Starting phenix.real_space_refine on Sun Feb 8 10:05:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uzk_26914/02_2026/7uzk_26914.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzk_26914/02_2026/7uzk_26914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uzk_26914/02_2026/7uzk_26914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzk_26914/02_2026/7uzk_26914.map" model { file = "/net/cci-nas-00/data/ceres_data/7uzk_26914/02_2026/7uzk_26914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzk_26914/02_2026/7uzk_26914.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 1.197 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 2 5.49 5 Mg 1 5.21 5 S 226 5.16 5 C 28656 2.51 5 N 7766 2.21 5 O 8595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 204 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: 45246 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4568 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 558} Chain breaks: 2 Chain: "B" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4657 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 570} Chain: "C" Number of atoms: 4648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4648 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 3603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3603 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Chain: "E" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3632 Classifications: {'peptide': 464} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 436} Chain breaks: 1 Chain: "F" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3576 Classifications: {'peptide': 457} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 429} Chain breaks: 1 Chain: "G" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2919 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 9, 'TRANS': 348} Chain breaks: 1 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1689 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 3, 'TRANS': 203} Chain breaks: 1 Chain: "I" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1341 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain: "J" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1807 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain: "K" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1773 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 5, 'TRANS': 212} Chain: "L" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "M" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "N" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 929 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "O" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 929 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "Q" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2122 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 9, 'TRANS': 252} Chain: "R" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2126 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain: "S" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2147 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 9, 'TRANS': 256} Chain: "T" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1376 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} 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} Time building chain proxies: 10.16, per 1000 atoms: 0.22 Number of scatterers: 45246 At special positions: 0 Unit cell: (173.84, 185.5, 195.04, 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 226 16.00 P 2 15.00 Mg 1 11.99 O 8595 8.00 N 7766 7.00 C 28656 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: 4.97 Conformation dependent library (CDL) restraints added in 1.7 seconds 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10716 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 33 sheets defined 54.2% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 259 through 266 Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.554A pdb=" N ARG A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 319 through 340 removed outlier: 3.579A pdb=" N GLU A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 365 removed outlier: 3.637A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 387 Processing helix chain 'A' and resid 419 through 427 removed outlier: 3.525A pdb=" N GLY A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 471 through 497 removed outlier: 3.837A pdb=" N LEU A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 519 Processing helix chain 'A' and resid 533 through 557 Processing helix chain 'A' and resid 566 through 583 removed outlier: 6.897A pdb=" N GLU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 587 removed outlier: 3.523A pdb=" N LYS A 587 " --> pdb=" O MET A 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 584 through 587' Processing helix chain 'A' and resid 593 through 615 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 256 through 267 removed outlier: 3.723A pdb=" N SER B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 291 Processing helix chain 'B' and resid 319 through 340 removed outlier: 5.120A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 365 removed outlier: 3.539A pdb=" N TRP B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 4.072A pdb=" N GLY B 373 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 387 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 419 through 429 Processing helix chain 'B' and resid 436 through 442 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 471 through 497 removed outlier: 3.731A pdb=" N LEU B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 519 Processing helix chain 'B' and resid 533 through 559 Processing helix chain 'B' and resid 566 through 584 removed outlier: 6.844A pdb=" N GLU B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 587 No H-bonds generated for 'chain 'B' and resid 585 through 587' Processing helix chain 'B' and resid 593 through 616 Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 255 through 266 Processing helix chain 'C' and resid 280 through 291 removed outlier: 3.884A pdb=" N MET C 284 " --> pdb=" O ARG C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 339 removed outlier: 3.789A pdb=" N ALA C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 365 removed outlier: 4.095A pdb=" N TRP C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.624A pdb=" N GLY C 373 " --> pdb=" O ALA C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 412 through 416 removed outlier: 3.558A pdb=" N ASP C 416 " --> pdb=" O PRO C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 427 removed outlier: 3.521A pdb=" N GLY C 427 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 442 removed outlier: 3.607A pdb=" N ARG C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 471 through 497 removed outlier: 4.021A pdb=" N LEU C 475 " --> pdb=" O GLU C 471 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 519 Processing helix chain 'C' and resid 533 through 559 Processing helix chain 'C' and resid 566 through 584 removed outlier: 6.688A pdb=" N GLU C 576 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 587 No H-bonds generated for 'chain 'C' and resid 585 through 587' Processing helix chain 'C' and resid 593 through 615 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 198 through 210 Processing helix chain 'D' and resid 237 through 251 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 268 through 272 Processing helix chain 'D' and resid 273 through 288 Processing helix chain 'D' and resid 299 through 314 Processing helix chain 'D' and resid 319 through 323 removed outlier: 3.587A pdb=" N GLY D 322 " --> pdb=" O GLY D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 336 removed outlier: 3.579A pdb=" N ILE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 360 Processing helix chain 'D' and resid 363 through 371 removed outlier: 3.622A pdb=" N TYR D 371 " --> pdb=" O ASP D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 386 Processing helix chain 'D' and resid 401 through 406 removed outlier: 3.702A pdb=" N ALA D 405 " --> pdb=" O LEU D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 440 removed outlier: 4.198A pdb=" N VAL D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 444 Processing helix chain 'D' and resid 445 through 462 Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 486 through 487 No H-bonds generated for 'chain 'D' and resid 486 through 487' Processing helix chain 'D' and resid 488 through 492 Processing helix chain 'D' and resid 496 through 504 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 237 through 251 Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 267 through 288 removed outlier: 3.543A pdb=" N ARG E 271 " --> pdb=" O PRO E 267 " (cutoff:3.500A) Proline residue: E 275 - end of helix Processing helix chain 'E' and resid 299 through 314 Processing helix chain 'E' and resid 319 through 323 removed outlier: 3.511A pdb=" N PHE E 323 " --> pdb=" O ARG E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 325 No H-bonds generated for 'chain 'E' and resid 324 through 325' Processing helix chain 'E' and resid 326 through 336 Processing helix chain 'E' and resid 357 through 360 Processing helix chain 'E' and resid 363 through 373 Processing helix chain 'E' and resid 380 through 386 Processing helix chain 'E' and resid 401 through 406 removed outlier: 3.622A pdb=" N ALA E 405 " --> pdb=" O LEU E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 440 removed outlier: 3.728A pdb=" N ASP E 431 " --> pdb=" O ALA E 427 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA E 437 " --> pdb=" O GLN E 433 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 444 Processing helix chain 'E' and resid 445 through 462 removed outlier: 3.753A pdb=" N GLN E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'E' and resid 486 through 487 No H-bonds generated for 'chain 'E' and resid 486 through 487' Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 496 through 504 Processing helix chain 'F' and resid 124 through 128 Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 198 through 210 Processing helix chain 'F' and resid 237 through 251 Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 269 through 288 removed outlier: 3.980A pdb=" N ILE F 273 " --> pdb=" O ILE F 269 " (cutoff:3.500A) Proline residue: F 275 - end of helix Processing helix chain 'F' and resid 299 through 314 Processing helix chain 'F' and resid 319 through 323 Processing helix chain 'F' and resid 326 through 336 removed outlier: 3.570A pdb=" N ILE F 334 " --> pdb=" O ASP F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 360 Processing helix chain 'F' and resid 363 through 371 Processing helix chain 'F' and resid 380 through 386 Processing helix chain 'F' and resid 401 through 405 Processing helix chain 'F' and resid 414 through 440 removed outlier: 3.501A pdb=" N ALA F 437 " --> pdb=" O GLN F 433 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 444 Processing helix chain 'F' and resid 445 through 462 removed outlier: 3.519A pdb=" N GLN F 456 " --> pdb=" O LEU F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 486 through 487 No H-bonds generated for 'chain 'F' and resid 486 through 487' Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 496 through 504 Processing helix chain 'G' and resid 14 through 27 removed outlier: 3.807A pdb=" N THR G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 81 removed outlier: 4.072A pdb=" N GLY G 53 " --> pdb=" O ASP G 49 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET G 76 " --> pdb=" O VAL G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 90 Processing helix chain 'G' and resid 97 through 104 Processing helix chain 'G' and resid 117 through 158 removed outlier: 3.994A pdb=" N LEU G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 169 removed outlier: 3.685A pdb=" N GLU G 168 " --> pdb=" O SER G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 175 Processing helix chain 'G' and resid 193 through 201 Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 254 through 310 removed outlier: 3.575A pdb=" N MET G 265 " --> pdb=" O ASP G 261 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN G 266 " --> pdb=" O LYS G 262 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY G 277 " --> pdb=" O LYS G 273 " (cutoff:3.500A) Proline residue: G 278 - end of helix Processing helix chain 'G' and resid 327 through 340 Processing helix chain 'G' and resid 341 through 343 No H-bonds generated for 'chain 'G' and resid 341 through 343' Processing helix chain 'H' and resid 12 through 77 removed outlier: 3.955A pdb=" N LYS H 49 " --> pdb=" O ARG H 45 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY H 59 " --> pdb=" O LYS H 55 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU H 60 " --> pdb=" O MET H 56 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 175 removed outlier: 4.007A pdb=" N ALA H 141 " --> pdb=" O ASN H 137 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU H 144 " --> pdb=" O LYS H 140 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU H 160 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA H 161 " --> pdb=" O THR H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 223 removed outlier: 3.630A pdb=" N ARG H 179 " --> pdb=" O VAL H 175 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS H 204 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE H 205 " --> pdb=" O ARG H 201 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU H 207 " --> pdb=" O LYS H 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 108 removed outlier: 3.849A pdb=" N GLU I 65 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL I 105 " --> pdb=" O ARG I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 128 removed outlier: 3.695A pdb=" N VAL I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 160 Proline residue: I 153 - end of helix Processing helix chain 'I' and resid 196 through 207 removed outlier: 4.007A pdb=" N GLN I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 217 Processing helix chain 'J' and resid 5 through 63 removed outlier: 3.525A pdb=" N LYS J 52 " --> pdb=" O THR J 48 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 108 removed outlier: 3.701A pdb=" N GLN J 71 " --> pdb=" O GLN J 67 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS J 107 " --> pdb=" O SER J 103 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP J 108 " --> pdb=" O LYS J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 128 removed outlier: 3.667A pdb=" N LEU J 121 " --> pdb=" O ASP J 117 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN J 126 " --> pdb=" O GLN J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 139 No H-bonds generated for 'chain 'J' and resid 137 through 139' Processing helix chain 'J' and resid 140 through 160 Proline residue: J 153 - end of helix Processing helix chain 'J' and resid 196 through 207 Processing helix chain 'J' and resid 207 through 217 removed outlier: 3.615A pdb=" N GLY J 213 " --> pdb=" O PRO J 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 108 removed outlier: 4.187A pdb=" N GLY K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS K 59 " --> pdb=" O GLU K 55 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL K 83 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS K 104 " --> pdb=" O GLN K 100 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL K 105 " --> pdb=" O ARG K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 128 removed outlier: 3.604A pdb=" N LEU K 121 " --> pdb=" O ASP K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 139 No H-bonds generated for 'chain 'K' and resid 137 through 139' Processing helix chain 'K' and resid 140 through 160 Proline residue: K 153 - end of helix Processing helix chain 'K' and resid 196 through 217 removed outlier: 3.561A pdb=" N GLN K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Proline residue: K 209 - end of helix Processing helix chain 'L' and resid 13 through 17 Processing helix chain 'L' and resid 46 through 57 removed outlier: 4.347A pdb=" N PHE L 52 " --> pdb=" O ILE L 48 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN L 54 " --> pdb=" O ASP L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 