Starting phenix.real_space_refine on Fri Feb 6 19:43:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u6o_63915/02_2026/9u6o_63915.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u6o_63915/02_2026/9u6o_63915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u6o_63915/02_2026/9u6o_63915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u6o_63915/02_2026/9u6o_63915.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u6o_63915/02_2026/9u6o_63915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u6o_63915/02_2026/9u6o_63915.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.049 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 7 5.49 5 Mg 3 5.21 5 S 101 5.16 5 C 17124 2.51 5 N 4648 2.21 5 O 5098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26981 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4478 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4478 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4478 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3683 Classifications: {'peptide': 470} Modifications used: {'COO': 1} 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: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1620 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.83, per 1000 atoms: 0.22 Number of scatterers: 26981 At special positions: 0 Unit cell: (138.06, 145.14, 159.3, 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 101 16.00 P 7 15.00 Mg 3 11.99 O 5098 8.00 N 4648 7.00 C 17124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 1.1 seconds 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6278 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 24 sheets defined 43.2% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.756A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 4.102A 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 315 removed outlier: 4.482A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.607A pdb=" N ALA A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) 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: 3.682A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.517A pdb=" N ALA A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 removed outlier: 3.594A pdb=" N GLU A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 472 removed outlier: 4.546A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 removed outlier: 3.506A pdb=" N LEU A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 477 through 494 removed outlier: 3.803A pdb=" N VAL A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 533 removed outlier: 3.759A pdb=" N LYS A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.830A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 removed outlier: 3.509A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 575 removed outlier: 3.518A pdb=" N TYR A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 571 " --> pdb=" O MET A 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.666A pdb=" N LYS B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 removed outlier: 3.550A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 301 Processing helix chain 'B' and resid 301 through 315 Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.826A 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: 3.896A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 443 removed outlier: 4.164A pdb=" N GLU B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 463 removed outlier: 3.507A pdb=" N ALA B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.689A pdb=" N LEU B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 494 removed outlier: 3.862A 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 removed outlier: 3.658A pdb=" N ILE B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.690A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 577 removed outlier: 3.801A pdb=" N TYR B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.923A pdb=" N GLU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) 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: 4.365A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 315 removed outlier: 4.291A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.570A pdb=" N GLY C 389 " --> pdb=" O PRO C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.784A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 435 through 443 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: 4.226A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN C 469 " --> pdb=" O GLN C 465 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 removed outlier: 3.553A 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 531 removed outlier: 3.909A pdb=" N LYS C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.581A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 removed outlier: 4.101A 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 576 removed outlier: 4.481A pdb=" N GLN C 571 " --> pdb=" O MET C 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.513A pdb=" N MET D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.529A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 210 Processing helix chain 'D' and resid 212 through 215 removed outlier: 3.725A pdb=" N SER D 215 " --> pdb=" O GLY D 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 212 through 215' Processing helix chain 'D' and resid 227 through 250 removed outlier: 3.529A pdb=" N ARG D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.864A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.794A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.656A pdb=" N ILE D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 331 removed outlier: 3.613A pdb=" N TYR D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.736A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 467 through 472 Processing helix chain 'E' and resid 85 through 89 removed outlier: 4.065A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.659A pdb=" N LEU E 177 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 212 removed outlier: 3.842A pdb=" N TYR E 203 " --> pdb=" O ARG E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.787A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.846A 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 273 removed outlier: 3.992A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.771A 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 removed outlier: 3.583A pdb=" N LYS E 346 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 365 removed outlier: 3.689A pdb=" N ASN E 364 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 400 removed outlier: 4.069A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 removed outlier: 3.579A pdb=" N ARG E 420 " --> pdb=" O ASP E 416 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 455 through 460 Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 197 through 212 removed outlier: 3.608A pdb=" N TYR F 203 " --> pdb=" O ARG F 199 " (cutoff:3.500A) 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 227 through 232 removed outlier: 3.726A pdb=" N GLU F 230 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.907A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 