Starting phenix.real_space_refine on Thu Nov 20 21:06:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8p_44351/11_2025/9b8p_44351.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8p_44351/11_2025/9b8p_44351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b8p_44351/11_2025/9b8p_44351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8p_44351/11_2025/9b8p_44351.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b8p_44351/11_2025/9b8p_44351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8p_44351/11_2025/9b8p_44351.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 212 5.16 5 C 24778 2.51 5 N 6739 2.21 5 O 7417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39148 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "B" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "C" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4651 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "E" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "F" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3595 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 431} Chain breaks: 1 Chain: "H" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1573 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 25 Chain: "I" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1408 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 5, 'TRANS': 168} Chain: "J" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1476 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "K" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1383 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain: "L" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "M" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "N" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 519 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "O" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 390 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "Q" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2130 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain: "R" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2155 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 9, 'TRANS': 257} Chain: "S" 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: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.27, per 1000 atoms: 0.24 Number of scatterers: 39148 At special positions: 0 Unit cell: (181.28, 183.34, 173.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 212 16.00 P 2 15.00 O 7417 8.00 N 6739 7.00 C 24778 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: 3.45 Conformation dependent library (CDL) restraints added in 1.7 seconds 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9286 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 32 sheets defined 54.3% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 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 255 through 266 Processing helix chain 'A' and resid 280 through 291 removed outlier: 4.041A pdb=" N MET A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 removed outlier: 4.152A pdb=" N ALA A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 366 removed outlier: 3.796A pdb=" N TRP A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 377 through 387 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.628A pdb=" N ASP A 416 " --> pdb=" O PRO A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 457 through 469 removed outlier: 4.586A pdb=" N GLU A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TYR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 497 removed outlier: 4.015A pdb=" N LEU A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 4.118A 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 558 removed outlier: 3.732A pdb=" N LEU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 593 through 616 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 254 through 257 removed outlier: 3.917A pdb=" N THR B 257 " --> pdb=" O CYS B 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 254 through 257' Processing helix chain 'B' and resid 258 through 266 Processing helix chain 'B' and resid 280 through 291 Processing helix chain 'B' and resid 319 through 340 removed outlier: 4.580A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 366 removed outlier: 3.529A pdb=" N TRP B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.579A pdb=" N TYR B 374 " --> pdb=" O ASP B 371 " (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 427 removed outlier: 3.530A pdb=" N GLY B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 443 Processing helix chain 'B' and resid 457 through 469 removed outlier: 4.493A pdb=" N GLU B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 496 removed outlier: 3.783A pdb=" N LEU B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (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 574 Processing helix chain 'B' and resid 574 through 584 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 removed outlier: 3.766A pdb=" N SER C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.984A pdb=" N ILE C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Proline residue: C 292 - end of helix Processing helix chain 'C' and resid 319 through 325 Processing helix chain 'C' and resid 325 through 340 Processing helix chain 'C' and resid 350 through 366 removed outlier: 3.624A pdb=" N TRP C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 412 through 416 Processing helix chain 'C' and resid 419 through 429 Processing helix chain 'C' and resid 436 through 442 Processing helix chain 'C' and resid 457 through 469 removed outlier: 4.957A pdb=" N GLU C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TYR C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 497 removed outlier: 4.230A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 519 removed outlier: 3.690A pdb=" N LEU C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 558 Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 574 through 584 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 616 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 198 through 209 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 315 Processing helix chain 'D' and resid 319 through 323 removed outlier: 3.548A pdb=" N GLY D 322 " --> pdb=" O GLY D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 336 Processing helix chain 'D' and resid 357 through 360 Processing helix chain 'D' and resid 363 through 