73 removed outlier: 3.597A pdb=" N MET L 73 " --> pdb=" O TYR L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 80 removed outlier: 3.548A pdb=" N ALA L 80 " --> pdb=" O HIS L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 110 Processing helix chain 'M' and resid 56 through 104 removed outlier: 3.662A pdb=" N SER M 71 " --> pdb=" O GLY M 67 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ASP M 93 " --> pdb=" O GLU M 89 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU M 94 " --> pdb=" O GLN M 90 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA M 101 " --> pdb=" O ASP M 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 70 removed outlier: 3.710A pdb=" N ALA N 36 " --> pdb=" O ARG N 32 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS N 37 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA N 42 " --> pdb=" O GLU N 38 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N SER N 65 " --> pdb=" O ALA N 61 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N HIS N 66 " --> pdb=" O ALA N 62 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER N 68 " --> pdb=" O GLY N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 105 removed outlier: 4.327A pdb=" N GLU N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP N 93 " --> pdb=" O GLU N 89 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU N 94 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 90 removed outlier: 3.936A pdb=" N LYS O 34 " --> pdb=" O ASN O 30 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU O 45 " --> pdb=" O GLN O 41 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER O 71 " --> pdb=" O GLY O 67 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU O 72 " --> pdb=" O SER O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 105 Processing helix chain 'Q' and resid 14 through 37 Processing helix chain 'Q' and resid 42 through 49 removed outlier: 3.714A pdb=" N ARG Q 46 " --> pdb=" O LEU Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 54 Processing helix chain 'Q' and resid 62 through 71 Processing helix chain 'Q' and resid 77 through 98 removed outlier: 3.519A pdb=" N LEU Q 88 " --> pdb=" O ARG Q 84 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU Q 94 " --> pdb=" O GLU Q 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 118 removed outlier: 3.611A pdb=" N HIS Q 118 " --> pdb=" O LYS Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 123 Processing helix chain 'Q' and resid 124 through 140 removed outlier: 3.940A pdb=" N LEU Q 140 " --> pdb=" O LEU Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 167 Processing helix chain 'Q' and resid 172 through 188 removed outlier: 3.715A pdb=" N LYS Q 180 " --> pdb=" O ASN Q 176 " (cutoff:3.500A) Processing helix chain 'Q' and resid 192 through 207 Processing helix chain 'Q' and resid 218 through 234 removed outlier: 3.748A pdb=" N TYR Q 232 " --> pdb=" O THR Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 250 Processing helix chain 'Q' and resid 256 through 274 Processing helix chain 'R' and resid 14 through 37 Processing helix chain 'R' and resid 42 through 54 removed outlier: 3.928A pdb=" N ASP R 48 " --> pdb=" O LYS R 44 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASP R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL R 52 " --> pdb=" O ASP R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 71 Processing helix chain 'R' and resid 77 through 98 Processing helix chain 'R' and resid 104 through 118 Processing helix chain 'R' and resid 124 through 141 removed outlier: 3.898A pdb=" N TYR R 139 " --> pdb=" O GLN R 135 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS R 141 " --> pdb=" O THR R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 167 Processing helix chain 'R' and resid 172 through 188 Processing helix chain 'R' and resid 192 through 207 Processing helix chain 'R' and resid 218 through 234 removed outlier: 3.516A pdb=" N MET R 229 " --> pdb=" O LEU R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 237 No H-bonds generated for 'chain 'R' and resid 235 through 237' Processing helix chain 'R' and resid 239 through 250 removed outlier: 3.751A pdb=" N SER R 250 " --> pdb=" O LEU R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 274 Processing helix chain 'S' and resid 14 through 37 Processing helix chain 'S' and resid 42 through 49 Processing helix chain 'S' and resid 49 through 54 Processing helix chain 'S' and resid 61 through 71 Processing helix chain 'S' and resid 77 through 98 removed outlier: 3.606A pdb=" N LEU S 88 " --> pdb=" O ARG S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 117 Processing helix chain 'S' and resid 120 through 123 Processing helix chain 'S' and resid 124 through 141 removed outlier: 3.532A pdb=" N TYR S 139 " --> pdb=" O GLN S 135 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 167 Processing helix chain 'S' and resid 172 through 188 Processing helix chain 'S' and resid 192 through 207 Processing helix chain 'S' and resid 218 through 234 removed outlier: 3.830A pdb=" N TYR S 232 " --> pdb=" O THR S 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 239 through 251 Processing helix chain 'S' and resid 256 through 274 Processing helix chain 'T' and resid 63 through 72 removed outlier: 3.556A pdb=" N GLN T 69 " --> pdb=" O MET T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 79 Processing helix chain 'T' and resid 89 through 93 Processing helix chain 'T' and resid 95 through 104 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 25 removed outlier: 5.711A pdb=" N VAL A 21 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N CYS A 32 " --> pdb=" O VAL A 21 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 28 through 32 current: chain 'A' and resid 50 through 58 removed outlier: 6.547A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N MET A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 61 through 66 current: chain 'B' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 28 through 32 current: chain 'B' and resid 50 through 58 removed outlier: 6.651A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 61 through 66 current: chain 'C' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 28 through 32 current: chain 'C' and resid 50 through 58 removed outlier: 6.623A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 61 through 66 current: chain 'D' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 60 current: chain 'D' and resid 81 through 90 removed outlier: 6.695A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 93 through 98 current: chain 'E' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 57 through 60 current: chain 'E' and resid 81 through 90 removed outlier: 5.732A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU E 88 " --> pdb=" O VAL E 95 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 93 through 98 current: chain 'F' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 57 through 60 current: chain 'F' and resid 81 through 90 removed outlier: 5.710A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 93 through 98 current: chain 'I' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 164 through 167 current: chain 'I' and resid 190 through 195 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 190 through 195 current: chain 'J' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 164 through 167 current: chain 'J' and resid 190 through 195 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 190 through 195 current: chain 'K' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 164 through 167 current: chain 'K' and resid 190 through 195 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 98 through 99 current: chain 'A' and resid 309 through 315 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 309 through 315 current: chain 'A' and resid 401 through 410 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 401 through 410 current: chain 'A' and resid 454 through 455 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 167 removed outlier: 3.573A pdb=" N GLY A 154 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLU A 134 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 6.212A pdb=" N GLU A 193 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 298 Processing sheet with id=AA7, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 98 through 99 current: chain 'B' and resid 309 through 312 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 309 through 312 current: chain 'B' and resid 401 through 410 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 401 through 410 current: chain 'B' and resid 454 through 455 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 167 removed outlier: 3.539A pdb=" N GLY B 154 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU B 134 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 148 removed outlier: 5.598A pdb=" N VAL B 176 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU B 195 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AB3, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AB4, first strand: chain 'C' and resid 98 through 100 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 98 through 100 current: chain 'C' and resid 309 through 314 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 309 through 314 current: chain 'C' and resid 401 through 410 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 401 through 410 current: chain 'C' and resid 454 through 455 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 164 through 167 Processing sheet with id=AB6, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.240A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 226 through 227 removed outlier: 4.558A pdb=" N CYS C 240 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AB9, first strand: chain 'D' and resid 120 through 123 Processing sheet with id=AC1, first strand: chain 'D' and resid 130 through 133 removed outlier: 6.743A pdb=" N ARG D 130 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N LEU D 261 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE D 132 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LEU D 263 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE D 191 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 163 through 164 removed outlier: 4.391A pdb=" N ARG D 340 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 183 through 184 removed outlier: 4.407A pdb=" N ILE D 183 " --> pdb=" O ILE D 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 120 through 123 Processing sheet with id=AC5, first strand: chain 'E' and resid 131 through 133 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 131 through 133 current: chain 'E' and resid 257 through 263 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 257 through 263 current: chain 'E' and resid 347 through 355 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 347 through 355 current: chain 'E' and resid 398 through 399 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 170 removed outlier: 4.622A pdb=" N ILE E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 120 through 123 Processing sheet with id=AC8, first strand: chain 'F' and resid 130 through 133 removed outlier: 3.905A pdb=" N ARG F 130 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA F 228 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE F 296 " --> pdb=" O ALA F 228 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL F 230 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N THR F 298 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA F 232 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL F 293 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE F 351 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL F 295 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE F 353 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU F 297 " --> pdb=" O ILE F 353 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N THR F 355 " --> pdb=" O LEU F 297 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE F 191 " --> pdb=" O LEU F 354 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 163 through 164 removed outlier: 4.292A pdb=" N ARG F 340 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 183 through 184 removed outlier: 4.395A pdb=" N ILE F 183 " --> pdb=" O ILE F 170 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 33 through 37 removed outlier: 6.533A pdb=" N GLU G 3 " --> pdb=" O PRO G 323 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 214 through 218 removed outlier: 6.114A pdb=" N VAL G 215 " --> pdb=" O ASN G 226 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN G 226 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU G 186 " --> pdb=" O ARG G 249 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 92 through 101 Processing sheet with id=AD5, first strand: chain 'L' and resid 36 through 38 removed outlier: 6.036A pdb=" N LEU L 7 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE L 63 " --> pdb=" O LEU L 7 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 83 through 88 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 83 through 88 current: chain 'T' and resid 121 through 126 removed outlier: 4.236A pdb=" N ILE T 121 " --> pdb=" O PHE T 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 151 through 155 current: chain 'T' and resid 170 through 173 removed outlier: 6.246A pdb=" N HIS T 190 " --> pdb=" O ASP T 185 " (cutoff:3.500A) 2382 hydrogen bonds defined for protein. 6924 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: 9.09 Time building geometry restraints manager: 6.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 9259 1.32 - 1.45: 9796 1.45 - 1.57: 26581 1.57 - 1.70: 1 1.70 - 1.83: 398 Bond restraints: 46035 Sorted by residual: bond pdb=" C ALA T 76 " pdb=" N ARG T 77 " ideal model delta sigma weight residual 1.335 1.474 -0.139 1.30e-02 5.92e+03 1.15e+02 bond pdb=" C PRO G 113 " pdb=" N ILE G 114 " ideal model delta sigma weight residual 1.334 1.459 -0.125 1.26e-02 6.30e+03 9.84e+01 bond pdb=" C LEU F 484 " pdb=" N ARG F 485 " ideal model delta sigma weight residual 1.334 1.205 0.129 1.38e-02 5.25e+03 8.72e+01 bond pdb=" C ARG T 77 " pdb=" N VAL T 78 " ideal model delta sigma weight residual 1.332 1.249 0.084 1.06e-02 8.90e+03 6.21e+01 bond pdb=" C4 ADP C 701 " pdb=" C5 ADP C 701 " ideal model delta sigma weight residual 1.490 1.348 0.142 2.00e-02 2.50e+03 5.07e+01 ... (remaining 46030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 55996 2.90 - 5.81: 6034 5.81 - 8.71: 93 8.71 - 11.61: 7 11.61 - 14.52: 2 Bond angle restraints: 62132 Sorted by residual: angle pdb=" O LEU F 484 " pdb=" C LEU F 484 " pdb=" N ARG F 485 " ideal model delta sigma weight residual 122.22 113.99 8.23 1.17e+00 7.31e-01 4.95e+01 angle pdb=" CA LEU F 484 " pdb=" C LEU F 484 " pdb=" N ARG F 485 " ideal model delta sigma weight residual 117.63 125.31 -7.68 1.25e+00 6.40e-01 3.78e+01 angle pdb=" CA ASP D 359 " pdb=" CB ASP D 359 " pdb=" CG ASP D 359 " ideal model delta sigma weight residual 112.60 118.56 -5.96 1.00e+00 1.00e+00 3.55e+01 angle pdb=" O PRO G 113 " pdb=" C PRO G 113 " pdb=" N ILE G 114 " ideal model delta sigma weight residual 123.03 129.75 -6.72 1.13e+00 7.83e-01 3.54e+01 angle pdb=" N GLN H 91 " pdb=" CA GLN H 91 " pdb=" C GLN H 91 " ideal model delta sigma weight residual 112.92 120.02 -7.10 1.23e+00 6.61e-01 3.34e+01 ... (remaining 62127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.57: 27172 22.57 - 45.14: 938 45.14 - 67.70: 153 67.70 - 90.27: 58 90.27 - 112.84: 1 Dihedral angle restraints: 28322 sinusoidal: 11711 harmonic: 16611 Sorted by residual: dihedral pdb=" CA GLY B 396 " pdb=" C GLY B 396 " pdb=" N ASN B 397 " pdb=" CA ASN B 397 " ideal model delta harmonic sigma weight residual -180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ASP C 349 " pdb=" C ASP C 349 " pdb=" N SER C 350 " pdb=" CA SER C 350 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ALA H 90 " pdb=" C ALA H 90 " pdb=" N GLN H 91 " pdb=" CA GLN H 91 " ideal model delta harmonic sigma weight residual 180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 28319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 5815 0.119 - 0.237: 1045 