270 " --> pdb=" O ALA F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 4.028A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.798A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 320 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: 3.889A pdb=" N GLY F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) removed outlier: 3.529A 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: 3.571A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 removed outlier: 3.648A pdb=" N LEU F 404 " --> pdb=" O GLU F 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 401 through 404' Processing helix chain 'F' and resid 405 through 422 removed outlier: 3.569A pdb=" N ARG F 409 " --> pdb=" O THR F 405 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG F 410 " --> pdb=" O GLU F 406 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR F 411 " --> pdb=" O ASN F 407 " (cutoff:3.500A) 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: 3.647A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 removed outlier: 3.529A pdb=" N LYS F 461 " --> pdb=" O ASP F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 470 Processing helix chain 'G' and resid 7 through 72 removed outlier: 3.957A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN G 55 " --> pdb=" O LYS G 51 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 122 through 205 removed outlier: 4.068A pdb=" N ARG G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix removed outlier: 3.765A pdb=" N GLU G 205 " --> pdb=" O ILE G 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 16 removed outlier: 3.611A pdb=" N PHE H 13 " --> pdb=" O THR H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.700A pdb=" N ARG H 39 " --> pdb=" O THR H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 81 removed outlier: 3.691A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 98 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.654A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.210A 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: 5.668A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.708A 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: 5.970A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.749A 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: 5.789A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 50 removed outlier: 6.623A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.153A 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: 5.608A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.566A 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: 5.732A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) 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: 3.900A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.889A 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: 3.594A pdb=" N GLY A 155 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 7.012A 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 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 82 through 84 current: chain 'B' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 291 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: 3.837A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 164 " --> pdb=" O TRP B 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.938A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB2, first strand: chain 'C' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.552A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.590A 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: 6.917A 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 Processing sheet with id=AB6, first strand: chain 'D' and resid 92 through 93 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 92 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: 4.686A 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 removed outlier: 3.629A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 92 through 93 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 92 through 93 current: chain 'E' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 217 through 223 current: chain 'E' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 307 through 315 current: chain 'E' and resid 358 through 359 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.448A 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: 3.529A 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 93 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 92 through 93 current: chain 'F' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 217 through 223 current: chain 'F' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 307 through 315 current: chain 'F' and resid 358 through 359 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AC5, first strand: chain 'G' and resid 89 through 96 Processing sheet with id=AC6, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.299A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) 1012 hydrogen bonds defined for protein. 2901 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.91 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4613 1.31 - 1.44: 6771 1.44 - 1.57: 15918 1.57 - 1.69: 16 1.69 - 1.82: 190 Bond restraints: 27508 Sorted by residual: bond pdb=" CA SER C 232 " pdb=" CB SER C 232 " ideal model delta sigma weight residual 1.534 1.465 0.069 1.45e-02 4.76e+03 2.25e+01 bond pdb=" CA SER B 232 " pdb=" CB SER B 232 " ideal model delta sigma weight residual 1.532 1.460 0.072 1.78e-02 3.16e+03 1.65e+01 bond pdb=" CA SER A 232 " pdb=" CB SER A 232 " ideal model delta sigma weight residual 1.534 1.482 0.052 1.45e-02 4.76e+03 1.26e+01 bond pdb=" C LEU H 68 " pdb=" N PRO H 69 " ideal model delta sigma weight residual 1.335 1.362 -0.027 8.70e-03 1.32e+04 9.31e+00 bond pdb=" O3 PO4 D 501 " pdb=" P PO4 D 501 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.02e+00 ... (remaining 27503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 36967 3.10 - 6.20: 267 6.20 - 9.30: 47 9.30 - 12.40: 6 12.40 - 15.50: 2 Bond angle restraints: 37289 Sorted by residual: angle pdb=" CA PHE C 230 " pdb=" CB PHE C 230 " pdb=" CG PHE C 230 " ideal model delta sigma weight residual 113.80 120.36 -6.56 1.00e+00 1.00e+00 4.31e+01 angle pdb=" CA GLU D 275 " pdb=" CB GLU D 275 " pdb=" CG GLU D 275 " ideal model delta sigma weight residual 114.10 124.78 -10.68 2.00e+00 2.50e-01 2.85e+01 angle pdb=" C GLU B 347 " pdb=" CA GLU B 347 " pdb=" CB GLU B 347 " ideal model delta sigma weight residual 116.54 110.54 6.00 1.15e+00 7.56e-01 2.72e+01 angle pdb=" C GLU D 182 " pdb=" CA GLU D 182 " pdb=" CB GLU D 182 " ideal model delta sigma weight residual 116.54 110.67 5.87 1.15e+00 7.56e-01 2.60e+01 angle pdb=" CB GLU D 275 " pdb=" CG GLU D 275 " pdb=" CD GLU D 275 " ideal model delta sigma weight residual 112.60 120.56 -7.96 1.70e+00 3.46e-01 2.20e+01 ... (remaining 37284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.27: 15189 19.27 - 38.54: 1188 38.54 - 57.82: 245 57.82 - 77.09: 46 77.09 - 96.36: 27 Dihedral angle restraints: 16695 sinusoidal: 6846 harmonic: 9849 Sorted by residual: dihedral pdb=" O1B ADP A 602 " pdb=" O3A ADP A 602 " pdb=" PB