLN cc_start: 0.6287 (tt0) cc_final: 0.5824 (mt0) REVERT: L 94 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5540 (mm) REVERT: L 150 LEU cc_start: 0.5315 (OUTLIER) cc_final: 0.5056 (pp) outliers start: 69 outliers final: 54 residues processed: 386 average time/residue: 0.2313 time to fit residues: 135.0867 Evaluate side-chains 383 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 319 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 150 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 295 optimal weight: 1.9990 chunk 339 optimal weight: 30.0000 chunk 288 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 325 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 chunk 284 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 286 optimal weight: 0.6980 chunk 250 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.101306 restraints weight = 38157.991| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.44 r_work: 0.2837 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30115 Z= 0.122 Angle : 0.513 10.093 40813 Z= 0.263 Chirality : 0.043 0.161 4572 Planarity : 0.005 0.049 5333 Dihedral : 5.774 84.721 4259 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.08 % Allowed : 11.81 % Favored : 86.12 % 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: 0.95 (0.14), residues: 3764 helix: 1.72 (0.13), residues: 1584 sheet: 0.18 (0.22), residues: 550 loop : -0.24 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 321 TYR 0.019 0.001 TYR E 13 PHE 0.013 0.001 PHE A 230 TRP 0.011 0.001 TRP A 119 HIS 0.005 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00284 (30114) covalent geometry : angle 0.51279 (40813) hydrogen bonds : bond 0.04288 ( 1298) hydrogen bonds : angle 4.33456 ( 3702) Misc. bond : bond 0.00003 ( 1) ********************** 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 385 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 321 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6329 (mmt) cc_final: 0.6044 (mpp) REVERT: A 20 LEU cc_start: 0.8476 (tp) cc_final: 0.8130 (tp) REVERT: A 28 CYS cc_start: 0.8617 (m) cc_final: 0.8401 (m) REVERT: A 124 LYS cc_start: 0.7995 (mtmm) cc_final: 0.7377 (mptt) REVERT: A 183 MET cc_start: 0.9036 (mtt) cc_final: 0.8579 (mtt) REVERT: A 456 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7341 (mt-10) REVERT: A 491 ARG cc_start: 0.7518 (mmt180) cc_final: 0.7069 (ttp-110) REVERT: A 530 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7633 (mt) REVERT: A 537 ASP cc_start: 0.6791 (t70) cc_final: 0.6366 (m-30) REVERT: A 546 GLU cc_start: 0.6323 (pp20) cc_final: 0.5933 (tm-30) REVERT: B 108 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8135 (t) REVERT: B 130 ARG cc_start: 0.7559 (mtm110) cc_final: 0.7205 (mtp85) REVERT: B 154 ARG cc_start: 0.7655 (mtm110) cc_final: 0.7033 (mtt90) REVERT: B 220 MET cc_start: 0.8347 (ttp) cc_final: 0.8136 (tpp) REVERT: B 329 ARG cc_start: 0.8061 (mmt-90) cc_final: 0.7775 (mmp80) REVERT: B 341 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7763 (mp) REVERT: B 342 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7709 (mt-10) REVERT: B 409 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7094 (tp) REVERT: B 477 GLN cc_start: 0.4815 (pp30) cc_final: 0.4071 (mm-40) REVERT: B 481 ARG cc_start: 0.6388 (mtp180) cc_final: 0.6016 (mtp-110) REVERT: B 485 GLU cc_start: 0.6856 (mm-30) cc_final: 0.5247 (pt0) REVERT: B 509 MET cc_start: 0.7635 (mmp) cc_final: 0.7425 (mmt) REVERT: B 558 GLU cc_start: 0.6760 (tt0) cc_final: 0.6365 (mt-10) REVERT: C 1 MET cc_start: 0.7286 (mpp) cc_final: 0.6371 (mmm) REVERT: C 209 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8346 (mtm) REVERT: C 292 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8385 (p) REVERT: C 424 TRP cc_start: 0.8096 (p90) cc_final: 0.7583 (p-90) REVERT: C 456 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7761 (tp30) REVERT: C 541 GLN cc_start: 0.7096 (mp-120) cc_final: 0.6783 (mt0) REVERT: C 546 GLU cc_start: 0.7552 (tp30) cc_final: 0.7281 (tp30) REVERT: C 550 ARG cc_start: 0.8326 (mmt180) cc_final: 0.7933 (mmt180) REVERT: D 206 GLN cc_start: 0.7851 (tp40) cc_final: 0.7496 (mm-40) REVERT: D 269 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7550 (mt-10) REVERT: D 461 LYS cc_start: 0.7791 (tttm) cc_final: 0.7311 (ttpt) REVERT: E 380 ASP cc_start: 0.8067 (m-30) cc_final: 0.7627 (m-30) REVERT: E 409 ARG cc_start: 0.7068 (ttm-80) cc_final: 0.6617 (mtt-85) REVERT: E 468 GLU cc_start: 0.3480 (OUTLIER) cc_final: 0.3216 (pm20) REVERT: F 7 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7560 (mm-30) REVERT: F 162 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: F 200 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7683 (mp0) REVERT: F 206 GLN cc_start: 0.7918 (mt0) cc_final: 0.7642 (mp10) REVERT: F 280 ARG cc_start: 0.8762 (mtt180) cc_final: 0.7648 (mtm110) REVERT: F 455 SER cc_start: 0.8692 (t) cc_final: 0.8276 (p) REVERT: G 148 LYS cc_start: 0.5960 (pttt) cc_final: 0.5335 (mttt) REVERT: G 155 LYS cc_start: 0.6898 (mttt) cc_final: 0.6642 (ttpt) REVERT: G 177 ARG cc_start: 0.7445 (ttp80) cc_final: 0.6814 (mtm-85) REVERT: G 185 GLN cc_start: 0.7695 (tp40) cc_final: 0.7331 (tp40) REVERT: G 190 ASP cc_start: 0.7880 (m-30) cc_final: 0.7612 (m-30) REVERT: G 207 GLU cc_start: 0.3073 (OUTLIER) cc_final: 0.2386 (tm-30) REVERT: J 85 ARG cc_start: 0.4517 (mtp180) cc_final: 0.4247 (ptp-170) REVERT: J 164 GLU cc_start: 0.6954 (tp30) cc_final: 0.6376 (tp30) REVERT: L 74 GLN cc_start: 0.6390 (tt0) cc_final: 0.5921 (mt0) REVERT: L 94 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5528 (mm) REVERT: L 121 LEU cc_start: 0.7051 (tt) cc_final: 0.6694 (tp) outliers start: 64 outliers final: 49 residues processed: 372 average time/residue: 0.2236 time to fit residues: 126.4479 Evaluate side-chains 377 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 318 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 280 ARG Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain E residue 468 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 86 LYS Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 416 ASP Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain L residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 31 optimal weight: 9.9990 chunk 361 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 367 optimal weight: 7.9990 chunk 210 optimal weight: 7.9990 chunk 254 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.134839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.100060 restraints weight = 38095.266| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.45 r_work: 0.2811 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30115 Z= 0.204 Angle : 0.601 10.608 40813 Z= 0.307 Chirality : 0.047 0.198 4572 Planarity : 0.005 0.048 5333 Dihedral : 6.069 86.639 4259 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.14 % Allowed : 11.81 % Favored : 86.05 % 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: 0.60 (0.14), residues: 3764 helix: 1.45 (0.13), residues: 1569 sheet: -0.17 (0.21), residues: 585 loop : -0.35 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 460 TYR 0.021 0.002 TYR E 13 PHE 0.021 0.002 PHE C 230 TRP 0.012 0.002 TRP A 119 HIS 0.009 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00501 (30114) covalent geometry : angle 0.60135 (40813) hydrogen bonds : bond 0.05353 ( 1298) hydrogen bonds : angle 4.55328 ( 3702) Misc. bond : bond 0.00041 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8351.40 seconds wall clock time: 143 minutes 4.89 seconds (8584.89 seconds total)