0.237 - 0.356: 97 0.356 - 0.475: 10 0.475 - 0.593: 2 Chirality restraints: 6969 Sorted by residual: chirality pdb=" CA ASN C 397 " pdb=" N ASN C 397 " pdb=" C ASN C 397 " pdb=" CB ASN C 397 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.80e+00 chirality pdb=" CA ASP E 299 " pdb=" N ASP E 299 " pdb=" C ASP E 299 " pdb=" CB ASP E 299 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.29e+00 chirality pdb=" CA LYS A 139 " pdb=" N LYS A 139 " pdb=" C LYS A 139 " pdb=" CB LYS A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.07e+00 ... (remaining 6966 not shown) Planarity restraints: 8036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 303 " -0.163 2.00e-02 2.50e+03 9.20e-02 1.69e+02 pdb=" CG TYR D 303 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR D 303 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR D 303 " 0.073 2.00e-02 2.50e+03 pdb=" CE1 TYR D 303 " 0.066 2.00e-02 2.50e+03 pdb=" CE2 TYR D 303 " 0.055 2.00e-02 2.50e+03 pdb=" CZ TYR D 303 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 303 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 122 " -0.137 2.00e-02 2.50e+03 7.88e-02 1.55e+02 pdb=" CG TRP R 122 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP R 122 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP R 122 " 0.051 2.00e-02 2.50e+03 pdb=" NE1 TRP R 122 " 0.080 2.00e-02 2.50e+03 pdb=" CE2 TRP R 122 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 122 " 0.107 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 122 " -0.106 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 122 " 0.054 2.00e-02 2.50e+03 pdb=" CH2 TRP R 122 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 122 " -0.130 2.00e-02 2.50e+03 7.69e-02 1.48e+02 pdb=" CG TRP Q 122 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 122 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 122 " 0.042 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 122 " 0.082 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 122 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 122 " 0.104 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 122 " -0.103 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 122 " 0.057 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 122 " -0.085 2.00e-02 2.50e+03 ... (remaining 8033 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5611 2.80 - 3.32: 44775 3.32 - 3.85: 72911 3.85 - 4.37: 91376 4.37 - 4.90: 153504 Nonbonded interactions: 368177 Sorted by model distance: nonbonded pdb=" OH TYR H 112 " pdb=" O ARG L 4 " model vdw 2.272 3.040 nonbonded pdb=" OH TYR F 303 " pdb=" OD1 ASP F 330 " model vdw 2.508 3.040 nonbonded pdb=" OG SER G 179 " pdb=" OE1 GLU O 15 " model vdw 2.521 3.040 nonbonded pdb=" OE2 GLU L 90 " pdb=" OG SER L 104 " model vdw 2.527 3.040 nonbonded pdb=" OG SER G 83 " pdb=" OD1 ASP G 85 " model vdw 2.528 3.040 ... (remaining 368172 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 16 through 250 or resid 258 through 412 or resid 418 throu \ gh 615)) selection = (chain 'C' and (resid 16 through 250 or resid 258 through 412 or resid 418 throu \ gh 615)) } ncs_group { reference = (chain 'D' and (resid 38 through 213 or resid 226 through 506)) selection = (chain 'E' and (resid 38 through 213 or resid 226 through 506)) selection = chain 'F' } ncs_group { reference = (chain 'J' and resid 9 through 226) selection = chain 'K' } ncs_group { reference = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'Q' selection = (chain 'R' and resid 13 through 274) selection = (chain 'S' and resid 13 through 274) } 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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 41.750 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.150 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:7.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.012 0.142 46035 Z= 0.735 Angle : 1.741 14.518 62132 Z= 1.182 Chirality : 0.089 0.593 6969 Planarity : 0.014 0.142 8036 Dihedral : 12.770 112.840 17606 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 0.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.64 % Favored : 97.20 % Rotamer: Outliers : 0.30 % Allowed : 2.94 % Favored : 96.75 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 2.95 % 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: -0.44 (0.10), residues: 5650 helix: -0.23 (0.09), residues: 2840 sheet: 0.29 (0.19), residues: 631 loop : -0.31 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 471 TYR 0.163 0.018 TYR D 303 PHE 0.072 0.012 PHE R 213 TRP 0.163 0.023 TRP C 567 HIS 0.010 0.003 HIS D 415 Details of bonding type rmsd covalent geometry : bond 0.01204 (46035) covalent geometry : angle 1.74111 (62132) hydrogen bonds : bond 0.17414 ( 2382) hydrogen bonds : angle 6.81762 ( 6924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1286 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 1271 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLN cc_start: 0.8758 (tp40) cc_final: 0.8376 (pt0) REVERT: A 163 LYS cc_start: 0.8857 (mmtm) cc_final: 0.8457 (mmtt) REVERT: A 173 ARG cc_start: 0.8467 (ptt-90) cc_final: 0.8082 (ptt180) REVERT: A 193 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7387 (mp0) REVERT: A 401 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8193 (mt-10) REVERT: A 492 ILE cc_start: 0.8155 (mt) cc_final: 0.7875 (mp) REVERT: A 584 MET cc_start: 0.8821 (mtm) cc_final: 0.8449 (mtm) REVERT: B 136 ILE cc_start: 0.8938 (mm) cc_final: 0.8659 (mp) REVERT: B 195 GLU cc_start: 0.7468 (tt0) cc_final: 0.6774 (tt0) REVERT: B 297 GLU cc_start: 0.7874 (tt0) cc_final: 0.7670 (tt0) REVERT: B 393 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8081 (tptt) REVERT: B 401 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7927 (mt-10) REVERT: B 484 GLN cc_start: 0.8216 (tp40) cc_final: 0.7859 (tp-100) REVERT: C 56 ARG cc_start: 0.8459 (ttm170) cc_final: 0.8042 (ttp-170) REVERT: C 84 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8600 (mmtp) REVERT: C 108 ASP cc_start: 0.8016 (m-30) cc_final: 0.7754 (m-30) REVERT: C 130 ASP cc_start: 0.8141 (m-30) cc_final: 0.7885 (m-30) REVERT: C 289 ARG cc_start: 0.8839 (ttp80) cc_final: 0.8613 (ttp-170) REVERT: C 293 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7581 (mm-30) REVERT: C 356 GLU cc_start: 0.8410 (tt0) cc_final: 0.8118 (mt-10) REVERT: C 371 ASP cc_start: 0.8740 (m-30) cc_final: 0.8486 (m-30) REVERT: C 438 LYS cc_start: 0.8313 (mttt) cc_final: 0.7961 (mmtm) REVERT: C 484 GLN cc_start: 0.8429 (tp40) cc_final: 0.8059 (mm-40) REVERT: C 485 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6913 (mt-10) REVERT: C 487 GLU cc_start: 0.8129 (tp30) cc_final: 0.7542 (tm-30) REVERT: C 517 ASP cc_start: 0.7868 (m-30) cc_final: 0.7567 (m-30) REVERT: C 584 MET cc_start: 0.8500 (mtm) cc_final: 0.8147 (mtm) REVERT: D 48 LYS cc_start: 0.8986 (mttt) cc_final: 0.8693 (mmmm) REVERT: D 93 LYS cc_start: 0.9018 (tttt) cc_final: 0.8772 (ttmt) REVERT: D 245 LYS cc_start: 0.8429 (tttm) cc_final: 0.8176 (ttpt) REVERT: D 250 GLU cc_start: 0.7714 (tt0) cc_final: 0.7468 (pt0) REVERT: D 321 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.7899 (mmm-85) REVERT: D 493 LYS cc_start: 0.8214 (mttt) cc_final: 0.7922 (pmtt) REVERT: D 494 ARG cc_start: 0.8464 (mmp80) cc_final: 0.8258 (mmt180) REVERT: E 126 ASP cc_start: 0.8588 (m-30) cc_final: 0.8346 (m-30) REVERT: E 315 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7763 (mp0) REVERT: E 460 LYS cc_start: 0.8860 (mttt) cc_final: 0.8454 (mtpm) REVERT: F 168 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7735 (mp0) REVERT: F 242 ARG cc_start: 0.7997 (mtt90) cc_final: 0.7427 (mtt90) REVERT: F 245 LYS cc_start: 0.7978 (tttm) cc_final: 0.7585 (ttmt) REVERT: F 410 MET cc_start: 0.8449 (mmt) cc_final: 0.8071 (mmt) REVERT: F 435 MET cc_start: 0.8852 (ttp) cc_final: 0.8553 (ttm) REVERT: F 452 LEU cc_start: 0.8756 (tp) cc_final: 0.8543 (mt) REVERT: F 491 MET cc_start: 0.8776 (mtp) cc_final: 0.8552 (mtp) REVERT: G 111 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9152 (mtpt) REVERT: G 114 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8456 (pt) REVERT: G 194 HIS cc_start: 0.7657 (t-90) cc_final: 0.7185 (t70) REVERT: H 62 MET cc_start: 0.8267 (mmt) cc_final: 0.8023 (mpt) REVERT: H 130 GLN cc_start: 0.7832 (mm110) cc_final: 0.7356 (pm20) REVERT: I 89 ASP cc_start: 0.7550 (m-30) cc_final: 0.6822 (m-30) REVERT: I 93 ASP cc_start: 0.7999 (m-30) cc_final: 0.7749 (m-30) REVERT: I 99 LYS cc_start: 0.8083 (tttt) cc_final: 0.7465 (mttt) REVERT: I 161 LYS cc_start: 0.8119 (mttp) cc_final: 0.7572 (ptmt) REVERT: I 185 ASN cc_start: 0.7731 (t0) cc_final: 0.7412 (t0) REVERT: I 208 MET cc_start: 0.9102 (mmt) cc_final: 0.8637 (mmm) REVERT: J 41 GLU cc_start: 0.7957 (tp30) cc_final: 0.7663 (tp30) REVERT: J 57 TYR cc_start: 0.8150 (m-80) cc_final: 0.7851 (m-80) REVERT: J 61 GLU cc_start: 0.7845 (tt0) cc_final: 0.7577 (mt-10) REVERT: J 76 MET cc_start: 0.7341 (mtm) cc_final: 0.6766 (tmm) REVERT: J 85 ARG cc_start: 0.7585 (mtt180) cc_final: 0.7128 (mmt180) REVERT: J 94 LEU cc_start: 0.8265 (tm) cc_final: 0.8056 (tp) REVERT: J 182 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8343 (mt-10) REVERT: J 191 LYS cc_start: 0.8840 (pttt) cc_final: 0.8501 (pttp) REVERT: J 197 GLU cc_start: 0.8178 (mp0) cc_final: 0.7207 (mp0) REVERT: J 201 ASP cc_start: 0.7722 (t0) cc_final: 0.7276 (m-30) REVERT: J 207 MET cc_start: 0.8115 (ptm) cc_final: 0.7830 (ptm) REVERT: K 60 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7820 (ttmm) REVERT: K 93 ASP cc_start: 0.7896 (m-30) cc_final: 0.7653 (m-30) REVERT: K 108 ASP cc_start: 0.7118 (t0) cc_final: 0.6433 (t0) REVERT: K 212 ARG cc_start: 0.8356 (ttt-90) cc_final: 0.8128 (ttt180) REVERT: M 98 ASN cc_start: 0.8352 (m-40) cc_final: 0.8115 (m-40) REVERT: M 112 GLU cc_start: 0.8174 (pm20) cc_final: 0.7973 (pt0) REVERT: N 48 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7540 (ttp-170) REVERT: O 80 LYS cc_start: 0.8100 (mttt) cc_final: 0.7792 (mttm) REVERT: O 97 ASP cc_start: 0.7969 (m-30) cc_final: 0.7740 (m-30) REVERT: Q 16 GLU cc_start: 0.8096 (tp30) cc_final: 0.7857 (tp30) REVERT: R 50 GLN cc_start: 0.7976 (tp40) cc_final: 0.7279 (tp40) REVERT: R 54 ILE cc_start: 0.8956 (tt) cc_final: 0.8685 (pt) REVERT: R 105 LEU cc_start: 0.7625 (mt) cc_final: 0.6935 (mp) REVERT: R 117 GLN cc_start: 0.8583 (mt0) cc_final: 0.8363 (mt0) REVERT: R 135 GLN cc_start: 0.8375 (tt0) cc_final: 0.7881 (tt0) REVERT: R 231 ASP cc_start: 0.8881 (m-30) cc_final: 0.8669 (m-30) REVERT: S 60 TYR cc_start: 0.8209 (m-80) cc_final: 0.7872 (m-80) REVERT: S 67 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6930 (mm-30) REVERT: T 185 ASP cc_start: 0.8809 (p0) cc_final: 0.8547 (p0) outliers start: 15 outliers final: 8 residues processed: 1280 average time/residue: 0.9105 time to fit residues: 1390.0186 Evaluate side-chains 838 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 828 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain T residue 153 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 0.0970 chunk 41 optimal weight: 0.7980 chunk 265 optimal weight: 0.5980 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 1.9990 chunk 414 optimal weight: 0.9980 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 0.8980 chunk 223 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 HIS C 523 ASN D 38 ASN F 382 GLN F 482 GLN G 88 GLN ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 ASN H 113 HIS I 100 GLN I 219 ASN J 39 ASN J 67 GLN J 205 GLN J 219 ASN J 221 ASN L 46 ASN L 57 ASN L 81 HIS M 90 GLN N 66 HIS O 90 GLN Q 117 GLN R 142 ASN S 149 ASN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 135 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.178184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.140694 restraints weight = 56010.661| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.50 r_work: 0.3215 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 46035 Z= 0.150 Angle : 0.627 7.571 62132 Z= 0.332 Chirality : 0.044 0.193 6969 Planarity : 0.005 0.049 8036 Dihedral : 5.854 114.001 6236 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.00 % Favored : 97.98 % Rotamer: Outliers : 2.32 % Allowed : 11.72 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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: 1.12 (0.11), residues: 5650 helix: 1.59 (0.09), residues: 2850 sheet: 0.33 (0.19), residues: 675 loop : -0.18 (0.14), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 107 TYR 0.029 0.001 TYR H 112 PHE 0.024 0.002 PHE G 230 TRP 0.028 0.002 TRP C 567 HIS 0.012 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00319 (46035) covalent geometry : angle 0.62716 (62132) hydrogen bonds : bond 0.05762 ( 2382) hydrogen bonds : angle 4.68741 ( 6924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 860 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 THR cc_start: 0.6455 (m) cc_final: 0.6227 (p) REVERT: A 18 PHE cc_start: 0.8388 (p90) cc_final: 0.8057 (p90) REVERT: A 65 GLN cc_start: 0.8562 (tp40) cc_final: 0.8346 (pt0) REVERT: A 163 LYS cc_start: 0.8891 (mmtm) cc_final: 0.8459 (mmtt) REVERT: A 173 ARG cc_start: 0.8790 (ptt-90) cc_final: 0.8379 (ptt180) REVERT: A 193 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7862 (mt-10) REVERT: A 492 ILE cc_start: 0.8347 (mt) cc_final: 0.8130 (mp) REVERT: A 521 GLN cc_start: 0.8847 (tt0) cc_final: 0.8599 (tt0) REVERT: A 584 MET cc_start: 0.8859 (mtm) cc_final: 0.8585 (mtm) REVERT: B 195 GLU cc_start: 0.7904 (tt0) cc_final: 0.7324 (tt0) REVERT: B 297 GLU cc_start: 0.8293 (tt0) cc_final: 0.8058 (tt0) REVERT: B 452 ILE cc_start: 0.8508 (tp) cc_final: 0.8109 (pt) REVERT: B 466 ASP cc_start: 0.8251 (t70) cc_final: 0.7961 (m-30) REVERT: B 471 GLU cc_start: 0.8302 (pm20) cc_final: 0.8015 (pm20) REVERT: B 540 MET cc_start: 0.8320 (mtp) cc_final: 0.8038 (mtm) REVERT: B 604 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7126 (tm) REVERT: C 17 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7848 (m) REVERT: C 56 ARG cc_start: 0.8653 (ttm170) cc_final: 0.8211 (ttp-170) REVERT: C 84 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8690 (mmtp) REVERT: C 108 ASP cc_start: 0.8208 (m-30) cc_final: 0.7931 (m-30) REVERT: C 139 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8265 (pttt) REVERT: C 286 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.6765 (tp30) REVERT: C 289 ARG cc_start: 0.8816 (ttp80) cc_final: 0.8331 (ttp-170) REVERT: C 293 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8004 (mm-30) REVERT: C 294 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8460 (tt) REVERT: C 297 GLU cc_start: 0.8575 (tt0) cc_final: 0.8331 (tt0) REVERT: C 301 LYS cc_start: 0.7696 (tttm) cc_final: 0.7477 (ttpp) REVERT: C 303 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8138 (mm-30) REVERT: C 356 GLU cc_start: 0.7982 (tt0) cc_final: 0.7678 (mt-10) REVERT: C 438 LYS cc_start: 0.8723 (mttt) cc_final: 0.8156 (mmtm) REVERT: C 485 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7349 (mt-10) REVERT: C 487 GLU cc_start: 0.8260 (tp30) cc_final: 0.7514 (tt0) REVERT: C 513 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6947 (ttmt) REVERT: C 540 MET cc_start: 0.8614 (mtp) cc_final: 0.8256 (mtp) REVERT: D 41 SER cc_start: 0.8437 (p) cc_final: 0.8206 (m) REVERT: D 93 LYS cc_start: 0.9037 (tttt) cc_final: 0.8649 (ttmt) REVERT: D 245 LYS cc_start: 0.8368 (tttm) cc_final: 0.8139 (ttpt) REVERT: D 250 GLU cc_start: 0.8034 (tt0) cc_final: 0.7504 (pt0) REVERT: D 382 GLN cc_start: 0.8403 (mm110) cc_final: 0.8108 (mt0) REVERT: E 127 MET cc_start: 0.9118 (mtp) cc_final: 0.8870 (mtp) REVERT: E 137 LYS cc_start: 0.8580 (ttpp) cc_final: 0.8296 (mtpm) REVERT: E 315 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7866 (mt-10) REVERT: E 410 MET cc_start: 0.9012 (mtm) cc_final: 0.8785 (mtp) REVERT: E 460 LYS cc_start: 0.8708 (mttt) cc_final: 0.8273 (ttpt) REVERT: F 108 LYS cc_start: 0.8993 (tttt) cc_final: 0.8715 (ttpp) REVERT: F 154 MET cc_start: 0.9109 (mmm) cc_final: 0.8892 (tpt) REVERT: F 156 GLN cc_start: 0.8431 (tt0) cc_final: 0.8073 (mt0) REVERT: F 168 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7997 (mp0) REVERT: F 242 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7610 (mtt90) REVERT: F 245 LYS cc_start: 0.8205 (tttm) cc_final: 0.7837 (ttpt) REVERT: F 299 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7852 (t0) REVERT: F 358 ASN cc_start: 0.8498 (m-40) cc_final: 0.8172 (t0) REVERT: F 435 MET cc_start: 0.8934 (ttp) cc_final: 0.8718 (ttm) REVERT: F 441 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7198 (tm-30) REVERT: F 449 LEU cc_start: 0.8079 (mt) cc_final: 0.7878 (mt) REVERT: G 211 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7814 (mmt180) REVERT: H 64 GLU cc_start: 0.6280 (pp20) cc_final: 0.5819 (tt0) REVERT: H 198 GLU cc_start: 0.7934 (tt0) cc_final: 0.7687 (tp30) REVERT: I 89 ASP cc_start: 0.7796 (m-30) cc_final: 0.7108 (m-30) REVERT: I 115 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7349 (mp) REVERT: I 117 ASP cc_start: 0.8009 (m-30) cc_final: 0.7677 (m-30) REVERT: I 161 LYS cc_start: 0.8217 (mttp) cc_final: 0.7662 (pttt) REVERT: I 201 ASP cc_start: 0.8068 (t0) cc_final: 0.7623 (m-30) REVERT: I 208 MET cc_start: 0.8824 (mmt) cc_final: 0.8511 (mmm) REVERT: I 226 ASP cc_start: 0.7810 (t0) cc_final: 0.7322 (m-30) REVERT: J 22 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8119 (tm-30) REVERT: J 41 GLU cc_start: 0.8495 (tp30) cc_final: 0.8052 (tp30) REVERT: J 44 ARG cc_start: 0.8133 (tmm-80) cc_final: 0.7895 (tmm-80) REVERT: J 61 GLU cc_start: 0.8118 (tt0) cc_final: 0.7622 (mt-10) REVERT: J 76 MET cc_start: 0.7611 (mtm) cc_final: 0.7058 (tmm) REVERT: J 85 ARG cc_start: 0.7744 (mtt180) cc_final: 0.7215 (mtt-85) REVERT: J 99 LYS cc_start: 0.8024 (tttt) cc_final: 0.7581 (ttmp) REVERT: J 197 GLU cc_start: 0.8061 (mp0) cc_final: 0.7455 (mp0) REVERT: J 201 ASP cc_start: 0.7966 (t0) cc_final: 0.7562 (m-30) REVERT: K 16 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8089 (mpp) REVERT: K 60 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7408 (ttmt) REVERT: K 61 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: K 63 GLN cc_start: 0.7342 (mt0) cc_final: 0.6848 (pt0) REVERT: K 117 ASP cc_start: 0.8277 (m-30) cc_final: 0.8032 (t0) REVERT: K 168 ASP cc_start: 0.8172 (t70) cc_final: 0.7954 (t70) REVERT: K 207 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8234 (mtp) REVERT: L 8 ILE cc_start: 0.7685 (mt) cc_final: 0.7349 (mt) REVERT: N 53 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8126 (ttpp) REVERT: N 93 ASP cc_start: 0.7598 (m-30) cc_final: 0.7392 (m-30) REVERT: Q 47 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7423 (mm-30) REVERT: Q 64 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: Q 117 GLN cc_start: 0.8483 (mm-40) cc_final: 0.7988 (mp-120) REVERT: Q 205 LYS cc_start: 0.7841 (tptt) cc_final: 0.7033 (mptt) REVERT: R 34 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6949 (tm-30) REVERT: R 50 GLN cc_start: 0.7629 (tp40) cc_final: 0.6998 (tp40) REVERT: R 117 GLN cc_start: 0.8670 (mt0) cc_final: 0.8314 (mp10) REVERT: R 135 GLN cc_start: 0.8276 (tt0) cc_final: 0.8008 (tt0) REVERT: R 264 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8354 (p0) REVERT: S 34 GLN cc_start: 0.7403 (tt0) cc_final: 0.7044 (tm-30) REVERT: S 49 TYR cc_start: 0.8700 (m-80) cc_final: 0.8470 (m-80) REVERT: S 67 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7214 (mm-30) REVERT: S 77 ASP cc_start: 0.7578 (t0) cc_final: 0.7082 (t0) REVERT: S 161 MET cc_start: 0.7407 (ttp) cc_final: 0.7111 (ttp) REVERT: S 197 TYR cc_start: 0.6616 (m-80) cc_final: 0.6325 (m-80) REVERT: S 210 GLU cc_start: 0.7865 (pm20) cc_final: 0.7404 (tp30) REVERT: S 221 ASP cc_start: 0.8775 (m-30) cc_final: 0.8509 (m-30) outliers start: 115 outliers final: 28 residues processed: 915 average time/residue: 0.8537 time to fit residues: 960.2623 Evaluate side-chains 774 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 732 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 207 MET Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 264 ASP Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain T residue 135 HIS Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 331 optimal weight: 0.2980 chunk 131 optimal weight: 5.9990 chunk 521 optimal weight: 2.9990 chunk 427 optimal weight: 3.9990 chunk 502 optimal weight: 3.9990 chunk 318 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 528 optimal weight: 6.9990 chunk 534 optimal weight: 10.0000 chunk 286 optimal weight: 0.9990 chunk 562 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS A 242 GLN A 573 HIS C 157 ASN C 164 HIS D 42 GLN D 54 ASN E 209 GLN E 345 ASN F 382 GLN G 88 GLN ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 HIS H 137 ASN I 100 GLN J 39 ASN J 221 ASN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN Q 142 ASN Q 222 GLN R 50 GLN R 142 ASN R 165 GLN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 135 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.177322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.138691 restraints weight = 55465.837| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.17 r_work: 0.3190 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 46035 Z= 0.220 Angle : 0.637 11.171 62132 Z= 0.332 Chirality : 0.045 0.188 6969 Planarity : 0.005 0.071 8036 Dihedral : 5.458 116.166 6220 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.11 % Allowed : 13.19 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.11), residues: 5650 helix: 1.81 (0.10), residues: 2853 sheet: 0.24 (0.19), residues: 682 loop : -0.39 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 107 TYR 0.026 0.002 TYR S 139 PHE 0.031 0.002 PHE H 155 TRP 0.021 0.002 TRP C 567 HIS 0.019 0.001 HIS L 96 Details of bonding type rmsd covalent geometry : bond 0.00535 (46035) covalent geometry : angle 0.63736 (62132) hydrogen bonds : bond 0.05693 ( 2382) hydrogen bonds : angle 4.50634 ( 6924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 777 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 THR cc_start: 0.6741 (m) cc_final: 0.6456 (p) REVERT: A 18 PHE cc_start: 0.8163 (p90) cc_final: 0.7867 (p90) REVERT: A 65 GLN cc_start: 0.8603 (tp40) cc_final: 0.8244 (pt0) REVERT: A 163 LYS cc_start: 0.8834 (mmtm) cc_final: 0.8430 (mmtt) REVERT: A 173 ARG cc_start: 0.8615 (ptt-90) cc_final: 0.8282 (ptt180) REVERT: A 193 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7770 (mt-10) REVERT: A 492 ILE cc_start: 0.8333 (mt) cc_final: 0.8119 (mp) REVERT: A 521 GLN cc_start: 0.8809 (tt0) cc_final: 0.8556 (tt0) REVERT: A 571 ARG cc_start: 0.7737 (ttp-170) cc_final: 0.7466 (ttm170) REVERT: A 584 MET cc_start: 0.8906 (mtm) cc_final: 0.8474 (mtm) REVERT: B 195 GLU cc_start: 0.7930 (tt0) cc_final: 0.7318 (tt0) REVERT: B 297 GLU cc_start: 0.8245 (tt0) cc_final: 0.7970 (tt0) REVERT: B 437 LYS cc_start: 0.8065 (tppp) cc_final: 0.7750 (tptm) REVERT: B 481 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7666 (mm-30) REVERT: B 584 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8095 (ttm) REVERT: C 17 THR cc_start: 0.8165 (p) cc_final: 0.7838 (m) REVERT: C 56 ARG cc_start: 0.8580 (ttm170) cc_final: 0.8034 (ttp-170) REVERT: C 84 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8543 (mmtp) REVERT: C 100 ASP cc_start: 0.9095 (p0) cc_final: 0.8792 (p0) REVERT: C 108 ASP cc_start: 0.8045 (m-30) cc_final: 0.7720 (m-30) REVERT: C 286 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.6732 (tp30) REVERT: C 289 ARG cc_start: 0.8820 (ttp80) cc_final: 0.8155 (ttp-170) REVERT: C 293 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7778 (mm-30) REVERT: C 297 GLU cc_start: 0.8624 (tt0) cc_final: 0.8312 (tt0) REVERT: C 301 LYS cc_start: 0.7506 (tttm) cc_final: 0.7292 (ttpp) REVERT: C 303 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8035 (mm-30) REVERT: C 356 GLU cc_start: 0.8038 (tt0) cc_final: 0.7496 (mt-10) REVERT: C 438 LYS cc_start: 0.8589 (mttt) cc_final: 0.8002 (mmtm) REVERT: C 463 GLU cc_start: 0.7816 (mp0) cc_final: 0.7570 (mp0) REVERT: C 485 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7139 (mt-10) REVERT: C 487 GLU cc_start: 0.8047 (tp30) cc_final: 0.7294 (tt0) REVERT: C 513 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6705 (ttmt) REVERT: C 574 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6850 (mtm) REVERT: C 591 LYS cc_start: 0.8259 (tppp) cc_final: 0.8047 (ttpp) REVERT: D 93 LYS cc_start: 0.8977 (tttt) cc_final: 0.8516 (ttmt) REVERT: D 250 GLU cc_start: 0.7717 (tt0) cc_final: 0.7098 (pt0) REVERT: D 382 GLN cc_start: 0.8203 (mm110) cc_final: 0.7866 (mt0) REVERT: D 403 LYS cc_start: 0.8629 (pttt) cc_final: 0.8219 (pttp) REVERT: D 485 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.5052 (mpp-170) REVERT: E 95 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8748 (t) REVERT: E 127 MET cc_start: 0.9140 (mtp) cc_final: 0.8931 (mtp) REVERT: E 137 LYS cc_start: 0.8409 (ttpp) cc_final: 0.8100 (mtpm) REVERT: E 141 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7968 (ptm160) REVERT: E 315 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7964 (mt-10) REVERT: E 342 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: E 374 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8795 (pm20) REVERT: E 410 MET cc_start: 0.8897 (mtm) cc_final: 0.8640 (mtp) REVERT: E 460 LYS cc_start: 0.8591 (mttt) cc_final: 0.8110 (ttpt) REVERT: F 81 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8363 (mttp) REVERT: F 96 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8276 (m) REVERT: F 108 LYS cc_start: 0.8932 (tttt) cc_final: 0.8606 (ttpp) REVERT: F 154 MET cc_start: 0.9000 (mmm) cc_final: 0.8760 (tpt) REVERT: F 168 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7902 (mp0) REVERT: F 242 ARG cc_start: 0.7887 (mtt90) cc_final: 0.7365 (mtt90) REVERT: F 245 LYS cc_start: 0.7981 (tttm) cc_final: 0.7534 (ttmt) REVERT: F 250 GLU cc_start: 0.8091 (tt0) cc_final: 0.7838 (tt0) REVERT: F 299 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7843 (t0) REVERT: F 358 ASN cc_start: 0.8453 (m-40) cc_final: 0.8070 (t0) REVERT: F 441 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7170 (tm-30) REVERT: G 211 ARG cc_start: 0.8249 (mtt180) cc_final: 0.7934 (mmt180) REVERT: H 130 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7643 (pm20) REVERT: H 137 ASN cc_start: 0.7966 (t0) cc_final: 0.7658 (m-40) REVERT: H 198 GLU cc_start: 0.7767 (tt0) cc_final: 0.7401 (mm-30) REVERT: I 89 ASP cc_start: 0.7719 (m-30) cc_final: 0.7075 (m-30) REVERT: I 99 LYS cc_start: 0.8020 (tttt) cc_final: 0.7467 (mttm) REVERT: I 115 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7087 (mp) REVERT: I 117 ASP cc_start: 0.8040 (m-30) cc_final: 0.7584 (m-30) REVERT: I 161 LYS cc_start: 0.8227 (mttp) cc_final: 0.7695 (ptmt) REVERT: I 208 MET cc_start: 0.8796 (mmt) cc_final: 0.8363 (mmm) REVERT: J 22 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8156 (tm-30) REVERT: J 41 GLU cc_start: 0.8387 (tp30) cc_final: 0.7936 (tp30) REVERT: J 59 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7391 (ttmt) REVERT: J 61 GLU cc_start: 0.8000 (tt0) cc_final: 0.7575 (mt-10) REVERT: J 76 MET cc_start: 0.7579 (mtm) cc_final: 0.6919 (tmm) REVERT: J 85 ARG cc_start: 0.7458 (mtt180) cc_final: 0.6748 (mmt-90) REVERT: J 99 LYS cc_start: 0.7836 (tttt) cc_final: 0.7325 (ttmm) REVERT: J 197 GLU cc_start: 0.7892 (mp0) cc_final: 0.7303 (mp0) REVERT: J 201 ASP cc_start: 0.7817 (t0) cc_final: 0.7341 (m-30) REVERT: K 15 MET cc_start: 0.7245 (mtt) cc_final: 0.6817 (mmt) REVERT: K 16 MET cc_start: 0.8507 (mtt) cc_final: 0.7992 (mpp) REVERT: K 54 MET cc_start: 0.6639 (mmt) cc_final: 0.6340 (mmm) REVERT: K 60 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7276 (ttmt) REVERT: K 63 GLN cc_start: 0.7166 (mt0) cc_final: 0.6747 (pt0) REVERT: K 69 LYS cc_start: 0.7344 (mttt) cc_final: 0.7143 (mtmt) REVERT: K 117 ASP cc_start: 0.8093 (m-30) cc_final: 0.7739 (m-30) REVERT: L 8 ILE cc_start: 0.7688 (mt) cc_final: 0.7311 (mt) REVERT: L 42 ASP cc_start: 0.8283 (m-30) cc_final: 0.7785 (m-30) REVERT: L 57 ASN cc_start: 0.7313 (t0) cc_final: 0.7025 (t0) REVERT: N 53 LYS cc_start: 0.8522 (ttmm) cc_final: 0.8113 (ttpp) REVERT: O 54 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7475 (pm20) REVERT: Q 47 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7515 (mm-30) REVERT: Q 117 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8007 (mp10) REVERT: Q 205 LYS cc_start: 0.7809 (tptt) cc_final: 0.6995 (mptt) REVERT: R 34 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.6783 (tm130) REVERT: R 50 GLN cc_start: 0.7328 (tp-100) cc_final: 0.6791 (tp40) REVERT: R 58 LYS cc_start: 0.7948 (tppt) cc_final: 0.7539 (tptp) REVERT: R 117 GLN cc_start: 0.8652 (mt0) cc_final: 0.8262 (mp10) REVERT: R 135 GLN cc_start: 0.8131 (tt0) cc_final: 0.7831 (tt0) REVERT: R 205 LYS cc_start: 0.7742 (tptt) cc_final: 0.7475 (mmtp) REVERT: S 34 GLN cc_start: 0.7325 (tt0) cc_final: 0.6959 (tm-30) REVERT: S 67 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7108 (mm-30) REVERT: S 77 ASP cc_start: 0.7736 (t0) cc_final: 0.7304 (t70) REVERT: S 161 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7036 (ttp) REVERT: S 165 GLN cc_start: 0.8192 (tt0) cc_final: 0.7948 (tt0) REVERT: S 195 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7134 (mp0) REVERT: S 197 TYR cc_start: 0.6609 (m-80) cc_final: 0.6279 (m-80) REVERT: S 199 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8769 (tm) REVERT: S 221 ASP cc_start: 0.8767 (m-30) cc_final: 0.8474 (m-30) REVERT: S 223 LYS cc_start: 0.8611 (tptt) cc_final: 0.8358 (tptt) REVERT: T 79 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8387 (mt0) outliers start: 154 outliers final: 58 residues processed: 857 average time/residue: 0.8440 time to fit residues: 874.7984 Evaluate side-chains 803 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 725 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 489 LYS Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 111 HIS Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 199 LEU Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 161 MET Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain S residue 201 LYS Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 79 GLN Chi-restraints excluded: chain T residue 97 LYS Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 400 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 482 optimal weight: 9.9990 chunk 509 optimal weight: 0.9980 chunk 292 optimal weight: 3.9990 chunk 552 optimal weight: 0.7980 chunk 286 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 573 HIS B 224 ASN C 65 GLN C 157 ASN D 42 GLN D 345 ASN E 433 GLN F 382 GLN F 482 GLN G 88 GLN ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN J 39 ASN J 67 GLN J 221 ASN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 142 ASN S 134 ASN S 142 ASN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.180074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.141762 restraints weight = 55773.253| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.06 r_work: 0.3286 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 46035 Z= 0.132 Angle : 0.542 11.032 62132 Z= 0.282 Chirality : 0.042 0.172 6969 Planarity : 0.004 0.045 8036 Dihedral : 5.007 111.444 6220 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.52 % Allowed : 14.40 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.11), residues: 5650 helix: 2.13 (0.10), residues: 2855 sheet: 0.15 (0.19), residues: 696 loop : -0.38 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 142 TYR 0.024 0.001 TYR H 112 PHE 0.020 0.001 PHE B 547 TRP 0.019 0.001 TRP G 19 HIS 0.014 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00290 (46035) covalent geometry : angle 0.54173 (62132) hydrogen bonds : bond 0.04857 ( 2382) hydrogen bonds : angle 4.23869 ( 6924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 780 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8293 (p90) cc_final: 0.8090 (p90) REVERT: A 43 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8849 (m) REVERT: A 163 LYS cc_start: 0.8945 (mmtm) cc_final: 0.8587 (mmtt) REVERT: A 173 ARG cc_start: 0.8739 (ptt-90) cc_final: 0.8355 (ptt180) REVERT: A 193 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7926 (mt-10) REVERT: A 521 GLN cc_start: 0.8970 (tt0) cc_final: 0.8768 (tt0) REVERT: A 571 ARG cc_start: 0.7851 (ttp-170) cc_final: 0.7519 (ttm170) REVERT: A 584 MET cc_start: 0.9027 (mtm) cc_final: 0.8638 (mtm) REVERT: B 195 GLU cc_start: 