ADP A 602 " pdb=" PA ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 -156.36 96.36 1 2.00e+01 2.50e-03 2.67e+01 dihedral pdb=" O1B ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PB ADP B 601 " pdb=" PA ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 -140.39 80.39 1 2.00e+01 2.50e-03 2.00e+01 dihedral pdb=" CA ASP B 213 " pdb=" C ASP B 213 " pdb=" N VAL B 214 " pdb=" CA VAL B 214 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 16692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3226 0.052 - 0.104: 741 0.104 - 0.156: 180 0.156 - 0.208: 8 0.208 - 0.260: 6 Chirality restraints: 4161 Sorted by residual: chirality pdb=" CA ASP B 436 " pdb=" N ASP B 436 " pdb=" C ASP B 436 " pdb=" CB ASP B 436 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 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 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CG LEU C 577 " pdb=" CB LEU C 577 " pdb=" CD1 LEU C 577 " pdb=" CD2 LEU C 577 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 4158 not shown) Planarity restraints: 4874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 275 " 0.016 2.00e-02 2.50e+03 3.11e-02 9.69e+00 pdb=" C GLU D 275 " -0.054 2.00e-02 2.50e+03 pdb=" O GLU D 275 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU D 276 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 13 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.06e+00 pdb=" CD GLN G 13 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLN G 13 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN G 13 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 200 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" CG ASP B 200 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP B 200 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP B 200 " -0.013 2.00e-02 2.50e+03 ... (remaining 4871 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 79 2.50 - 3.10: 18172 3.10 - 3.70: 39173 3.70 - 4.30: 56621 4.30 - 4.90: 98403 Nonbonded interactions: 212448 Sorted by model distance: nonbonded pdb=" OG1 THR B 235 " pdb="MG MG B 602 " model vdw 1.895 2.170 nonbonded pdb="MG MG A 601 " pdb=" O2B ADP A 602 " model vdw 2.046 2.170 nonbonded pdb=" OG1 THR C 235 " pdb="MG MG C 601 " model vdw 2.047 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1B ADP C 602 " model vdw 2.048 2.170 nonbonded pdb=" OG1 THR A 235 " pdb="MG MG A 601 " model vdw 2.060 2.170 ... (remaining 212443 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) } 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 23.470 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 33.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 27508 Z= 0.189 Angle : 0.748 15.497 37289 Z= 0.413 Chirality : 0.047 0.260 4161 Planarity : 0.006 0.074 4874 Dihedral : 14.857 96.359 10417 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.95 % Allowed : 14.12 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.24 (0.14), residues: 3437 helix: 0.59 (0.15), residues: 1292 sheet: 0.49 (0.23), residues: 542 loop : -0.19 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 95 TYR 0.017 0.001 TYR H 21 PHE 0.034 0.001 PHE C 230 TRP 0.007 0.001 TRP C 438 HIS 0.002 0.001 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00372 (27508) covalent geometry : angle 0.74814 (37289) hydrogen bonds : bond 0.19156 ( 1012) hydrogen bonds : angle 6.53174 ( 2901) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 427 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.7866 (mtm) cc_final: 0.7597 (mtt) REVERT: A 337 ILE cc_start: 0.8390 (mm) cc_final: 0.8086 (mp) REVERT: A 379 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8389 (m) REVERT: A 441 GLU cc_start: 0.8569 (mp0) cc_final: 0.8282 (mp0) REVERT: A 466 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7439 (tm-30) REVERT: A 469 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8371 (mp10) REVERT: A 518 MET cc_start: 0.8409 (mtp) cc_final: 0.8187 (mtp) REVERT: A 558 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8364 (tp30) REVERT: B 191 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7890 (ttp80) REVERT: B 348 GLU cc_start: 0.6763 (tm-30) cc_final: 0.5952 (tm-30) REVERT: B 481 ARG cc_start: 0.7388 (ttt180) cc_final: 0.7116 (ttm170) REVERT: B 518 MET cc_start: 0.7988 (mtp) cc_final: 0.7773 (mtt) REVERT: C 262 MET cc_start: 0.8292 (mmt) cc_final: 0.8025 (mmm) REVERT: C 456 GLU cc_start: 0.8268 (tm-30) cc_final: 0.8026 (tm-30) REVERT: C 558 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7676 (tm-30) REVERT: D 162 GLU cc_start: 0.8477 (mp0) cc_final: 0.8202 (mp0) REVERT: D 265 GLU cc_start: 0.8257 (mp0) cc_final: 0.7834 (mp0) REVERT: D 269 GLU cc_start: 0.7636 (mp0) cc_final: 0.6816 (pm20) REVERT: D 420 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7747 (mtp180) REVERT: E 49 GLU cc_start: 0.8759 (tt0) cc_final: 0.8557 (tt0) REVERT: E 128 GLU cc_start: 0.8578 (pm20) cc_final: 0.8218 (pm20) REVERT: E 198 GLN cc_start: 0.8088 (tp40) cc_final: 0.7674 (tp40) REVERT: E 230 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7920 (mt-10) REVERT: E 388 ASN cc_start: 0.7964 (m-40) cc_final: 0.7713 (t0) REVERT: E 394 LYS cc_start: 0.8889 (ttmm) cc_final: 0.8549 (mtpt) REVERT: E 420 ARG cc_start: 0.6854 (tpm-80) cc_final: 0.6553 (tpm170) REVERT: F 276 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8203 (mm-30) REVERT: F 334 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7862 (mt-10) REVERT: F 465 GLN cc_start: 0.7421 (tm-30) cc_final: 0.6923 (tp40) REVERT: G 133 TYR cc_start: 0.6971 (t80) cc_final: 0.6769 (t80) REVERT: H 3 VAL cc_start: 0.7079 (p) cc_final: 0.6820 (t) REVERT: H 13 PHE cc_start: 0.8474 (m-80) cc_final: 0.7572 (m-80) REVERT: H 42 TYR cc_start: 0.6459 (m-80) cc_final: 0.6050 (m-80) REVERT: H 63 MET cc_start: 0.7243 (pmm) cc_final: 0.6884 (mtm) outliers start: 27 outliers final: 4 residues processed: 448 average time/residue: 0.8338 time to fit residues: 422.3230 Evaluate side-chains 269 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 264 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 402 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN A 418 HIS B 81 ASN B 425 ASN B 442 ASN B 459 GLN C 498 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN D 407 ASN D 428 GLN D 465 GLN E 170 GLN E 363 ASN E 425 GLN E 458 HIS G 55 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.095565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.070207 restraints weight = 48267.184| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.61 r_work: 0.2762 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 27508 Z= 0.258 Angle : 0.690 8.813 37289 Z= 0.355 Chirality : 0.049 0.221 4161 Planarity : 0.006 0.056 4874 Dihedral : 5.728 90.606 3856 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.81 % Allowed : 13.59 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3437 helix: 0.81 (0.15), residues: 1323 sheet: 0.31 (0.22), residues: 557 loop : -0.40 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 130 TYR 0.017 0.002 TYR C 428 PHE 0.019 0.002 PHE B 574 TRP 0.017 0.002 TRP B 119 HIS 0.006 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00621 (27508) covalent geometry : angle 0.69009 (37289) hydrogen bonds : bond 0.06395 ( 1012) hydrogen bonds : angle 4.83185 ( 2901) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 286 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.8933 (mtm) cc_final: 0.8702 (mtt) REVERT: A 393 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7180 (tt0) REVERT: A 557 GLU cc_start: 0.8487 (pm20) cc_final: 0.7657 (pm20) REVERT: A 558 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8375 (mp0) REVERT: B 269 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8644 (t80) REVERT: B 392 SER cc_start: 0.9246 (OUTLIER) cc_final: 0.8874 (t) REVERT: B 397 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8364 (mm110) REVERT: B 408 ARG cc_start: 0.8779 (ttm-80) cc_final: 0.8435 (ttt180) REVERT: B 442 ASN cc_start: 0.8168 (m-40) cc_final: 0.7965 (m110) REVERT: B 518 MET cc_start: 0.8416 (mtp) cc_final: 0.8199 (mtt) REVERT: C 209 MET cc_start: 0.8293 (mtp) cc_final: 0.7927 (mtm) REVERT: C 268 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: C 348 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8740 (tt0) REVERT: D 88 MET cc_start: 0.8796 (mtm) cc_final: 0.8589 (mtm) REVERT: D 334 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8950 (mt-10) REVERT: D 420 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8112 (mtp-110) REVERT: E 61 GLU cc_start: 0.8349 (pm20) cc_final: 0.8027 (pm20) REVERT: E 128 GLU cc_start: 0.8862 (pm20) cc_final: 0.8464 (pm20) REVERT: E 226 ASP cc_start: 0.8642 (m-30) cc_final: 0.7899 (m-30) REVERT: E 269 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7530 (mt-10) REVERT: E 345 ARG cc_start: 0.8588 (tpp80) cc_final: 0.8313 (ttm-80) REVERT: F 209 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8447 (mm-30) REVERT: F 276 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8592 (mm-30) REVERT: F 465 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7595 (tm-30) REVERT: G 13 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8347 (tm130) REVERT: G 81 LEU cc_start: 0.6911 (tm) cc_final: 0.6361 (mt) REVERT: G 144 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: H 13 PHE cc_start: 0.8439 (m-80) cc_final: 0.7724 (m-80) REVERT: H 63 MET cc_start: 0.7625 (pmm) cc_final: 0.7164 (mtm) REVERT: H 93 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9156 (mm) outliers start: 108 outliers final: 36 residues processed: 359 average time/residue: 0.7651 time to fit residues: 313.9009 Evaluate side-chains 288 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 465 GLN Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 93 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 151 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 339 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 541 GLN B 571 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 424 ASN F 166 GLN F 170 GLN F 437 GLN G 181 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.095918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.070389 restraints weight = 47945.261| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.62 r_work: 0.2778 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27508 Z= 0.165 Angle : 0.568 8.804 37289 Z= 0.287 Chirality : 0.045 0.214 4161 Planarity : 0.004 0.051 4874 Dihedral : 5.234 85.117 3852 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.14 % Allowed : 14.27 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.56 (0.14), residues: 3437 helix: 1.29 (0.15), residues: 1309 sheet: 0.34 (0.22), residues: 560 loop : -0.33 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 95 TYR 0.011 0.001 TYR A 562 PHE 0.016 0.001 PHE C 230 TRP 0.015 0.001 TRP B 119 HIS 0.003 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00391 (27508) covalent geometry : angle 0.56799 (37289) hydrogen bonds : bond 0.05479 ( 1012) hydrogen bonds : angle 4.51199 ( 2901) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 264 time to evaluate : 1.089 Fit side-chains REVERT: A 133 MET cc_start: 0.8945 (mtm) cc_final: 0.8690 (mtt) REVERT: A 558 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8262 (tp30) REVERT: B 239 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8139 (mt0) REVERT: B 243 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7706 (tptm) REVERT: B 269 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8795 (t80) REVERT: B 323 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8641 (mtt) REVERT: B 397 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8497 (mm110) REVERT: B 442 ASN cc_start: 0.8390 (m-40) cc_final: 0.8151 (m110) REVERT: B 518 MET cc_start: 0.8617 (mtp) cc_final: 0.8254 (mtt) REVERT: C 268 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: C 348 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8733 (tt0) REVERT: D 88 MET cc_start: 0.8987 (mtm) cc_final: 0.8747 (mtm) REVERT: D 265 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: D 269 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7805 (mp0) REVERT: D 327 ASP cc_start: 0.8850 (t0) cc_final: 0.8584 (t0) REVERT: D 334 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8921 (mt-10) REVERT: D 394 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8948 (ttmm) REVERT: D 420 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8114 (mtp-110) REVERT: E 61 GLU cc_start: 0.8356 (pm20) cc_final: 0.7954 (pm20) REVERT: E 128 GLU cc_start: 0.8906 (pm20) cc_final: 0.8480 (pm20) REVERT: E 226 ASP cc_start: 0.8552 (m-30) cc_final: 0.7825 (m-30) REVERT: E 345 ARG cc_start: 0.8602 (tpp80) cc_final: 0.8339 (ttm-80) REVERT: E 469 GLU cc_start: 0.6458 (tt0) cc_final: 0.6103 (tt0) REVERT: F 276 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8594 (mm-30) REVERT: F 465 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: G 13 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8276 (tm130) REVERT: G 81 LEU cc_start: 0.7217 (tm) cc_final: 0.6711 (mt) REVERT: G 144 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: G 190 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8451 (t0) REVERT: G 197 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.8042 (mp) REVERT: H 13 PHE cc_start: 0.8425 (m-80) cc_final: 0.7653 (m-80) REVERT: H 63 MET cc_start: 0.7538 (pmm) cc_final: 0.7064 (mtm) REVERT: H 93 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9110 (mm) outliers start: 89 outliers final: 35 residues processed: 323 average time/residue: 0.7295 time to fit residues: 269.4916 Evaluate side-chains 290 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 465 GLN Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 93 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 195 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 289 optimal weight: 5.9990 chunk 307 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 287 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 21 optimal weight: 0.0470 overall best weight: 2.3484 ------------------------------------------------------------------------------- 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** F 23 ASN F 166 GLN G 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.094863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.069144 restraints weight = 