373 Processing helix chain 'D' and resid 380 through 386 Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 414 through 440 removed outlier: 3.781A 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 removed outlier: 3.594A pdb=" N GLU D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 159 through 163 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 269 through 272 Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 299 through 315 Processing helix chain 'E' and resid 319 through 323 removed outlier: 3.554A pdb=" N GLY E 322 " --> pdb=" O GLY E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 336 removed outlier: 3.601A pdb=" N ILE E 334 " --> pdb=" O ASP E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 360 Processing helix chain 'E' and resid 363 through 373 removed outlier: 3.586A pdb=" N ILE E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 386 Processing helix chain 'E' and resid 414 through 440 removed outlier: 3.675A 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 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 removed outlier: 3.941A pdb=" N GLU E 502 " --> pdb=" O SER E 498 " (cutoff:3.500A) 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 267 through 288 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 324 through 325 No H-bonds generated for 'chain 'F' and resid 324 through 325' Processing helix chain 'F' and resid 326 through 336 Processing helix chain 'F' and resid 357 through 360 Processing helix chain 'F' and resid 363 through 373 Processing helix chain 'F' and resid 380 through 386 Processing helix chain 'F' and resid 402 through 406 removed outlier: 3.684A pdb=" N ILE F 406 " --> pdb=" O LYS F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 440 removed outlier: 3.635A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 462 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 removed outlier: 3.962A pdb=" N GLU F 502 " --> pdb=" O SER F 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 77 removed outlier: 3.561A pdb=" N GLU H 60 " --> pdb=" O MET H 56 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 86 Processing helix chain 'H' and resid 131 through 217 removed outlier: 3.701A pdb=" N GLU H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ILE H 177 " --> pdb=" O GLU H 173 " (cutoff:3.500A) Proline residue: H 178 - end of helix Processing helix chain 'I' and resid 54 through 108 removed outlier: 3.655A pdb=" N LYS I 107 " --> pdb=" O SER I 103 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP I 108 " --> pdb=" O LYS I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 128 Processing helix chain 'I' and resid 140 through 160 Proline residue: I 153 - end of helix Processing helix chain 'I' and resid 196 through 217 removed outlier: 3.597A pdb=" N GLN I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Proline residue: I 209 - end of helix Processing helix chain 'J' and resid 46 through 108 removed outlier: 3.929A pdb=" N LYS J 107 " --> pdb=" O SER J 103 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP J 108 " --> pdb=" O LYS J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 128 removed outlier: 3.817A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 160 Proline residue: J 153 - end of helix Processing helix chain 'J' and resid 196 through 216 removed outlier: 3.695A pdb=" N ASP J 201 " --> pdb=" O GLU J 197 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Proline residue: J 209 - end of helix Processing helix chain 'K' and resid 57 through 106 removed outlier: 3.511A pdb=" N LYS K 104 " --> pdb=" O GLN K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 128 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: 3.580A 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 24 Processing helix chain 'L' and resid 44 through 58 Processing helix chain 'L' and resid 68 through 74 Processing helix chain 'L' and resid 74 through 81 Processing helix chain 'L' and resid 105 through 109 Processing helix chain 'M' and resid 71 through 91 Processing helix chain 'M' and resid 91 through 105 removed outlier: 3.852A pdb=" N VAL M 95 " --> pdb=" O ASN M 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 105 removed outlier: 3.676A pdb=" N ARG N 90 " --> pdb=" O SER N 86 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN N 91 " --> pdb=" O SER N 87 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU N 93 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ARG N 94 " --> pdb=" O ARG N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 105 removed outlier: 3.659A pdb=" N ASN O 91 " --> pdb=" O SER O 87 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLU O 93 " --> pdb=" O GLN O 89 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 37 Processing helix chain 'Q' and resid 42 through 49 Processing helix chain 'Q' and resid 49 through 58 removed outlier: 5.227A pdb=" N TRP Q 55 " --> pdb=" O ASP Q 51 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA Q 56 " --> pdb=" O VAL Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 71 Processing helix chain 'Q' and resid 77 through 98 Processing helix chain 'Q' and resid 104 through 118 Processing helix chain 'Q' and resid 120 through 123 Processing helix chain 'Q' and resid 124 through 143 removed outlier: 4.051A pdb=" N ASN Q 142 " --> pdb=" O ASP Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 167 Processing helix chain 'Q' and resid 172 through 188 Processing helix chain 'Q' and resid 192 through 207 Processing helix chain 'Q' and resid 218 through 234 Processing helix chain 'Q' and resid 235 through 237 No H-bonds generated for 'chain 'Q' and resid 235 through 237' Processing helix chain 'Q' and resid 239 through 249 removed outlier: 3.633A pdb=" N LEU Q 249 " --> pdb=" O LYS Q 245 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 252 No H-bonds generated for 'chain 'Q' and resid 250 through 252' Processing helix chain 'Q' and resid 256 through 273 Processing helix chain 'R' and resid 14 through 37 removed outlier: 3.704A pdb=" N VAL R 23 " --> pdb=" O HIS R 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 49 Processing helix chain 'R' and resid 49 through 58 removed outlier: 5.089A pdb=" N TRP R 55 " --> pdb=" O ASP R 51 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA R 56 " --> pdb=" O VAL R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 71 Processing helix chain 'R' and resid 77 through 98 removed outlier: 3.582A pdb=" N ILE R 98 " --> pdb=" O LEU