0.8059 (tt0) cc_final: 0.7599 (tt0) REVERT: B 417 PHE cc_start: 0.8112 (m-80) cc_final: 0.7908 (m-10) REVERT: B 452 ILE cc_start: 0.8541 (tp) cc_final: 0.8176 (pt) REVERT: B 481 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7827 (mm-30) REVERT: B 530 ARG cc_start: 0.8278 (ptp-110) cc_final: 0.8077 (ptp-170) REVERT: C 56 ARG cc_start: 0.8705 (ttm170) cc_final: 0.8235 (ttp-170) REVERT: C 84 LYS cc_start: 0.9030 (mmtt) cc_final: 0.8816 (mmtp) REVERT: C 108 ASP cc_start: 0.8122 (m-30) cc_final: 0.7843 (m-30) REVERT: C 123 ASN cc_start: 0.8791 (t0) cc_final: 0.8544 (t0) REVERT: C 139 LYS cc_start: 0.8477 (ttpp) cc_final: 0.8247 (pttt) REVERT: C 279 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7925 (tp30) REVERT: C 286 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.6939 (tp30) REVERT: C 289 ARG cc_start: 0.8971 (ttp80) cc_final: 0.8251 (ttp-170) REVERT: C 293 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7966 (mm-30) REVERT: C 297 GLU cc_start: 0.8452 (tt0) cc_final: 0.8182 (tt0) REVERT: C 303 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8306 (mm-30) REVERT: C 318 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8624 (mtp) REVERT: C 356 GLU cc_start: 0.8286 (tt0) cc_final: 0.7978 (mt-10) REVERT: C 438 LYS cc_start: 0.8748 (mttt) cc_final: 0.8281 (mmtm) REVERT: C 463 GLU cc_start: 0.8042 (mp0) cc_final: 0.7800 (mp0) REVERT: C 485 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7385 (mt-10) REVERT: C 487 GLU cc_start: 0.8146 (tp30) cc_final: 0.7520 (tt0) REVERT: C 513 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7084 (ttmt) REVERT: C 540 MET cc_start: 0.8505 (mtp) cc_final: 0.8221 (mtp) REVERT: C 574 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7076 (mtm) REVERT: D 88 GLU cc_start: 0.9070 (tt0) cc_final: 0.8768 (tm-30) REVERT: D 93 LYS cc_start: 0.8958 (tttt) cc_final: 0.8676 (ttmt) REVERT: D 250 GLU cc_start: 0.7998 (tt0) cc_final: 0.7436 (pt0) REVERT: D 382 GLN cc_start: 0.8445 (mm110) cc_final: 0.8122 (mt0) REVERT: D 403 LYS cc_start: 0.8670 (pttt) cc_final: 0.8320 (pttp) REVERT: D 438 VAL cc_start: 0.8299 (t) cc_final: 0.8032 (p) REVERT: E 137 LYS cc_start: 0.8534 (ttpp) cc_final: 0.8320 (mtpm) REVERT: E 249 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7861 (mt-10) REVERT: E 315 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8084 (mt-10) REVERT: E 342 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8081 (tm-30) REVERT: E 374 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8634 (pm20) REVERT: E 460 LYS cc_start: 0.8692 (mttt) cc_final: 0.8434 (ttpt) REVERT: F 81 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8490 (mttp) REVERT: F 96 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8356 (m) REVERT: F 108 LYS cc_start: 0.9063 (tttt) cc_final: 0.8816 (ttpp) REVERT: F 168 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7982 (mp0) REVERT: F 242 ARG cc_start: 0.8116 (mtt90) cc_final: 0.7734 (mtt90) REVERT: F 245 LYS cc_start: 0.8230 (tttm) cc_final: 0.7886 (ttmt) REVERT: F 250 GLU cc_start: 0.8176 (tt0) cc_final: 0.7964 (tt0) REVERT: F 305 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8045 (mt-10) REVERT: F 358 ASN cc_start: 0.8472 (m-40) cc_final: 0.8107 (t0) REVERT: F 410 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8161 (mmt) REVERT: F 441 GLU cc_start: 0.7349 (tm-30) cc_final: 0.7126 (tm-30) REVERT: G 207 MET cc_start: 0.5567 (mmm) cc_final: 0.5207 (mmm) REVERT: H 137 ASN cc_start: 0.7663 (t0) cc_final: 0.7387 (m-40) REVERT: H 198 GLU cc_start: 0.7905 (tt0) cc_final: 0.7671 (mm-30) REVERT: I 89 ASP cc_start: 0.7790 (m-30) cc_final: 0.7139 (m-30) REVERT: I 99 LYS cc_start: 0.8232 (tttt) cc_final: 0.7760 (mttm) REVERT: I 115 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7333 (mp) REVERT: I 117 ASP cc_start: 0.8048 (m-30) cc_final: 0.7581 (m-30) REVERT: I 140 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: I 161 LYS cc_start: 0.8224 (mttp) cc_final: 0.7869 (ptmt) REVERT: I 208 MET cc_start: 0.8957 (mmt) cc_final: 0.8630 (mmm) REVERT: I 226 ASP cc_start: 0.7924 (m-30) cc_final: 0.7684 (m-30) REVERT: J 22 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8074 (tm-30) REVERT: J 41 GLU cc_start: 0.8378 (tp30) cc_final: 0.8072 (tp30) REVERT: J 59 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7614 (ttmt) REVERT: J 61 GLU cc_start: 0.8153 (tt0) cc_final: 0.7793 (mt-10) REVERT: J 76 MET cc_start: 0.7658 (mtm) cc_final: 0.7098 (tmm) REVERT: J 85 ARG cc_start: 0.7788 (mtt180) cc_final: 0.7119 (mmt-90) REVERT: J 99 LYS cc_start: 0.8096 (tttt) cc_final: 0.7621 (ttmm) REVERT: J 197 GLU cc_start: 0.8004 (mp0) cc_final: 0.7468 (mp0) REVERT: J 201 ASP cc_start: 0.8028 (t0) cc_final: 0.7656 (m-30) REVERT: K 15 MET cc_start: 0.6515 (mtt) cc_final: 0.6294 (mmt) REVERT: K 54 MET cc_start: 0.6799 (mmt) cc_final: 0.6438 (mmm) REVERT: K 117 ASP cc_start: 0.8276 (m-30) cc_final: 0.7960 (m-30) REVERT: L 57 ASN cc_start: 0.6773 (t0) cc_final: 0.6561 (t0) REVERT: N 53 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8183 (ttpp) REVERT: O 54 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7142 (pt0) REVERT: O 114 TYR cc_start: 0.8924 (t80) cc_final: 0.8699 (t80) REVERT: Q 117 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8018 (mp10) REVERT: Q 205 LYS cc_start: 0.7974 (tptt) cc_final: 0.7158 (mptt) REVERT: Q 239 SER cc_start: 0.6791 (OUTLIER) cc_final: 0.6546 (p) REVERT: R 34 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7087 (tm130) REVERT: R 50 GLN cc_start: 0.7481 (tp-100) cc_final: 0.6922 (tp40) REVERT: R 58 LYS cc_start: 0.7916 (tppt) cc_final: 0.7647 (tptm) REVERT: R 117 GLN cc_start: 0.8607 (mt0) cc_final: 0.8323 (mp10) REVERT: R 135 GLN cc_start: 0.8353 (tt0) cc_final: 0.7741 (tt0) REVERT: R 205 LYS cc_start: 0.7878 (tptt) cc_final: 0.7630 (mmtp) REVERT: S 34 GLN cc_start: 0.7526 (tt0) cc_final: 0.7325 (tm-30) REVERT: S 67 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7337 (mm-30) REVERT: S 77 ASP cc_start: 0.7895 (t0) cc_final: 0.7580 (t70) REVERT: S 141 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8434 (tptt) REVERT: S 161 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7319 (ttp) REVERT: S 165 GLN cc_start: 0.8244 (tt0) cc_final: 0.7977 (tt0) REVERT: S 195 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7327 (mp0) REVERT: S 197 TYR cc_start: 0.6761 (m-80) cc_final: 0.6386 (m-80) REVERT: S 199 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8813 (tm) REVERT: S 221 ASP cc_start: 0.8666 (m-30) cc_final: 0.8440 (m-30) outliers start: 125 outliers final: 43 residues processed: 852 average time/residue: 0.8214 time to fit residues: 849.7907 Evaluate side-chains 786 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 723 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 256 LYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 111 HIS Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 140 ASP Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 239 SER Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 161 MET Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 97 LYS Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 11 optimal weight: 0.0070 chunk 25 optimal weight: 5.9990 chunk 505 optimal weight: 2.9990 chunk 366 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 453 optimal weight: 10.0000 chunk 561 optimal weight: 1.9990 chunk 128 optimal weight: 0.0170 chunk 275 optimal weight: 0.7980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 HIS B 224 ASN B 603 GLN C 157 ASN D 42 GLN E 133 ASN F 382 GLN F 482 GLN G 23 HIS G 88 GLN ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 HIS I 100 GLN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 HIS Q 132 GLN Q 142 ASN R 142 ASN R 184 HIS S 134 ASN T 56 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.180168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.142101 restraints weight = 55611.079| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.09 r_work: 0.3268 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 46035 Z= 0.124 Angle : 0.534 10.903 62132 Z= 0.276 Chirality : 0.041 0.191 6969 Planarity : 0.004 0.045 8036 Dihedral : 4.804 108.213 6220 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.42 % Allowed : 15.17 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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: 1.62 (0.11), residues: 5650 helix: 2.32 (0.10), residues: 2853 sheet: 0.19 (0.19), residues: 703 loop : -0.35 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 142 TYR 0.025 0.001 TYR L 98 PHE 0.027 0.001 PHE K 18 TRP 0.017 0.001 TRP C 567 HIS 0.019 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00273 (46035) covalent geometry : angle 0.53438 (62132) hydrogen bonds : bond 0.04604 ( 2382) hydrogen bonds : angle 4.14755 ( 6924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 760 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8691 (m) REVERT: A 163 LYS cc_start: 0.8799 (mmtm) cc_final: 0.8372 (mmtt) REVERT: A 193 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7620 (mt-10) REVERT: A 521 GLN cc_start: 0.8837 (tt0) cc_final: 0.8609 (tt0) REVERT: A 571 ARG cc_start: 0.7797 (ttp-170) cc_final: 0.7467 (ttm170) REVERT: A 584 MET cc_start: 0.8924 (mtm) cc_final: 0.8537 (mtm) REVERT: B 84 LYS cc_start: 0.8791 (mtmm) cc_final: 0.8301 (pttp) REVERT: B 195 GLU cc_start: 0.7901 (tt0) cc_final: 0.7352 (tt0) REVERT: B 297 GLU cc_start: 0.8233 (tt0) cc_final: 0.8010 (tp30) REVERT: B 346 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.8866 (ttt) REVERT: B 452 ILE cc_start: 0.8497 (tp) cc_final: 0.8084 (pt) REVERT: B 530 ARG cc_start: 0.8099 (ptp-110) cc_final: 0.7887 (ptp-170) REVERT: C 56 ARG cc_start: 0.8579 (ttm170) cc_final: 0.8164 (ttp-170) REVERT: C 84 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8631 (mmtp) REVERT: C 108 ASP cc_start: 0.7936 (m-30) cc_final: 0.7614 (m-30) REVERT: C 123 ASN cc_start: 0.8784 (t0) cc_final: 0.8529 (t0) REVERT: C 139 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8245 (pttt) REVERT: C 220 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8737 (mtpp) REVERT: C 279 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7778 (mp0) REVERT: C 286 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.6707 (tp30) REVERT: C 289 ARG cc_start: 0.8898 (ttp80) cc_final: 0.8002 (ttp-170) REVERT: C 293 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7792 (mm-30) REVERT: C 297 GLU cc_start: 0.8359 (tt0) cc_final: 0.8022 (tt0) REVERT: C 303 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8325 (mm-30) REVERT: C 318 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8383 (mtp) REVERT: C 356 GLU cc_start: 0.8125 (tt0) cc_final: 0.7611 (mt-10) REVERT: C 399 GLU cc_start: 0.8275 (tp30) cc_final: 0.7886 (tp30) REVERT: C 438 LYS cc_start: 0.8591 (mttt) cc_final: 0.8034 (mmtm) REVERT: C 463 GLU cc_start: 0.7884 (mp0) cc_final: 0.7594 (mp0) REVERT: C 485 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7250 (mt-10) REVERT: C 487 GLU cc_start: 0.8038 (tp30) cc_final: 0.7333 (tt0) REVERT: C 491 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: C 540 MET cc_start: 0.8431 (mtp) cc_final: 0.8184 (mtp) REVERT: C 552 ARG cc_start: 0.7374 (ttt-90) cc_final: 0.7062 (mtp-110) REVERT: D 88 GLU cc_start: 0.9095 (tt0) cc_final: 0.8726 (tm-30) REVERT: D 93 LYS cc_start: 0.8901 (tttt) cc_final: 0.8490 (ttmt) REVERT: D 250 GLU cc_start: 0.7682 (tt0) cc_final: 0.7074 (pt0) REVERT: D 382 GLN cc_start: 0.8150 (mm110) cc_final: 0.7852 (mt0) REVERT: D 403 LYS cc_start: 0.8627 (pttt) cc_final: 0.8280 (pttp) REVERT: E 95 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8805 (t) REVERT: E 137 LYS cc_start: 0.8544 (ttpp) cc_final: 0.8312 (mtpm) REVERT: E 141 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8053 (ptm160) REVERT: E 315 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7974 (mt-10) REVERT: E 342 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: E 460 LYS cc_start: 0.8511 (mttt) cc_final: 0.8091 (ttpt) REVERT: F 81 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8463 (mttp) REVERT: F 96 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8224 (m) REVERT: F 108 LYS cc_start: 0.8934 (tttt) cc_final: 0.8586 (ttpp) REVERT: F 168 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7891 (mp0) REVERT: F 242 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7486 (mtt90) REVERT: F 245 LYS cc_start: 0.7918 (tttm) cc_final: 0.7538 (ttmt) REVERT: F 250 GLU cc_start: 0.8080 (tt0) cc_final: 0.7855 (tt0) REVERT: F 305 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7813 (mt-10) REVERT: F 358 ASN cc_start: 0.8430 (m-40) cc_final: 0.7960 (t0) REVERT: F 410 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8152 (mmt) REVERT: F 441 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6976 (tm-30) REVERT: G 261 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8346 (t70) REVERT: H 198 GLU cc_start: 0.7651 (tt0) cc_final: 0.7329 (mm-30) REVERT: I 89 ASP cc_start: 0.7646 (m-30) cc_final: 0.7010 (m-30) REVERT: I 99 LYS cc_start: 0.8030 (tttt) cc_final: 0.7490 (mttm) REVERT: I 117 ASP cc_start: 0.7935 (m-30) cc_final: 0.7448 (m-30) REVERT: I 161 LYS cc_start: 0.8179 (mttp) cc_final: 0.7755 (ptmt) REVERT: I 182 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7908 (mt-10) REVERT: I 189 LYS cc_start: 0.8719 (mttt) cc_final: 0.8493 (mtpt) REVERT: I 208 MET cc_start: 0.8746 (mmt) cc_final: 0.8380 (mmm) REVERT: I 226 ASP cc_start: 0.7900 (m-30) cc_final: 0.7324 (m-30) REVERT: J 22 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8117 (tm-30) REVERT: J 39 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.8051 (t0) REVERT: J 41 GLU cc_start: 0.8403 (tp30) cc_final: 0.7963 (tp30) REVERT: J 59 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7422 (ttmt) REVERT: J 61 GLU cc_start: 0.8142 (tt0) cc_final: 0.7659 (mt-10) REVERT: J 76 MET cc_start: 0.7736 (mtm) cc_final: 0.7078 (tmm) REVERT: J 85 ARG cc_start: 0.7582 (mtt180) cc_final: 0.6755 (mmt-90) REVERT: J 99 LYS cc_start: 0.7900 (tttt) cc_final: 0.7398 (ttmm) REVERT: J 177 ILE cc_start: 0.7497 (mm) cc_final: 0.7297 (OUTLIER) REVERT: J 197 GLU cc_start: 0.7825 (mp0) cc_final: 0.7244 (mp0) REVERT: J 201 ASP cc_start: 0.7852 (t0) cc_final: 0.7432 (m-30) REVERT: K 54 MET cc_start: 0.6570 (mmt) cc_final: 0.6267 (mmm) REVERT: K 117 ASP cc_start: 0.8183 (m-30) cc_final: 0.7876 (m-30) REVERT: L 57 ASN cc_start: 0.7179 (t0) cc_final: 0.6905 (t0) REVERT: N 48 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7672 (ttp-170) REVERT: N 53 LYS cc_start: 0.8437 (ttmm) cc_final: 0.8007 (ttpp) REVERT: O 53 LYS cc_start: 0.8308 (mtmm) cc_final: 0.8091 (mtmm) REVERT: Q 42 LEU cc_start: 0.7552 (mt) cc_final: 0.7347 (mp) REVERT: Q 109 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: Q 117 GLN cc_start: 0.8483 (mm-40) cc_final: 0.7945 (mp10) REVERT: Q 205 LYS cc_start: 0.7807 (tptt) cc_final: 0.7015 (mptt) REVERT: R 34 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6748 (tm130) REVERT: R 58 LYS cc_start: 0.7987 (tppt) cc_final: 0.7719 (tptm) REVERT: R 117 GLN cc_start: 0.8578 (mt0) cc_final: 0.8221 (mp10) REVERT: R 135 GLN cc_start: 0.8095 (tt0) cc_final: 0.7583 (tt0) REVERT: R 205 LYS cc_start: 0.7682 (tptt) cc_final: 0.7434 (mmtp) REVERT: S 34 GLN cc_start: 0.7287 (tt0) cc_final: 0.7063 (tm-30) REVERT: S 67 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7181 (mm-30) REVERT: S 77 ASP cc_start: 0.7900 (t0) cc_final: 0.7514 (t70) REVERT: S 141 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8436 (tptt) REVERT: S 165 GLN cc_start: 0.8191 (tt0) cc_final: 0.7873 (tt0) REVERT: S 195 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7150 (mp0) REVERT: S 197 TYR cc_start: 0.6543 (m-80) cc_final: 0.6295 (m-80) REVERT: S 199 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8628 (tm) REVERT: S 221 ASP cc_start: 0.8726 (m-30) cc_final: 0.8443 (m-30) outliers start: 120 outliers final: 41 residues processed: 822 average time/residue: 0.7286 time to fit residues: 728.6626 Evaluate side-chains 766 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 706 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 88 GLN Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 150 ASN Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 