48017.565| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.62 r_work: 0.2756 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 27508 Z= 0.200 Angle : 0.579 6.932 37289 Z= 0.293 Chirality : 0.046 0.184 4161 Planarity : 0.005 0.049 4874 Dihedral : 5.150 79.781 3852 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.32 % Allowed : 14.62 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3437 helix: 1.40 (0.15), residues: 1312 sheet: 0.25 (0.22), residues: 565 loop : -0.36 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 95 TYR 0.013 0.001 TYR G 122 PHE 0.018 0.001 PHE C 230 TRP 0.015 0.001 TRP B 119 HIS 0.003 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00489 (27508) covalent geometry : angle 0.57906 (37289) hydrogen bonds : bond 0.05567 ( 1012) hydrogen bonds : angle 4.41368 ( 2901) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 262 time to evaluate : 1.296 Fit side-chains REVERT: A 53 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8414 (mt-10) REVERT: A 469 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8805 (tm-30) REVERT: B 1 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7783 (pmm) REVERT: B 239 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8138 (mt0) REVERT: B 269 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8849 (t80) REVERT: B 347 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8162 (mm-30) REVERT: B 392 SER cc_start: 0.9372 (m) cc_final: 0.8830 (t) REVERT: B 397 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8480 (mm110) REVERT: B 442 ASN cc_start: 0.8395 (m-40) cc_final: 0.8147 (m110) REVERT: C 1 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8188 (ptp) REVERT: C 43 ASP cc_start: 0.8674 (t0) cc_final: 0.8405 (t0) REVERT: C 268 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: C 348 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8693 (tt0) REVERT: C 393 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7603 (pp20) REVERT: D 88 MET cc_start: 0.9045 (mtm) cc_final: 0.8825 (mtm) REVERT: D 296 GLU cc_start: 0.9364 (mm-30) cc_final: 0.9163 (mm-30) REVERT: D 327 ASP cc_start: 0.8855 (t0) cc_final: 0.8593 (t0) REVERT: D 334 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.9008 (mt-10) REVERT: D 394 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8926 (ttmm) REVERT: D 420 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8078 (mtp-110) REVERT: E 61 GLU cc_start: 0.8370 (pm20) cc_final: 0.8013 (pm20) REVERT: E 128 GLU cc_start: 0.8971 (pm20) cc_final: 0.8508 (pm20) REVERT: E 226 ASP cc_start: 0.8479 (m-30) cc_final: 0.7816 (m-30) REVERT: E 265 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: E 345 ARG cc_start: 0.8662 (tpp80) cc_final: 0.8350 (ttm-80) REVERT: E 416 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7278 (p0) REVERT: F 275 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8299 (mm-30) REVERT: F 276 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8617 (mm-30) REVERT: F 465 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: G 13 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8143 (tm-30) REVERT: G 81 LEU cc_start: 0.7478 (tm) cc_final: 0.6932 (mt) REVERT: G 144 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: G 190 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8416 (t0) REVERT: H 13 PHE cc_start: 0.8418 (m-80) cc_final: 0.7574 (m-80) REVERT: H 14 ARG cc_start: 0.8865 (mpp80) cc_final: 0.8586 (mpp80) REVERT: H 93 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9099 (mm) REVERT: H 103 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.6876 (tmmm) outliers start: 94 outliers final: 44 residues processed: 327 average time/residue: 0.7876 time to fit residues: 294.6835 Evaluate side-chains 305 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 244 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 465 GLN Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 103 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 329 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 chunk 311 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN F 437 GLN G 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.093580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.067941 restraints weight = 48250.049| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.62 r_work: 0.2728 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 27508 Z= 0.256 Angle : 0.616 7.001 37289 Z= 0.313 Chirality : 0.048 0.218 4161 Planarity : 0.005 0.050 4874 Dihedral : 5.265 80.101 3852 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.53 % Allowed : 15.01 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.46 (0.14), residues: 3437 helix: 1.37 (0.15), residues: 1312 sheet: 0.11 (0.22), residues: 563 loop : -0.47 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 95 TYR 0.014 0.001 TYR A 562 PHE 0.023 0.002 PHE C 574 TRP 0.015 0.001 TRP B 119 HIS 0.004 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00630 (27508) covalent geometry : angle 0.61650 (37289) hydrogen bonds : bond 0.06025 ( 1012) hydrogen bonds : angle 4.42010 ( 2901) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 255 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8433 (mt-10) REVERT: A 469 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8745 (tm-30) REVERT: B 1 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7936 (pmm) REVERT: B 239 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: B 269 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8875 (t80) REVERT: B 323 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8814 (mtt) REVERT: B 397 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8479 (mm110) REVERT: B 518 MET cc_start: 0.8819 (mtm) cc_final: 0.8545 (mtt) REVERT: C 268 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: C 348 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8728 (tt0) REVERT: C 558 GLU cc_start: 0.8691 (mt-10) cc_final: 0.7511 (tp30) REVERT: D 53 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: D 296 GLU cc_start: 0.9381 (mm-30) cc_final: 0.9177 (mm-30) REVERT: D 327 ASP cc_start: 0.8897 (t0) cc_final: 0.8640 (t0) REVERT: D 334 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.9013 (mt-10) REVERT: D 394 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8938 (ttmm) REVERT: D 420 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8104 (mtp-110) REVERT: E 61 GLU cc_start: 0.8450 (pm20) cc_final: 0.8150 (pm20) REVERT: E 128 GLU cc_start: 0.8956 (pm20) cc_final: 0.8510 (pm20) REVERT: E 226 ASP cc_start: 0.8439 (m-30) cc_final: 0.7768 (m-30) REVERT: E 345 ARG cc_start: 0.8644 (tpp80) cc_final: 0.8330 (ttm-80) REVERT: E 416 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7251 (p0) REVERT: F 275 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8423 (mm-30) REVERT: G 13 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8078 (tm-30) REVERT: G 81 LEU cc_start: 0.7734 (tm) cc_final: 0.7161 (mt) REVERT: G 144 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: G 190 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8376 (t0) REVERT: H 13 PHE cc_start: 0.8487 (m-80) cc_final: 0.7712 (m-80) REVERT: H 63 MET cc_start: 0.7757 (mtm) cc_final: 0.7001 (mtm) REVERT: H 93 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9113 (mm) outliers start: 100 outliers final: 47 residues processed: 323 average time/residue: 0.7785 time to fit residues: 288.4353 Evaluate side-chains 303 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 242 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 194 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 93 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 157 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 327 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 GLN C 397 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN F 437 GLN G 55 GLN G 181 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.096382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.070877 restraints weight = 47906.654| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.62 r_work: 0.2776 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27508 Z= 0.120 Angle : 0.537 8.379 37289 Z= 0.269 Chirality : 0.044 0.235 4161 Planarity : 0.004 0.048 4874 Dihedral : 4.930 77.807 3851 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.72 % Allowed : 16.21 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.76 (0.15), residues: 3437 helix: 1.69 (0.15), residues: 1304 sheet: 0.29 (0.23), residues: 543 loop : -0.37 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 95 TYR 0.012 0.001 TYR C 500 PHE 0.013 0.001 PHE A 230 TRP 0.013 0.001 TRP B 119 HIS 0.002 0.000 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00278 (27508) covalent geometry : angle 0.53725 (37289) hydrogen bonds : bond 0.04626 ( 1012) hydrogen bonds : angle 4.21209 ( 2901) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 258 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: A 393 GLU cc_start: 0.7584 (tt0) cc_final: 0.6857 (pt0) REVERT: A 469 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8757 (tm-30) REVERT: B 239 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8211 (mt0) REVERT: B 269 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8896 (t80) REVERT: B 323 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8775 (mtt) REVERT: B 397 GLN cc_start: 0.8708 (mm110) cc_final: 0.8450 (mm110) REVERT: B 442 ASN cc_start: 0.8404 (m-40) cc_final: 0.8110 (m110) REVERT: B 518 MET cc_start: 0.8798 (mtm) cc_final: 0.8502 (mtt) REVERT: C 268 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: C 338 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8947 (t) REVERT: C 348 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8724 (tt0) REVERT: C 393 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7633 (pp20) REVERT: C 558 GLU cc_start: 0.8692 (mt-10) cc_final: 0.7561 (tp30) REVERT: D 53 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: D 327 ASP cc_start: 0.8816 (t0) cc_final: 0.8555 (t0) REVERT: D 334 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8995 (mt-10) REVERT: D 394 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8914 (ttmm) REVERT: D 420 ARG cc_start: 0.8373 (ttp80) cc_final: 0.8026 (mtp-110) REVERT: E 61 GLU cc_start: 0.8412 (pm20) cc_final: 0.7982 (pm20) REVERT: E 128 GLU cc_start: 0.8914 (pm20) cc_final: 0.8491 (pm20) REVERT: E 226 ASP cc_start: 0.8433 (m-30) cc_final: 0.7747 (m-30) REVERT: E 230 GLU cc_start: 0.8478 (mp0) cc_final: 0.8242 (mp0) REVERT: E 345 ARG cc_start: 0.8640 (tpp80) cc_final: 0.8349 (ttm-80) REVERT: E 416 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7345 (p0) REVERT: E 469 GLU cc_start: 0.6400 (tt0) cc_final: 0.4968 (mp0) REVERT: G 13 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8236 (tp40) REVERT: G 81 LEU cc_start: 0.7783 (tm) cc_final: 0.7224 (mt) REVERT: G 144 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: G 190 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8386 (t0) REVERT: H 13 PHE cc_start: 0.8436 (m-80) cc_final: 0.7640 (m-80) REVERT: H 14 ARG cc_start: 0.8823 (mpp80) cc_final: 0.8532 (mpp80) REVERT: H 63 MET cc_start: 0.7804 (mtm) cc_final: 0.7201 (mtm) REVERT: H 93 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9092 (mm) outliers start: 77 outliers final: 25 residues processed: 304 average time/residue: 0.7946 time to fit residues: 276.7864 Evaluate side-chains 287 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 65 LEU 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 157 THR Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 93 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 294 optimal weight: 3.9990 chunk 309 optimal weight: 7.9990 chunk 330 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 156 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 chunk 135 optimal weight: 0.0770 chunk 62 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 148 optimal weight: 0.3980 overall best weight: 0.4940 ------------------------------------------------------------------------------- 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** E 407 ASN F 206 GLN G 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.097654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.072142 restraints weight = 47094.988| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.61 r_work: 0.2809 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 27508 Z= 0.099 Angle : 0.523 9.158 37289 Z= 0.259 Chirality : 0.043 0.230 4161 Planarity : 0.004 0.046 4874 Dihedral : 4.659 72.289 3851 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.19 % Allowed : 17.02 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.02 (0.15), residues: 3437 helix: 1.89 (0.15), residues: 1300 sheet: 0.44 (0.23), residues: 563 loop : -0.21 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 91 TYR 0.011 0.001 TYR H 21 PHE 0.011 0.001 PHE A 230 TRP 0.012 0.001 TRP B 119 HIS 0.001 0.000 HIS D 323 Details of bonding type rmsd covalent geometry : bond 0.00222 (27508) covalent geometry : angle 0.52276 (37289) hydrogen bonds : bond 0.03977 ( 1012) hydrogen bonds : angle 4.05958 ( 2901) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 255 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 393 GLU cc_start: 0.7529 (tt0) cc_final: 0.6805 (pt0) REVERT: A 469 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8809 (tm-30) REVERT: B 209 MET cc_start: 0.7698 (mtp) cc_final: 0.7202 (ttm) REVERT: B 239 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8225 (mt0) REVERT: B 269 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8906 (t80) REVERT: B 323 MET cc_start: 0.9154 (mtt) cc_final: 0.8752 (mtt) REVERT: B 397 GLN cc_start: 0.8642 (mm110) cc_final: 0.8293 (mm110) REVERT: C 268 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: C 348 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8686 (tt0) REVERT: D 53 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: D 200 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8104 (mt-10) REVERT: D 214 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8783 (tm) REVERT: D 327 ASP cc_start: 0.8716 (t0) cc_final: 0.8449 (t0) REVERT: D 334 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8937 (mt-10) REVERT: D 420 ARG cc_start: 0.8368 (ttp80) cc_final: 0.8018 (mtp-110) REVERT: E 61 GLU cc_start: 0.8363 (pm20) cc_final: 0.8016 (pm20) REVERT: E 128 GLU cc_start: 