464 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 455 optimal weight: 4.9990 chunk 233 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 HIS B 603 GLN C 157 ASN C 573 HIS D 42 GLN F 382 GLN F 482 GLN ** G 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN J 67 GLN J 122 GLN R 142 ASN T 56 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.177393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.138896 restraints weight = 55368.079| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.19 r_work: 0.3152 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 46035 Z= 0.240 Angle : 0.629 10.575 62132 Z= 0.324 Chirality : 0.046 0.199 6969 Planarity : 0.005 0.052 8036 Dihedral : 5.136 114.408 6220 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.92 % Allowed : 15.65 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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: 1.38 (0.11), residues: 5650 helix: 2.17 (0.10), residues: 2851 sheet: 0.01 (0.19), residues: 688 loop : -0.51 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 142 TYR 0.021 0.002 TYR R 139 PHE 0.033 0.002 PHE H 155 TRP 0.016 0.002 TRP C 567 HIS 0.006 0.001 HIS C 444 Details of bonding type rmsd covalent geometry : bond 0.00590 (46035) covalent geometry : angle 0.62908 (62132) hydrogen bonds : bond 0.05318 ( 2382) hydrogen bonds : angle 4.27412 ( 6924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 737 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8741 (m) REVERT: A 102 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8471 (mp) REVERT: A 159 ASN cc_start: 0.8163 (m110) cc_final: 0.7946 (m-40) REVERT: A 163 LYS cc_start: 0.8740 (mmtm) cc_final: 0.8376 (mmtt) REVERT: A 173 ARG cc_start: 0.8714 (ptt-90) cc_final: 0.8333 (ptt180) REVERT: A 193 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 487 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7716 (tp30) REVERT: A 565 ILE cc_start: 0.8922 (mt) cc_final: 0.8589 (mp) REVERT: A 571 ARG cc_start: 0.7802 (ttp-170) cc_final: 0.7470 (ttm170) REVERT: B 195 GLU cc_start: 0.8014 (tt0) cc_final: 0.7387 (tt0) REVERT: B 297 GLU cc_start: 0.8267 (tt0) cc_final: 0.8013 (tp30) REVERT: B 437 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7708 (tptm) REVERT: B 530 ARG cc_start: 0.8132 (ptp-110) cc_final: 0.7924 (ptp-170) REVERT: C 56 ARG cc_start: 0.8589 (ttm170) cc_final: 0.8029 (ttp-170) REVERT: C 84 LYS cc_start: 0.8916 (mmtt) cc_final: 0.8562 (mmtp) REVERT: C 100 ASP cc_start: 0.9030 (p0) cc_final: 0.8796 (p0) REVERT: C 108 ASP cc_start: 0.8012 (m-30) cc_final: 0.7661 (m-30) REVERT: C 220 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8676 (mtpp) REVERT: C 279 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7901 (tp30) REVERT: C 286 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.6627 (tp30) REVERT: C 289 ARG cc_start: 0.8830 (ttp80) cc_final: 0.7932 (ttp-170) REVERT: C 293 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7820 (mm-30) REVERT: C 297 GLU cc_start: 0.8430 (tt0) cc_final: 0.8117 (tt0) REVERT: C 303 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8381 (mm-30) REVERT: C 318 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8478 (mtp) REVERT: C 356 GLU cc_start: 0.8105 (tt0) cc_final: 0.7563 (mt-10) REVERT: C 399 GLU cc_start: 0.8352 (tp30) cc_final: 0.7971 (tp30) REVERT: C 438 LYS cc_start: 0.8671 (mttt) cc_final: 0.8091 (mmtm) REVERT: C 463 GLU cc_start: 0.7924 (mp0) cc_final: 0.7638 (mp0) REVERT: C 485 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7234 (mt-10) REVERT: C 487 GLU cc_start: 0.8133 (tp30) cc_final: 0.7327 (tt0) REVERT: C 552 ARG cc_start: 0.7293 (ttt-90) cc_final: 0.6989 (mtp-110) REVERT: D 88 GLU cc_start: 0.9023 (tt0) cc_final: 0.8674 (tm-30) REVERT: D 93 LYS cc_start: 0.8884 (tttt) cc_final: 0.8461 (ttmt) REVERT: D 250 GLU cc_start: 0.7769 (tt0) cc_final: 0.7104 (pt0) REVERT: D 382 GLN cc_start: 0.8190 (mm110) cc_final: 0.7939 (mt0) REVERT: D 403 LYS cc_start: 0.8766 (pttt) cc_final: 0.8454 (pttp) REVERT: D 485 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.4865 (mtp180) REVERT: E 41 SER cc_start: 0.8154 (m) cc_final: 0.7627 (p) REVERT: E 95 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8806 (t) REVERT: E 120 ARG cc_start: 0.9086 (mtt-85) cc_final: 0.8809 (mtt90) REVERT: E 137 LYS cc_start: 0.8492 (ttpp) cc_final: 0.8226 (mtpm) REVERT: E 141 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8044 (ptm160) REVERT: E 315 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8084 (mt-10) REVERT: E 342 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: E 460 LYS cc_start: 0.8669 (mttt) cc_final: 0.8177 (ttpt) REVERT: F 81 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8277 (mttp) REVERT: F 108 LYS cc_start: 0.8922 (tttt) cc_final: 0.8521 (ttpp) REVERT: F 168 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7941 (mp0) REVERT: F 242 ARG cc_start: 0.8076 (mtt90) cc_final: 0.7463 (mtt90) REVERT: F 245 LYS cc_start: 0.8000 (tttm) cc_final: 0.7579 (ttmt) REVERT: F 250 GLU cc_start: 0.8139 (tt0) cc_final: 0.7911 (tt0) REVERT: F 305 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7862 (mt-10) REVERT: F 410 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7777 (mmt) REVERT: G 27 THR cc_start: 0.6771 (m) cc_final: 0.6167 (p) REVERT: G 88 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: H 137 ASN cc_start: 0.8005 (t0) cc_final: 0.7601 (m-40) REVERT: H 198 GLU cc_start: 0.7746 (tt0) cc_final: 0.7398 (mm-30) REVERT: I 89 ASP cc_start: 0.7617 (m-30) cc_final: 0.6989 (m-30) REVERT: I 99 LYS cc_start: 0.8049 (tttt) cc_final: 0.7476 (mttm) REVERT: I 115 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7128 (mp) REVERT: I 117 ASP cc_start: 0.8019 (m-30) cc_final: 0.7456 (m-30) REVERT: I 161 LYS cc_start: 0.8149 (mttp) cc_final: 0.7644 (ptmt) REVERT: I 182 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7954 (mt-10) REVERT: I 201 ASP cc_start: 0.7930 (t0) cc_final: 0.7353 (m-30) REVERT: I 226 ASP cc_start: 0.7931 (m-30) cc_final: 0.7276 (m-30) REVERT: J 22 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8093 (tm-30) REVERT: J 41 GLU cc_start: 0.8403 (tp30) cc_final: 0.8002 (tp30) REVERT: J 59 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7445 (ttmt) REVERT: J 61 GLU cc_start: 0.8016 (tt0) cc_final: 0.7634 (mt-10) REVERT: J 76 MET cc_start: 0.7704 (mtm) cc_final: 0.7008 (tmm) REVERT: J 85 ARG cc_start: 0.7537 (mtt180) cc_final: 0.6807 (mmt-90) REVERT: J 99 LYS cc_start: 0.7864 (tttt) cc_final: 0.7365 (ttmm) REVERT: J 197 GLU cc_start: 0.7877 (mp0) cc_final: 0.7313 (mp0) REVERT: J 201 ASP cc_start: 0.7820 (t0) cc_final: 0.7356 (m-30) REVERT: K 15 MET cc_start: 0.7351 (mtt) cc_final: 0.6992 (mmt) REVERT: K 54 MET cc_start: 0.6626 (mmt) cc_final: 0.6321 (mmm) REVERT: K 117 ASP cc_start: 0.8116 (m-30) cc_final: 0.7836 (m-30) REVERT: L 57 ASN cc_start: 0.7532 (t0) cc_final: 0.7165 (t0) REVERT: N 48 ARG cc_start: 0.8278 (ttp80) cc_final: 0.7711 (ttp-170) REVERT: N 52 GLU cc_start: 0.8705 (tp30) cc_final: 0.8226 (tp30) REVERT: N 53 LYS cc_start: 0.8473 (ttmm) cc_final: 0.8021 (ttpp) REVERT: Q 42 LEU cc_start: 0.7704 (mt) cc_final: 0.7470 (mp) REVERT: Q 109 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: Q 117 GLN cc_start: 0.8513 (mm-40) cc_final: 0.7934 (mp10) REVERT: Q 205 LYS cc_start: 0.7896 (tptt) cc_final: 0.7182 (mptt) REVERT: R 34 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6796 (tm130) REVERT: R 47 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7445 (tm-30) REVERT: R 58 LYS cc_start: 0.8037 (tppt) cc_final: 0.7796 (tptm) REVERT: R 117 GLN cc_start: 0.8690 (mt0) cc_final: 0.8354 (mp10) REVERT: R 135 GLN cc_start: 0.8224 (tt0) cc_final: 0.7678 (tt0) REVERT: R 205 LYS cc_start: 0.7682 (tptt) cc_final: 0.7471 (mmtp) REVERT: S 34 GLN cc_start: 0.7371 (tt0) cc_final: 0.7131 (tm-30) REVERT: S 67 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7220 (mm-30) REVERT: S 77 ASP cc_start: 0.7996 (t0) cc_final: 0.7582 (t70) REVERT: S 141 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8462 (tptt) REVERT: S 165 GLN cc_start: 0.8200 (tt0) cc_final: 0.7894 (tt0) REVERT: S 195 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7119 (mp0) REVERT: S 197 TYR cc_start: 0.6587 (m-80) cc_final: 0.6367 (m-80) REVERT: S 221 ASP cc_start: 0.8720 (m-30) cc_final: 0.8423 (m-30) outliers start: 145 outliers final: 65 residues processed: 819 average time/residue: 0.6241 time to fit residues: 621.9748 Evaluate side-chains 792 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 707 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 437 LYS Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 88 GLN Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain S residue 103 MET Chi-restraints excluded: chain S residue 126 TYR Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain T residue 150 ASN Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 556 optimal weight: 0.9980 chunk 218 optimal weight: 6.9990 chunk 395 optimal weight: 6.9990 chunk 411 optimal weight: 20.0000 chunk 537 optimal weight: 10.0000 chunk 479 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 chunk 375 optimal weight: 3.9990 chunk 499 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 493 optimal weight: 20.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 HIS C 157 ASN D 42 GLN F 382 GLN F 482 GLN G 88 GLN G 194 HIS I 100 GLN Q 142 ASN R 142 ASN ** R 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 ASN T 56 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.178947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.140660 restraints weight = 55157.479| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.12 r_work: 0.3188 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 46035 Z= 0.137 Angle : 0.549 11.229 62132 Z= 0.283 Chirality : 0.042 0.201 6969 Planarity : 0.004 0.054 8036 Dihedral : 4.833 110.354 6220 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.24 % Allowed : 16.58 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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: 1.55 (0.11), residues: 5650 helix: 2.35 (0.10), residues: 2860 sheet: -0.01 (0.19), residues: 692 loop : -0.46 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 107 TYR 0.022 0.001 TYR L 98 PHE 0.027 0.001 PHE K 18 TRP 0.018 0.001 TRP G 19 HIS 0.004 0.001 HIS G 296 Details of bonding type rmsd covalent geometry : bond 0.00315 (46035) covalent geometry : angle 0.54860 (62132) hydrogen bonds : bond 0.04657 ( 2382) hydrogen bonds : angle 4.13254 ( 6924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 735 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8301 (p90) cc_final: 0.8078 (p90) REVERT: A 43 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8614 (m) REVERT: A 102 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8402 (mp) REVERT: A 163 LYS cc_start: 0.8653 (mmtm) cc_final: 0.8258 (mmtt) REVERT: A 193 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7652 (mt-10) REVERT: A 487 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7664 (tp30) REVERT: A 529 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7648 (t0) REVERT: A 565 ILE cc_start: 0.8900 (mt) cc_final: 0.8584 (mp) REVERT: A 571 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.7443 (ttm170) REVERT: B 195 GLU cc_start: 0.7899 (tt0) cc_final: 0.7229 (tt0) REVERT: B 297 GLU cc_start: 0.8302 (tt0) cc_final: 0.7994 (tp30) REVERT: B 346 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.9052 (ttt) REVERT: B 437 LYS cc_start: 0.8038 (tppp) cc_final: 0.7620 (tptm) REVERT: B 530 ARG cc_start: 0.8028 (ptp-110) cc_final: 0.7803 (ptp-170) REVERT: C 56 ARG cc_start: 0.8558 (ttm170) cc_final: 0.8117 (ttp-170) REVERT: C 84 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8573 (mmtp) REVERT: C 100 ASP cc_start: 0.9004 (p0) cc_final: 0.8713 (p0) REVERT: C 108 ASP cc_start: 0.7924 (m-30) cc_final: 0.7579 (m-30) REVERT: C 114 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8074 (mm-40) REVERT: C 123 ASN cc_start: 0.8839 (t0) cc_final: 0.8576 (t0) REVERT: C 220 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8625 (mtpp) REVERT: C 293 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7765 (mm-30) REVERT: C 297 GLU cc_start: 0.8327 (tt0) cc_final: 0.7986 (tt0) REVERT: C 303 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8376 (mm-30) REVERT: C 318 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8373 (mtp) REVERT: C 356 GLU cc_start: 0.8036 (tt0) cc_final: 0.7476 (mt-10) REVERT: C 399 GLU cc_start: 0.8331 (tp30) cc_final: 0.7938 (tp30) REVERT: C 438 LYS cc_start: 0.8606 (mttt) cc_final: 0.8011 (mmtm) REVERT: C 463 GLU cc_start: 0.8048 (mp0) cc_final: 0.7722 (mp0) REVERT: C 485 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7171 (mt-10) REVERT: C 487 GLU cc_start: 0.8061 (tp30) cc_final: 0.7304 (tt0) REVERT: C 513 LYS cc_start: 0.7045 (tttt) cc_final: 0.6674 (tttp) REVERT: C 540 MET cc_start: 0.8331 (mtp) cc_final: 0.8038 (mtp) REVERT: C 552 ARG cc_start: 0.7288 (ttt-90) cc_final: 0.7006 (mtp-110) REVERT: D 88 GLU cc_start: 0.8983 (tt0) cc_final: 0.8654 (tm-30) REVERT: D 93 LYS cc_start: 0.8892 (tttt) cc_final: 0.8458 (ttmt) REVERT: D 250 GLU cc_start: 0.7706 (tt0) cc_final: 0.7199 (mt-10) REVERT: D 382 GLN cc_start: 0.8063 (mm110) cc_final: 0.7782 (mt0) REVERT: D 403 LYS cc_start: 0.8734 (pttt) cc_final: 0.8407 (pttp) REVERT: D 485 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7107 (mtt-85) REVERT: E 41 SER cc_start: 0.8027 (m) cc_final: 0.7555 (p) REVERT: E 93 LYS cc_start: 0.8899 (ttmm) cc_final: 0.8492 (ttmt) REVERT: E 95 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8797 (t) REVERT: E 120 ARG cc_start: 0.8988 (mtt-85) cc_final: 0.8703 (mtt90) REVERT: E 137 LYS cc_start: 0.8404 (ttpp) cc_final: 0.8180 (mtpm) REVERT: E 315 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7955 (mt-10) REVERT: E 329 THR cc_start: 0.8699 (m) cc_final: 0.8370 (m) REVERT: E 342 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: E 431 ASP cc_start: 0.8418 (t70) cc_final: 0.8125 (t0) REVERT: E 456 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8251 (mp10) REVERT: E 460 LYS cc_start: 0.8598 (mttt) cc_final: 0.8120 (ttpt) REVERT: F 81 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8379 (mttp) REVERT: F 96 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8182 (m) REVERT: F 108 LYS cc_start: 0.8883 (tttt) cc_final: 0.8526 (ttpp) REVERT: F 168 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7846 (mp0) REVERT: F 242 ARG cc_start: 0.7967 (mtt90) cc_final: 0.7396 (mtt90) REVERT: F 245 LYS cc_start: 0.7931 (tttm) cc_final: 0.7508 (ttmt) REVERT: F 250 GLU cc_start: 0.8107 (tt0) cc_final: 0.7882 (tt0) REVERT: F 305 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7691 (mt-10) REVERT: G 27 THR cc_start: 0.6633 (m) cc_final: 0.6042 (p) REVERT: G 80 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8885 (mm) REVERT: H 137 ASN cc_start: 0.7950 (t0) cc_final: 0.7613 (m-40) REVERT: H 198 GLU cc_start: 0.7584 (tt0) cc_final: 0.7214 (mm-30) REVERT: I 89 ASP cc_start: 0.7570 (m-30) cc_final: 0.6984 (m-30) REVERT: I 99 LYS cc_start: 0.7941 (tttt) cc_final: 0.7385 (mttm) REVERT: I 117 ASP cc_start: 0.7891 (m-30) cc_final: 0.7420 (m-30) REVERT: I 161 LYS cc_start: 0.8102 (mttp) cc_final: 0.7634 (ptmt) REVERT: I 182 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7883 (mt-10) REVERT: I 202 LEU cc_start: 0.8178 (tp) cc_final: 0.7950 (tp) REVERT: I 226 ASP cc_start: 0.7917 (m-30) cc_final: 0.7270 (m-30) REVERT: J 22 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8104 (tm-30) REVERT: J 39 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.8101 (t0) REVERT: J 41 GLU cc_start: 0.8387 (tp30) cc_final: 0.7934 (tp30) REVERT: J 59 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7356 (ttmt) REVERT: J 61 GLU cc_start: 0.7961 (tt0) cc_final: 0.7576 (mt-10) REVERT: J 76 MET cc_start: 0.7692 (mtm) cc_final: 0.6978 (tmm) REVERT: J 85 ARG cc_start: 0.7465 (mtt180) cc_final: 0.6650 (mmt-90) REVERT: J 99 LYS cc_start: 0.7820 (tttt) cc_final: 0.7319 (ttmm) REVERT: J 197 GLU cc_start: 0.7810 (mp0) cc_final: 0.7224 (mp0) REVERT: J 201 ASP cc_start: 0.7777 (t0) cc_final: 0.7334 (m-30) REVERT: K 15 MET cc_start: 0.7427 (mtt) cc_final: 0.7084 (mmt) REVERT: K 16 