0.8906 (pm20) cc_final: 0.8471 (pm20) REVERT: E 226 ASP cc_start: 0.8419 (m-30) cc_final: 0.7710 (m-30) REVERT: E 230 GLU cc_start: 0.8486 (mp0) cc_final: 0.8251 (mp0) REVERT: E 265 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: E 345 ARG cc_start: 0.8611 (tpp80) cc_final: 0.8363 (ttm-80) REVERT: E 416 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7244 (p0) REVERT: F 87 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8363 (pm20) REVERT: F 206 GLN cc_start: 0.8944 (mt0) cc_final: 0.8714 (mp10) REVERT: F 465 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6977 (tp40) REVERT: G 13 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8140 (tp40) REVERT: G 81 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7303 (mt) REVERT: G 190 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8446 (t0) REVERT: H 13 PHE cc_start: 0.8410 (m-80) cc_final: 0.7626 (m-80) REVERT: H 14 ARG cc_start: 0.8827 (mpp80) cc_final: 0.8538 (mpp80) REVERT: H 63 MET cc_start: 0.7852 (mtm) cc_final: 0.7111 (mtm) REVERT: H 93 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9071 (mm) outliers start: 62 outliers final: 23 residues processed: 294 average time/residue: 0.8002 time to fit residues: 270.4356 Evaluate side-chains 278 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 156 SER Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 93 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 211 optimal weight: 0.5980 chunk 105 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 310 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 304 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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** G 55 GLN G 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.094547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.068898 restraints weight = 48244.414| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.63 r_work: 0.2745 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27508 Z= 0.221 Angle : 0.596 7.255 37289 Z= 0.300 Chirality : 0.046 0.214 4161 Planarity : 0.005 0.055 4874 Dihedral : 4.943 72.070 3851 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.22 % Allowed : 17.48 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 3437 helix: 1.68 (0.15), residues: 1311 sheet: 0.29 (0.22), residues: 563 loop : -0.32 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 95 TYR 0.013 0.001 TYR A 562 PHE 0.019 0.002 PHE C 230 TRP 0.015 0.001 TRP B 424 HIS 0.005 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00543 (27508) covalent geometry : angle 0.59573 (37289) hydrogen bonds : bond 0.05452 ( 1012) hydrogen bonds : angle 4.25086 ( 2901) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8423 (mt-10) REVERT: A 122 MET cc_start: 0.8926 (mtp) cc_final: 0.8679 (mtt) REVERT: A 294 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8260 (mtt) REVERT: A 469 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8799 (tm-30) REVERT: B 209 MET cc_start: 0.7750 (mtp) cc_final: 0.7332 (ttm) REVERT: B 239 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: B 269 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8893 (t80) REVERT: B 323 MET cc_start: 0.9219 (mtt) cc_final: 0.8829 (mtt) REVERT: B 397 GLN cc_start: 0.8724 (mm110) cc_final: 0.8342 (mm110) REVERT: C 268 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: C 348 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8728 (tt0) REVERT: C 558 GLU cc_start: 0.8698 (mt-10) cc_final: 0.7600 (tp30) REVERT: D 53 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: D 214 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8758 (tm) REVERT: D 327 ASP cc_start: 0.8878 (t0) cc_final: 0.8613 (t0) REVERT: D 334 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8966 (mt-10) REVERT: D 394 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8939 (ttmm) REVERT: D 420 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8091 (mtp-110) REVERT: E 61 GLU cc_start: 0.8390 (pm20) cc_final: 0.8101 (pm20) REVERT: E 128 GLU cc_start: 0.8906 (pm20) cc_final: 0.8458 (pm20) REVERT: E 226 ASP cc_start: 0.8374 (m-30) cc_final: 0.7739 (m-30) REVERT: E 230 GLU cc_start: 0.8556 (mp0) cc_final: 0.8244 (mp0) REVERT: E 345 ARG cc_start: 0.8623 (tpp80) cc_final: 0.8348 (ttm-80) REVERT: E 416 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7297 (p0) REVERT: E 469 GLU cc_start: 0.6525 (tt0) cc_final: 0.5071 (mp0) REVERT: F 401 GLU cc_start: 0.8082 (pp20) cc_final: 0.7604 (tm-30) REVERT: F 465 GLN cc_start: 0.7236 (tm-30) cc_final: 0.6750 (tp40) REVERT: G 13 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8170 (tp40) REVERT: G 81 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7358 (mt) REVERT: G 144 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8388 (mm-30) REVERT: H 13 PHE cc_start: 0.8387 (m-80) cc_final: 0.7586 (m-80) REVERT: H 14 ARG cc_start: 0.8812 (mpp80) cc_final: 0.8054 (mpp80) REVERT: H 66 ARG cc_start: 0.7314 (tmm-80) cc_final: 0.6928 (tmm-80) REVERT: H 93 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9086 (mm) outliers start: 63 outliers final: 33 residues processed: 293 average time/residue: 0.8291 time to fit residues: 277.7184 Evaluate side-chains 287 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 93 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 163 optimal weight: 0.5980 chunk 168 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 304 optimal weight: 0.1980 chunk 226 optimal weight: 6.9990 chunk 293 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN G 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.096880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.071287 restraints weight = 47690.101| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.62 r_work: 0.2790 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27508 Z= 0.114 Angle : 0.539 9.362 37289 Z= 0.269 Chirality : 0.043 0.245 4161 Planarity : 0.004 0.048 4874 Dihedral : 4.688 67.374 3851 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.69 % Allowed : 18.11 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.15), residues: 3437 helix: 1.86 (0.15), residues: 1301 sheet: 0.44 (0.22), residues: 563 loop : -0.21 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 130 TYR 0.011 0.001 TYR C 500 PHE 0.012 0.001 PHE A 230 TRP 0.012 0.001 TRP B 119 HIS 0.002 0.000 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00266 (27508) covalent geometry : angle 0.53863 (37289) hydrogen bonds : bond 0.04207 ( 1012) hydrogen bonds : angle 4.08979 ( 2901) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8893 (mtp) cc_final: 0.8642 (mtt) REVERT: A 393 GLU cc_start: 0.7637 (tt0) cc_final: 0.6940 (pt0) REVERT: A 469 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8824 (tm-30) REVERT: B 209 MET cc_start: 0.7532 (mtp) cc_final: 0.7317 (ttm) REVERT: B 239 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8216 (mt0) REVERT: B 269 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8914 (t80) REVERT: B 323 MET cc_start: 0.9196 (mtt) cc_final: 0.8819 (mtt) REVERT: B 397 GLN cc_start: 0.8637 (mm110) cc_final: 0.8378 (mm110) REVERT: B 467 ILE cc_start: 0.7220 (mp) cc_final: 0.6988 (mp) REVERT: C 268 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: C 348 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8733 (tt0) REVERT: C 558 GLU cc_start: 0.8706 (mt-10) cc_final: 0.7623 (tp30) REVERT: D 53 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: D 214 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8761 (tm) REVERT: D 327 ASP cc_start: 0.8721 (t0) cc_final: 0.8466 (t0) REVERT: D 334 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8938 (mt-10) REVERT: D 342 GLU cc_start: 0.8440 (pm20) cc_final: 0.8226 (pm20) REVERT: D 420 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8020 (mtp-110) REVERT: E 61 GLU cc_start: 0.8406 (pm20) cc_final: 0.8036 (pm20) REVERT: E 128 GLU cc_start: 0.8900 (pm20) cc_final: 0.8464 (pm20) REVERT: E 226 ASP cc_start: 0.8399 (m-30) cc_final: 0.7698 (m-30) REVERT: E 230 GLU cc_start: 0.8493 (mp0) cc_final: 0.8248 (mp0) REVERT: E 345 ARG cc_start: 0.8641 (tpp80) cc_final: 0.8406 (ttm-80) REVERT: E 416 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7262 (p0) REVERT: E 428 GLN cc_start: 0.7564 (tt0) cc_final: 0.7134 (mm-40) REVERT: F 401 GLU cc_start: 0.8013 (pp20) cc_final: 0.7559 (tm-30) REVERT: F 465 GLN cc_start: 0.7230 (tm-30) cc_final: 0.6817 (tp40) REVERT: G 13 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8201 (tp40) REVERT: G 81 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7287 (mt) REVERT: H 13 PHE cc_start: 0.8412 (m-80) cc_final: 0.7622 (m-80) REVERT: H 66 ARG cc_start: 0.7305 (tmm-80) cc_final: 0.7003 (tmm-80) REVERT: H 93 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9000 (mm) outliers start: 48 outliers final: 25 residues processed: 281 average time/residue: 0.8121 time to fit residues: 261.3689 Evaluate side-chains 272 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 93 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 116 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 320 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** G 55 GLN G 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.096533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.070914 restraints weight = 47515.705| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.61 r_work: 0.2784 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27508 Z= 0.129 Angle : 0.541 9.085 37289 Z= 0.269 Chirality : 0.044 0.244 4161 Planarity : 0.004 0.067 4874 Dihedral : 4.650 64.511 3851 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.34 % Allowed : 18.50 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.03 (0.15), residues: 3437 helix: 1.87 (0.15), residues: 1307 sheet: 0.43 (0.23), residues: 561 loop : -0.19 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG H 95 TYR 0.013 0.001 TYR H 21 PHE 0.013 0.001 PHE C 230 TRP 0.012 0.001 TRP B 119 HIS 0.002 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00309 (27508) covalent geometry : angle 0.54080 (37289) hydrogen bonds : bond 0.04345 ( 1012) hydrogen bonds : angle 4.07681 ( 2901) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8925 (mtp) cc_final: 0.8670 (mtt) REVERT: A 393 GLU cc_start: 0.7672 (tt0) cc_final: 0.6966 (pt0) REVERT: B 130 ARG cc_start: 0.8657 (mtm-85) cc_final: 0.8441 (mpp80) REVERT: B 209 MET cc_start: 0.7610 (mtp) cc_final: 0.7329 (ttm) REVERT: B 269 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8927 (t80) REVERT: B 323 MET cc_start: 0.9211 (mtt) cc_final: 0.8835 (mtt) REVERT: B 397 GLN cc_start: 0.8681 (mm110) cc_final: 0.8292 (mm110) REVERT: B 467 ILE cc_start: 0.7237 (mp) cc_final: 0.6976 (mp) REVERT: C 268 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: C 348 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8703 (tt0) REVERT: C 558 GLU cc_start: 0.8700 (mt-10) cc_final: 0.7883 (mm-30) REVERT: D 53 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: D 162 GLU cc_start: 0.8958 (mp0) cc_final: 0.8609 (mp0) REVERT: D 214 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8784 (tm) REVERT: D 327 ASP cc_start: 0.8741 (t0) cc_final: 0.8500 (t0) REVERT: D 334 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8948 (mt-10) REVERT: D 420 ARG cc_start: 0.8376 (ttp80) cc_final: 0.8026 (mtp-110) REVERT: E 61 GLU cc_start: 0.8411 (pm20) cc_final: 0.8039 (pm20) REVERT: E 128 GLU cc_start: 0.8908 (pm20) cc_final: 0.8460 (pm20) REVERT: E 226 ASP cc_start: 0.8392 (m-30) cc_final: 0.7709 (m-30) REVERT: E 230 GLU cc_start: 0.8542 (mp0) cc_final: 0.8289 (mp0) REVERT: E 345 ARG cc_start: 0.8623 (tpp80) cc_final: 0.8387 (ttm-80) REVERT: E 416 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7281 (p0) REVERT: E 428 GLN cc_start: 0.7558 (tt0) cc_final: 0.7130 (mm-40) REVERT: F 87 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: F 401 GLU cc_start: 0.8011 (pp20) cc_final: 0.7570 (tm-30) REVERT: F 465 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6791 (tp40) REVERT: G 13 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8076 (tp40) REVERT: G 81 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7287 (mt) REVERT: G 144 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8387 (mm-30) REVERT: G 165 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7365 (tt0) REVERT: H 13 PHE cc_start: 0.8365 (m-80) cc_final: 0.7553 (m-80) REVERT: H 66 ARG cc_start: 0.7306 (tmm-80) cc_final: 0.6975 (tmm-80) REVERT: H 97 THR cc_start: 0.7670 (m) cc_final: 0.7389 (p) outliers start: 38 outliers final: 24 residues processed: 274 average time/residue: 0.8313 time to fit residues: 260.1589 Evaluate side-chains 274 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 416 ASP Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 81 LEU 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 157 THR Chi-restraints excluded: chain H residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 163 optimal weight: 4.9990 chunk 314 optimal weight: 0.7980 chunk 322 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 chunk 315 optimal weight: 7.9990 chunk 211 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 226 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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** G 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.095951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.070366 restraints weight = 47784.382| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.61 r_work: 0.2761 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27508 Z= 0.164 Angle : 0.567 8.879 37289 Z= 0.284 Chirality : 0.045 0.243 4161 Planarity : 0.004 0.047 4874 Dihedral : 4.718 62.243 3851 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.41 % Allowed : 18.57 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.99 (0.15), residues: 3437 helix: 1.84 (0.15), residues: 1306 sheet: 0.47 (0.22), residues: 567 loop : -0.23 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 130 TYR 0.013 0.001 TYR C 500 PHE 0.015 0.001 PHE C 230 TRP 0.012 0.001 TRP B 119 HIS 0.003 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00402 (27508) covalent geometry : angle 0.56750 (37289) hydrogen bonds : bond 0.04747 ( 1012) hydrogen bonds : angle 4.13259 ( 2901) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10585.37 seconds wall clock time: 180 minutes 41.21 seconds (10841.21 seconds total)