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8570 (pmm) REVERT: K 54 MET cc_start: 0.6642 (mmt) cc_final: 0.6314 (mmm) REVERT: K 117 ASP cc_start: 0.8105 (m-30) cc_final: 0.7808 (m-30) REVERT: K 192 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8407 (m) REVERT: L 57 ASN cc_start: 0.7443 (t0) cc_final: 0.7146 (t0) REVERT: N 48 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7694 (ttp-170) REVERT: N 52 GLU cc_start: 0.8682 (tp30) cc_final: 0.8186 (tp30) REVERT: N 53 LYS cc_start: 0.8407 (ttmm) cc_final: 0.7956 (ttpp) REVERT: Q 42 LEU cc_start: 0.7682 (mt) cc_final: 0.7469 (mp) REVERT: Q 109 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6399 (mp0) REVERT: Q 117 GLN cc_start: 0.8468 (mm-40) cc_final: 0.7916 (mp10) REVERT: Q 205 LYS cc_start: 0.7955 (tptt) cc_final: 0.7227 (mptt) REVERT: Q 206 ASP cc_start: 0.7207 (m-30) cc_final: 0.6951 (m-30) REVERT: R 34 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6716 (tm130) REVERT: R 47 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7458 (tm-30) REVERT: R 58 LYS cc_start: 0.7939 (tppt) cc_final: 0.7731 (tptm) REVERT: R 117 GLN cc_start: 0.8619 (mt0) cc_final: 0.8296 (mp10) REVERT: R 135 GLN cc_start: 0.8061 (tt0) cc_final: 0.7572 (tt0) REVERT: S 67 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7188 (mm-30) REVERT: S 141 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8427 (tptt) REVERT: S 165 GLN cc_start: 0.8203 (tt0) cc_final: 0.7905 (tt0) REVERT: S 195 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7135 (mp0) REVERT: S 197 TYR cc_start: 0.6546 (m-80) cc_final: 0.6307 (m-80) REVERT: S 221 ASP cc_start: 0.8687 (m-30) cc_final: 0.8405 (m-30) outliers start: 111 outliers final: 51 residues processed: 803 average time/residue: 0.5015 time to fit residues: 492.5670 Evaluate side-chains 784 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 711 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 456 GLN Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 217 LEU Chi-restraints excluded: chain T residue 150 ASN Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 485 optimal weight: 0.8980 chunk 481 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 chunk 263 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 368 optimal weight: 4.9990 chunk 429 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 573 HIS C 157 ASN D 42 GLN F 382 GLN F 482 GLN G 88 GLN G 194 HIS I 100 GLN R 142 ASN R 165 GLN ** R 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 GLN S 134 ASN T 56 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.181595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.143196 restraints weight = 55652.839| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.93 r_work: 0.3202 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 46035 Z= 0.141 Angle : 0.556 12.165 62132 Z= 0.286 Chirality : 0.042 0.191 6969 Planarity : 0.004 0.056 8036 Dihedral : 4.725 108.682 6220 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.18 % Allowed : 17.18 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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: 1.62 (0.11), residues: 5650 helix: 2.41 (0.10), residues: 2862 sheet: -0.02 (0.19), residues: 715 loop : -0.42 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 267 TYR 0.025 0.001 TYR L 98 PHE 0.028 0.001 PHE K 18 TRP 0.016 0.001 TRP G 19 HIS 0.004 0.001 HIS T 66 Details of bonding type rmsd covalent geometry : bond 0.00328 (46035) covalent geometry : angle 0.55557 (62132) hydrogen bonds : bond 0.04582 ( 2382) hydrogen bonds : angle 4.08425 ( 6924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 734 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8342 (p90) cc_final: 0.8111 (p90) REVERT: A 102 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8435 (mp) REVERT: A 163 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8468 (mmtm) REVERT: A 193 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7747 (mt-10) REVERT: A 487 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7749 (tp30) REVERT: A 565 ILE cc_start: 0.8903 (mt) cc_final: 0.8617 (mp) REVERT: A 571 ARG cc_start: 0.7772 (ttp-170) cc_final: 0.7424 (ttm170) REVERT: B 61 MET cc_start: 0.8511 (ttm) cc_final: 0.8310 (mtp) REVERT: B 84 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8328 (pttp) REVERT: B 195 GLU cc_start: 0.7932 (tt0) cc_final: 0.7317 (tt0) REVERT: B 297 GLU cc_start: 0.8283 (tt0) cc_final: 0.8035 (tp30) REVERT: B 346 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.9041 (ttt) REVERT: B 437 LYS cc_start: 0.8223 (tppp) cc_final: 0.7845 (tptm) REVERT: B 530 ARG cc_start: 0.8129 (ptp-110) cc_final: 0.7885 (ptp-170) REVERT: B 540 MET cc_start: 0.8308 (mtp) cc_final: 0.7981 (mtm) REVERT: B 604 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7372 (tm) REVERT: C 56 ARG cc_start: 0.8587 (ttm170) cc_final: 0.8164 (ttp-170) REVERT: C 84 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8648 (mmtp) REVERT: C 100 ASP cc_start: 0.9015 (p0) cc_final: 0.8717 (p0) REVERT: C 108 ASP cc_start: 0.8016 (m-30) cc_final: 0.7691 (m-30) REVERT: C 114 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8096 (mm-40) REVERT: C 220 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8651 (mtpp) REVERT: C 279 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: C 293 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7777 (mm-30) REVERT: C 297 GLU cc_start: 0.8343 (tt0) cc_final: 0.8021 (tt0) REVERT: C 303 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8346 (mm-30) REVERT: C 318 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8470 (mtp) REVERT: C 356 GLU cc_start: 0.8126 (tt0) cc_final: 0.7594 (mt-10) REVERT: C 399 GLU cc_start: 0.8325 (tp30) cc_final: 0.7990 (tp30) REVERT: C 438 LYS cc_start: 0.8704 (mttt) cc_final: 0.8131 (mmtm) REVERT: C 485 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7208 (mt-10) REVERT: C 487 GLU cc_start: 0.8085 (tp30) cc_final: 0.7377 (tt0) REVERT: C 491 GLU cc_start: 0.7895 (tt0) cc_final: 0.7663 (tm-30) REVERT: C 513 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6882 (tttp) REVERT: C 540 MET cc_start: 0.8347 (mtp) cc_final: 0.8092 (mtp) REVERT: C 552 ARG cc_start: 0.7258 (ttt-90) cc_final: 0.6980 (mtp-110) REVERT: D 88 GLU cc_start: 0.8934 (tt0) cc_final: 0.8590 (tm-30) REVERT: D 93 LYS cc_start: 0.8888 (tttt) cc_final: 0.8526 (ttmt) REVERT: D 141 ARG cc_start: 0.7952 (mmm-85) cc_final: 0.7454 (mtm110) REVERT: D 250 GLU cc_start: 0.7825 (tt0) cc_final: 0.7309 (mt-10) REVERT: D 382 GLN cc_start: 0.8181 (mm110) cc_final: 0.7927 (mt0) REVERT: D 403 LYS cc_start: 0.8761 (pttt) cc_final: 0.8449 (pttp) REVERT: D 485 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7257 (mtt-85) REVERT: E 41 SER cc_start: 0.8117 (m) cc_final: 0.7695 (p) REVERT: E 95 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8837 (t) REVERT: E 120 ARG cc_start: 0.9013 (mtt-85) cc_final: 0.8737 (mtt90) REVERT: E 137 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8208 (mtpm) REVERT: E 141 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8082 (ptm160) REVERT: E 315 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7866 (mt-10) REVERT: E 329 THR cc_start: 0.8736 (m) cc_final: 0.8394 (m) REVERT: E 342 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: E 431 ASP cc_start: 0.8401 (t70) cc_final: 0.8121 (t0) REVERT: E 460 LYS cc_start: 0.8671 (mttt) cc_final: 0.8237 (ttpt) REVERT: F 81 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8406 (mttp) REVERT: F 96 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8187 (m) REVERT: F 108 LYS cc_start: 0.8942 (tttt) cc_final: 0.8609 (ttpp) REVERT: F 168 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7870 (mp0) REVERT: F 242 ARG cc_start: 0.8093 (mtt90) cc_final: 0.7524 (mtt90) REVERT: F 245 LYS cc_start: 0.8030 (tttm) cc_final: 0.7622 (ttmt) REVERT: F 250 GLU cc_start: 0.8177 (tt0) cc_final: 0.7959 (tt0) REVERT: F 305 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7785 (mt-10) REVERT: G 27 THR cc_start: 0.6614 (m) cc_final: 0.6240 (p) REVERT: H 198 GLU cc_start: 0.7612 (tt0) cc_final: 0.7394 (mm-30) REVERT: I 89 ASP cc_start: 0.7569 (m-30) cc_final: 0.6994 (m-30) REVERT: I 99 LYS cc_start: 0.8022 (tttt) cc_final: 0.7436 (mttm) REVERT: I 117 ASP cc_start: 0.7928 (m-30) cc_final: 0.7440 (m-30) REVERT: I 161 LYS cc_start: 0.8004 (mttp) cc_final: 0.7688 (ptmt) REVERT: I 182 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7975 (mt-10) REVERT: I 202 LEU cc_start: 0.8247 (tp) cc_final: 0.8028 (tp) REVERT: I 208 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8677 (mmm) REVERT: I 226 ASP cc_start: 0.7941 (m-30) cc_final: 0.7321 (m-30) REVERT: J 22 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8059 (tm-30) REVERT: J 41 GLU cc_start: 0.8346 (tp30) cc_final: 0.8000 (tp30) REVERT: J 59 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7470 (ttmt) REVERT: J 61 GLU cc_start: 0.8052 (tt0) cc_final: 0.7836 (mt-10) REVERT: J 76 MET cc_start: 0.7794 (mtm) cc_final: 0.7087 (tmm) REVERT: J 85 ARG cc_start: 0.7509 (mtt180) cc_final: 0.6727 (mmt-90) REVERT: J 99 LYS cc_start: 0.7880 (tttt) cc_final: 0.7377 (ttmm) REVERT: J 197 GLU cc_start: 0.7838 (mp0) cc_final: 0.7212 (mp0) REVERT: J 201 ASP cc_start: 0.7744 (t0) cc_final: 0.7340 (m-30) REVERT: J 208 MET cc_start: 0.8763 (mmm) cc_final: 0.8538 (mmm) REVERT: K 16 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8513 (pmm) REVERT: K 54 MET cc_start: 0.6817 (mmt) cc_final: 0.6473 (mmm) REVERT: K 117 ASP cc_start: 0.8168 (m-30) cc_final: 0.7886 (m-30) REVERT: K 192 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8431 (m) REVERT: L 57 ASN cc_start: 0.7295 (t0) cc_final: 0.7040 (t0) REVERT: N 48 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7687 (ttp-170) REVERT: N 52 GLU cc_start: 0.8650 (tp30) cc_final: 0.8189 (tp30) REVERT: N 53 LYS cc_start: 0.8449 (ttmm) cc_final: 0.7992 (ttpp) REVERT: Q 42 LEU cc_start: 0.7615 (mt) cc_final: 0.7410 (mp) REVERT: Q 109 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6553 (mp0) REVERT: Q 117 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8000 (mp10) REVERT: Q 205 LYS cc_start: 0.8019 (tptt) cc_final: 0.7373 (mptt) REVERT: R 34 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.6870 (tm130) REVERT: R 47 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7522 (tm-30) REVERT: R 117 GLN cc_start: 0.8572 (mt0) cc_final: 0.8304 (mp10) REVERT: R 135 GLN cc_start: 0.8193 (tt0) cc_final: 0.7708 (tt0) REVERT: S 67 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7214 (mm-30) REVERT: S 141 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8436 (tptt) REVERT: S 165 GLN cc_start: 0.8129 (tt0) cc_final: 0.7874 (tt0) REVERT: S 195 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7346 (mp0) REVERT: S 210 GLU cc_start: 0.8012 (pm20) cc_final: 0.7782 (tp30) REVERT: S 221 ASP cc_start: 0.8601 (m-30) cc_final: 0.8339 (m-30) REVERT: S 223 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8494 (mmtt) REVERT: T 214 ASP cc_start: 0.8694 (m-30) cc_final: 0.8347 (m-30) outliers start: 108 outliers final: 50 residues processed: 799 average time/residue: 0.5072 time to fit residues: 495.9923 Evaluate side-chains 781 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 708 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 88 GLN Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 223 LYS Chi-restraints excluded: chain T residue 150 ASN Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 426 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 385 optimal weight: 0.9980 chunk 269 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 383 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 423 optimal weight: 5.9990 chunk 337 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 573 HIS C 157 ASN D 42 GLN D 54 ASN F 482 GLN G 194 HIS I 100 GLN K 78 GLN Q 142 ASN R 142 ASN ** R 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 ASN ** T 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.178479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.140014 restraints weight = 55192.492| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.10 r_work: 0.3253 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 46035 Z= 0.163 Angle : 0.576 13.107 62132 Z= 0.297 Chirality : 0.042 0.191 6969 Planarity : 0.004 0.064 8036 Dihedral : 4.757 108.956 6220 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.88 % Allowed : 17.75 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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: 1.55 (0.11), residues: 5650 helix: 2.37 (0.10), residues: 2853 sheet: -0.05 (0.19), residues: 705 loop : -0.46 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 142 TYR 0.024 0.001 TYR R 139 PHE 0.028 0.001 PHE K 18 TRP 0.015 0.001 TRP C 567 HIS 0.013 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00387 (46035) covalent geometry : angle 0.57643 (62132) hydrogen bonds : bond 0.04695 ( 2382) hydrogen bonds : angle 4.09533 ( 6924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 716 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8354 (p90) cc_final: 0.8136 (p90) REVERT: A 163 LYS cc_start: 0.8713 (mmtm) cc_final: 0.8390 (mmtt) REVERT: A 193 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7796 (mt-10) REVERT: A 487 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7719 (tp30) REVERT: A 552 ARG cc_start: 0.8344 (mtp85) cc_final: 0.7976 (mtp-110) REVERT: A 565 ILE cc_start: 0.8912 (mt) cc_final: 0.8663 (mp) REVERT: A 571 ARG cc_start: 0.7827 (ttp-170) cc_final: 0.7481 (ttm170) REVERT: B 61 MET cc_start: 0.8620 (ttm) cc_final: 0.8378 (mtp) REVERT: B 195 GLU cc_start: 0.7996 (tt0) cc_final: 0.7371 (tt0) REVERT: B 297 GLU cc_start: 0.8323 (tt0) cc_final: 0.8061 (tp30) REVERT: B 346 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.9052 (ttt) REVERT: B 361 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8737 (mt) REVERT: B 437 LYS cc_start: 0.8171 (tppp) cc_final: 0.7777 (tptm) REVERT: B 530 ARG cc_start: 0.8127 (ptp-110) cc_final: 0.7879 (ptp-170) REVERT: B 540 MET cc_start: 0.8264 (mtp) cc_final: 0.7955 (mtm) REVERT: C 56 ARG cc_start: 0.8632 (ttm170) cc_final: 0.8178 (ttp-170) REVERT: C 84 LYS cc_start: 0.8977 (mmtt) cc_final: 0.8680 (mmtp) REVERT: C 100 ASP cc_start: 0.9047 (p0) cc_final: 0.8755 (p0) REVERT: C 108 ASP cc_start: 0.8018 (m-30) cc_final: 0.7691 (m-30) REVERT: C 114 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8115 (mm-40) REVERT: C 220 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8691 (mtpp) REVERT: C 279 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: C 293 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7789 (mm-30) REVERT: C 297 GLU cc_start: 0.8347 (tt0) cc_final: 0.8031 (tt0) REVERT: C 303 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8344 (mm-30) REVERT: C 318 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8472 (mtp) REVERT: C 356 GLU cc_start: 0.8143 (tt0) cc_final: 0.7617 (mt-10) REVERT: C 399 GLU cc_start: 0.8375 (tp30) cc_final: 0.8013 (tp30) REVERT: C 438 LYS cc_start: 0.8747 (mttt) cc_final: 0.8167 (mmtm) REVERT: C 463 GLU cc_start: 0.8008 (mp0) cc_final: 0.7740 (mp0) REVERT: C 485 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7267 (mt-10) REVERT: C 487 GLU cc_start: 0.8106 (tp30) cc_final: 0.7367 (tt0) REVERT: C 491 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: C 513 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6833 (tttp) REVERT: C 540 MET cc_start: 0.8422 (mtp) cc_final: 0.8170 (mtp) REVERT: C 552 ARG cc_start: 0.7305 (ttt-90) cc_final: 0.7022 (mtp-110) REVERT: D 88 GLU cc_start: 0.8975 (tt0) cc_final: 0.8625 (tm-30) REVERT: D 93 LYS cc_start: 0.8929 (tttt) cc_final: 0.8548 (ttmt) REVERT: D 141 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7495 (mtm110) REVERT: D 250 GLU cc_start: 0.7824 (tt0) cc_final: 0.7327 (mt-10) REVERT: D 382 GLN cc_start: 0.8148 (mm110) cc_final: 0.7914 (mt0) REVERT: D 403 LYS cc_start: 0.8742 (pttt) cc_final: 0.8190 (ptpp) REVERT: D 485 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7256 (mtt-85) REVERT: E 41 SER cc_start: 0.8171 (m) cc_final: 0.7698 (p) REVERT: E 93 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8622 (ttmt) REVERT: E 95 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8847 (t) REVERT: E 120 ARG cc_start: 0.9031 (mtt-85) cc_final: 0.8746 (mtt90) REVERT: E 137 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8240 (mtpm) REVERT: E 141 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8043 (ptm160) REVERT: E 315 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7942 (mt-10) REVERT: E 329 THR cc_start: 0.8794 (m) cc_final: 0.8442 (m) REVERT: E 342 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: E 431 ASP cc_start: 0.8455 (t70) cc_final: 0.8180 (t0) REVERT: E 460 LYS cc_start: 0.8704 (mttt) cc_final: 0.8272 (ttpt) REVERT: E 489 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8520 (ptmm) REVERT: F 81 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8391 (mttp) REVERT: F 96 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8249 (m) REVERT: F 108 LYS cc_start: 0.8912 (tttt) cc_final: 0.8557 (ttpp) REVERT: F 168 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7915 (mp0) REVERT: F 242 ARG cc_start: 0.8085 (mtt90) cc_final: 0.7525 (mtt90) REVERT: F 245 LYS cc_start: 0.8088 (tttm) cc_final: 0.7674 (ttmt) REVERT: F 250 GLU cc_start: 0.8183 (tt0) cc_final: 0.7962 (tt0) REVERT: F 305 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7810 (mt-10) REVERT: G 27 THR cc_start: 0.6824 (m) cc_final: 0.6338 (p) REVERT: H 137 ASN cc_start: 0.7816 (t0) cc_final: 0.7451 (m-40) REVERT: H 198 GLU cc_start: 0.7827 (tt0) cc_final: 0.7509 (mm-30) REVERT: I 89 ASP cc_start: 0.7652 (m-30) cc_final: 0.7095 (m-30) REVERT: I 99 LYS cc_start: 0.8030 (tttt) cc_final: 0.7461 (mttm) REVERT: I 117 ASP cc_start: 0.7972 (m-30) cc_final: 0.7435 (m-30) REVERT: I 161 LYS cc_start: 0.8046 (mttp) cc_final: 0.7691 (ptmt) REVERT: I 182 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7999 (mt-10) REVERT: I 202 LEU cc_start: 0.8262 (tp) cc_final: 0.8044 (tp) REVERT: I 208 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8716 (mmm) REVERT: I 226 ASP cc_start: 0.7999 (m-30) cc_final: 0.7362 (m-30) REVERT: J 22 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8088 (tm-30) REVERT: J 41 GLU cc_start: 0.8392 (tp30) cc_final: 0.8016 (tp30) REVERT: J 55 GLU cc_start: 0.8107 (pp20) cc_final: 0.7846 (OUTLIER) REVERT: J 61 GLU cc_start: 0.8055 (tt0) cc_final: 0.7800 (mt-10) REVERT: J 76 MET cc_start: 0.7839 (mtm) cc_final: 0.7105 (tmm) REVERT: J 85 ARG cc_start: 0.7595 (mtt180) cc_final: 0.6837 (mmt-90) REVERT: J 99 LYS cc_start: 0.7920 (tttt) cc_final: 0.7415 (ttmm) REVERT: J 197 GLU cc_start: 0.7857 (mp0) cc_final: 0.7331 (mp0) REVERT: J 201 ASP cc_start: 0.7868 (t0) cc_final: 0.7456 (m-30) REVERT: J 208 MET cc_start: 0.8833 (mmm) cc_final: 0.8631 (mmm) REVERT: J 221 ASN cc_start: 0.9006 (m-40) cc_final: 0.8786 (m110) REVERT: K 15 MET cc_start: 0.8278 (mmt) cc_final: 0.8001 (mmt) REVERT: K 16 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8347 (mpp) REVERT: K 54 MET cc_start: 0.6844 (mmt) cc_final: 0.6496 (mmm) REVERT: K 78 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7587 (mm110) REVERT: K 117 ASP cc_start: 0.8108 (m-30) cc_final: 0.7817 (m-30) REVERT: K 135 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7034 (ttp-170) REVERT: K 192 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8504 (m) REVERT: L 57 ASN cc_start: 0.7409 (t0) cc_final: 0.7134 (t0) REVERT: N 48 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7664 (ttp-170) REVERT: N 52 GLU cc_start: 0.8670 (tp30) cc_final: 0.8209 (tp30) REVERT: N 53 LYS cc_start: 0.8442 (ttmm) cc_final: 0.7985 (ttpp) REVERT: N 87 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.6706 (m-80) REVERT: O 58 LYS cc_start: 0.7944 (tttp) cc_final: 0.7604 (tttp) REVERT: Q 42 LEU cc_start: 0.7621 (mt) cc_final: 0.7391 (mp) REVERT: Q 45 ILE cc_start: 0.7109 (mt) cc_final: 0.6904 (mm) REVERT: Q 109 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6547 (mp0) REVERT: Q 117 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7984 (mp10) REVERT: Q 205 LYS cc_start: 0.8036 (tptt) cc_final: 0.7386 (mptt) REVERT: R 34 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.6827 (tm130) REVERT: R 47 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7488 (tm-30) REVERT: R 117 GLN cc_start: 0.8637 (mt0) cc_final: 0.8345 (mp10) REVERT: R 135 GLN cc_start: 0.8119 (tt0) cc_final: 0.7623 (tt0) REVERT: R 142 ASN cc_start: 0.8714 (t160) cc_final: 0.8174 (t0) REVERT: S 67 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7234 (mm-30) REVERT: S 141 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8357 (tptt) REVERT: S 165 GLN cc_start: 0.8135 (tt0) cc_final: 0.7883 (tt0) REVERT: S 195 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7447 (mp0) REVERT: S 221 ASP cc_start: 0.8586 (m-30) cc_final: 0.8306 (m-30) REVERT: S 223 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8539 (mmtt) REVERT: T 214 ASP cc_start: 0.8757 (m-30) cc_final: 0.8396 (m-30) outliers start: 93 outliers final: 53 residues processed: 769 average time/residue: 0.4977 time to fit residues: 469.1359 Evaluate side-chains 777 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 700 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 489 LYS Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 223 TYR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 135 ARG Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 223 LYS Chi-restraints excluded: chain T residue 90 LEU Chi-restraints excluded: chain T residue 150 ASN Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 206 optimal weight: 4.9990 chunk 432 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 186 optimal weight: 0.4980 chunk 315 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 377 optimal weight: 0.0270 chunk 230 optimal weight: 0.0870 chunk 486 optimal weight: 10.0000 chunk 397 optimal weight: 4.9990 chunk 246 optimal weight: 0.9980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 573 HIS C 157 ASN D 42 GLN F 482 GLN G 88 GLN G 194 HIS I 100 GLN L 35 ASN R 19 HIS ** R 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 GLN S 134 ASN ** T 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.182770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.144948 restraints weight = 55887.428| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.96 r_work: 0.3283 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 46035 Z= 0.112 Angle : 0.545 12.229 62132 Z= 0.280 Chirality : 0.041 0.225 6969 Planarity : 0.004 0.063 8036 Dihedral : 4.478 102.004 6220 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.33 % Allowed : 18.46 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % 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: 1.76 (0.11), residues: 5650 helix: 2.53 (0.10), residues: 2855 sheet: 0.05 (0.19), residues: 733 loop : -0.36 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M 107 TYR 0.025 0.001 TYR R 139 PHE 0.030 0.001 PHE K 18 TRP 0.017 0.001 TRP G 19 HIS 0.007 0.001 HIS T 66 Details of bonding type rmsd covalent geometry : bond 0.00242 (46035) covalent geometry : angle 0.54459 (62132) hydrogen bonds : bond 0.04183 ( 2382) hydrogen bonds : angle 3.98070 ( 6924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11300 Ramachandran restraints generated. 5650 Oldfield, 0 Emsley, 5650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 742 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8439 (p90) cc_final: 0.8232 (p90) REVERT: A 163 LYS cc_start: 0.8829 (mmtm) cc_final: 0.8561 (mmtm) REVERT: A 193 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7875 (mt-10) REVERT: A 487 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7923 (tp30) REVERT: A 571 ARG cc_start: 0.7890 (ttp-170) cc_final: 0.7558 (ttm170) REVERT: B 61 MET cc_start: 0.8621 (ttm) cc_final: 0.8409 (mtp) REVERT: B 84 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8443 (pttp) REVERT: B 194 LEU cc_start: 0.8508 (pp) cc_final: 0.8288 (pt) REVERT: B 195 GLU cc_start: 0.8025 (tt0) cc_final: 0.7527 (tt0) REVERT: B 297 GLU cc_start: 0.8247 (tt0) cc_final: 0.8035 (tp30) REVERT: B 346 MET cc_start: 0.9327 (ttp) cc_final: 0.9046 (ttt) REVERT: B 361 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8939 (mt) REVERT: B 437 LYS cc_start: 0.8338 (tppp) cc_final: 0.7990 (tptm) REVERT: B 438 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8166 (mtpp) REVERT: B 530 ARG cc_start: 0.8335 (ptp-110) cc_final: 0.8074 (ptp-170) REVERT: B 540 MET cc_start: 0.8390 (mtp) cc_final: 0.8084 (mtm) REVERT: C 56 ARG cc_start: 0.8589 (ttm170) cc_final: 0.8308 (ttp-170) REVERT: C 84 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8809 (mmtp) REVERT: C 108 ASP cc_start: 0.8126 (m-30) cc_final: 0.7864 (m-30) REVERT: C 114 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8164 (mm-40) REVERT: C 173 ARG cc_start: 0.8482 (ptp90) cc_final: 0.8263 (ptt-90) REVERT: C 279 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: C 293 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7862 (mm-30) REVERT: C 297 GLU cc_start: 0.8284 (tt0) cc_final: 0.7953 (tt0) REVERT: C 318 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8603 (mtp) REVERT: C 356 GLU cc_start: 0.8240 (tt0) cc_final: 0.7871 (mt-10) REVERT: C 399 GLU cc_start: 0.8433 (tp30) cc_final: 0.8150 (tp30) REVERT: C 438 LYS cc_start: 0.8883 (mttt) cc_final: 0.8417 (mmtm) REVERT: C 485 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7469 (mt-10) REVERT: C 487 GLU cc_start: 0.8156 (tp30) cc_final: 0.7562 (tt0) REVERT: C 491 GLU cc_start: 0.7970 (tt0) cc_final: 0.7756 (tm-30) REVERT: C 513 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7232 (tttp) REVERT: C 552 ARG cc_start: 0.7502 (ttt-90) cc_final: 0.7215 (mtp-110) REVERT: D 88 GLU cc_start: 0.8928 (tt0) cc_final: 0.8657 (tm-30) REVERT: D 93 LYS cc_start: 0.8865 (tttt) cc_final: 0.8626 (ttmt) REVERT: D 141 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7492 (mtm110) REVERT: D 161 GLN cc_start: 0.8589 (tp40) cc_final: 0.8172 (tp40) REVERT: D 250 GLU cc_start: 0.7939 (tt0) cc_final: 0.7469 (mt-10) REVERT: D 403 LYS cc_start: 0.8789 (pttt) cc_final: 0.8308 (ptpp) REVERT: E 41 SER cc_start: 0.8185 (m) cc_final: 0.7841 (p) REVERT: E 93 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8595 (ttmt) REVERT: E 95 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8883 (t) REVERT: E 137 LYS cc_start: 0.8507 (ttpp) cc_final: 0.8260 (mmtt) REVERT: E 141 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8058 (ptm160) REVERT: E 315 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8036 (mt-10) REVERT: E 329 THR cc_start: 0.8910 (m) cc_final: 0.8593 (m) REVERT: E 342 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: E 460 LYS cc_start: 0.8729 (mttt) cc_final: 0.8492 (ttpt) REVERT: F 96 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8269 (m) REVERT: F 108 LYS cc_start: 0.8964 (tttt) cc_final: 0.8694 (ttpp) REVERT: F 168 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7908 (mp0) REVERT: F 242 ARG cc_start: 0.8229 (mtt90) cc_final: 0.7753 (mtt90) REVERT: F 245 LYS cc_start: 0.8304 (tttm) cc_final: 0.7987 (ttmt) REVERT: F 305 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8046 (mt-10) REVERT: F 387 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7974 (mp-120) REVERT: F 410 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8019 (mtt) REVERT: G 27 THR cc_start: 0.6747 (m) cc_final: 0.6358 (p) REVERT: I 89 ASP cc_start: 0.7674 (m-30) cc_final: 0.7152 (m-30) REVERT: I 99 LYS cc_start: 0.8170 (tttt) cc_final: 0.7581 (mttt) REVERT: I 117 ASP cc_start: 0.8032 (m-30) cc_final: 0.7588 (m-30) REVERT: I 161 LYS cc_start: 0.8043 (mttp) cc_final: 0.7841 (ptmt) REVERT: I 182 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8105 (mt-10) REVERT: I 202 LEU cc_start: 0.8472 (tp) cc_final: 0.8260 (tp) REVERT: I 207 MET cc_start: 0.8694 (mtp) cc_final: 0.8464 (ttp) REVERT: I 208 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8833 (mmm) REVERT: I 226 ASP cc_start: 0.8054 (m-30) cc_final: 0.7534 (m-30) REVERT: J 22 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8148 (tm-30) REVERT: J 41 GLU cc_start: 0.8297 (tp30) cc_final: 0.8022 (tp30) REVERT: J 61 GLU cc_start: 0.8005 (tt0) cc_final: 0.7749 (mt-10) REVERT: J 76 MET cc_start: 0.7860 (mtm) cc_final: 0.7215 (tmm) REVERT: J 85 ARG cc_start: 0.7836 (mtt180) cc_final: 0.7080 (mmt-90) REVERT: J 99 LYS cc_start: 0.8176 (tttt) cc_final: 0.7687 (ttmm) REVERT: J 197 GLU cc_start: 0.7932 (mp0) cc_final: 0.7440 (mp0) REVERT: J 201 ASP cc_start: 0.7919 (t0) cc_final: 0.7562 (m-30) REVERT: K 54 MET cc_start: 0.6948 (mmt) cc_final: 0.6547 (mmm) REVERT: K 117 ASP cc_start: 0.8222 (m-30) cc_final: 0.7913 (m-30) REVERT: L 59 ASP cc_start: 0.7276 (p0) cc_final: 0.7060 (p0) REVERT: N 48 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7789 (ttp-170) REVERT: N 52 GLU cc_start: 0.8501 (tp30) cc_final: 0.8136 (tp30) REVERT: N 53 LYS cc_start: 0.8561 (ttmm) cc_final: 0.8134 (ttpp) REVERT: O 58 LYS cc_start: 0.8031 (tttp) cc_final: 0.7751 (tttp) REVERT: Q 109 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: Q 117 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7992 (mp10) REVERT: Q 205 LYS cc_start: 0.8099 (tptt) cc_final: 0.7444 (mptt) REVERT: R 34 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7168 (tm130) REVERT: R 47 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7589 (tm-30) REVERT: R 135 GLN cc_start: 0.8278 (tt0) cc_final: 0.8028 (tt0) REVERT: R 142 ASN cc_start: 0.8579 (t160) cc_final: 0.8016 (t0) REVERT: S 10 MET cc_start: 0.7799 (mtt) cc_final: 0.7444 (mtp) REVERT: S 67 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7386 (mm-30) REVERT: S 165 GLN cc_start: 0.8138 (tt0) cc_final: 0.7922 (tt0) REVERT: S 221 ASP cc_start: 0.8501 (m-30) cc_final: 0.8292 (m-30) REVERT: S 223 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8468 (mmtt) REVERT: T 214 ASP cc_start: 0.8649 (m-30) cc_final: 0.8417 (m-30) outliers start: 66 outliers final: 32 residues processed: 779 average time/residue: 0.4971 time to fit residues: 475.6162 Evaluate side-chains 757 residues out of total 4958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 710 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 513 LYS Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain F residue 410 MET Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 208 MET Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 34 GLN Chi-restraints excluded: chain S residue 168 ILE Chi-restraints excluded: chain S residue 223 LYS Chi-restraints excluded: chain T residue 150 ASN Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 168 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 529 optimal weight: 20.0000 chunk 213 optimal weight: 0.0770 chunk 109 optimal weight: 2.9990 chunk 311 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 444 optimal weight: 8.9990 chunk 343 optimal weight: 0.5980 chunk 413 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 330 optimal weight: 4.9990 overall best weight: 2.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 573 HIS C 157 ASN D 42 GLN F 482 GLN G 194 HIS ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN J 221 ASN L 35 ASN ** O 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 142 ASN R 19 HIS ** R 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.176254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.137348 restraints weight = 55564.918| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.16 r_work: 0.3192 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 46035 Z= 0.251 Angle : 0.662 11.914 62132 Z= 0.340 Chirality : 0.046 0.214 6969 Planarity : 0.005 0.064 8036 Dihedral : 4.959 110.312 6220 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.49 % Allowed : 18.68 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.11), residues: 5650 helix: 2.26 (0.10), residues: 2848 sheet: -0.04 (0.19), residues: 717 loop : -0.54 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 142 TYR 0.043 0.002 TYR S 197 PHE 0.035 0.002 PHE H 155 TRP 0.016 0.002 TRP A 450 HIS 0.008 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00619 (46035) covalent geometry : angle 0.66196 (62132) hydrogen bonds : bond 0.05195 ( 2382) hydrogen bonds : angle 4.22138 ( 6924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17721.79 seconds wall clock time: 300 minutes 51.06 seconds (18051.06 seconds total)