R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 102 removed outlier: 3.800A pdb=" N LYS R 102 " --> pdb=" O SER R 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 99 through 102' Processing helix chain 'R' and resid 104 through 118 Processing helix chain 'R' and resid 120 through 123 Processing helix chain 'R' and resid 124 through 142 removed outlier: 4.501A pdb=" N ASN R 142 " --> pdb=" O ASP R 138 " (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 Processing helix chain 'R' and resid 239 through 250 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 58 removed outlier: 4.738A pdb=" N TRP S 55 " --> pdb=" O ASP S 51 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA S 56 " --> pdb=" O VAL S 52 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS S 58 " --> pdb=" O ILE S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 72 Processing helix chain 'S' and resid 77 through 98 removed outlier: 3.541A pdb=" N LEU S 91 " --> pdb=" O ILE S 87 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE S 98 " --> pdb=" O LEU S 94 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 118 Processing helix chain 'S' and resid 120 through 123 Processing helix chain 'S' and resid 124 through 143 removed outlier: 3.931A pdb=" N ASN S 142 " --> pdb=" O ASP S 138 " (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 Processing helix chain 'S' and resid 235 through 237 No H-bonds generated for 'chain 'S' and resid 235 through 237' Processing helix chain 'S' and resid 239 through 250 Processing helix chain 'S' and resid 256 through 274 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 24 removed outlier: 6.472A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (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: 6.929A pdb=" N THR A 63 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU A 57 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 6.516A 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: 5.565A pdb=" N ILE B 54 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN B 65 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG B 56 " --> pdb=" O THR B 63 " (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: 6.492A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.781A 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: 6.570A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.749A 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: 6.715A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (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: 5.493A pdb=" N VAL F 86 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN F 97 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER F 90 " --> pdb=" O LYS F 93 " (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 removed outlier: 6.412A pdb=" N ILE A 272 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL A 312 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR A 274 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 271 " --> pdb=" O HIS A 343 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL A 344 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL A 407 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET A 346 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA A 409 " --> pdb=" O MET A 346 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA A 348 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 410 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A 245 " --> pdb=" O VAL A 431 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 167 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 removed outlier: 6.458A 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 315 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 309 through 315 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 164 through 167 removed outlier: 3.544A pdb=" N GLY B 154 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.677A pdb=" N GLU B 193 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 295 through 298 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 99 removed outlier: 4.229A pdb=" N ARG C 391 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU C 219 " --> pdb=" O LYS C 393 " (cutoff:3.500A) 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: 6.492A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE C 179 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N VAL C 191 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 409 through 410 removed outlier: 6.860A pdb=" N VAL C 410 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE C 248 " --> pdb=" O VAL C 410 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 295 through 298 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: 6.385A pdb=" N ARG D 130 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU D 261 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE D 132 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU D 263 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA D 228 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE D 296 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL D 230 " --> pdb=" O ILE D 296 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N THR D 298 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA D 232 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 163 through 164 removed outlier: 3.609A pdb=" N ILE D 164 " --> pdb=" O ARG D 340 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG D 340 " --> pdb=" O ILE D 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 170 removed outlier: 4.461A pdb=" N ILE D 183 " --> pdb=" O ILE D 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 353 through 355 Processing sheet with id=AC5, first strand: chain 'E' and resid 120 through 123 Processing sheet with id=AC6, first strand: chain 'E' and resid 130 through 133 removed outlier: 6.424A pdb=" N ARG E 130 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU E 261 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE E 132 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU E 263 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU E 297 " --> pdb=" O ILE E 351 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE E 191 " --> pdb=" O LEU E 354 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 169 through 170 removed outlier: 4.530A pdb=" N ILE E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 120 through 123 Processing sheet with id=AC9, first strand: chain 'F' and resid 131 through 133 removed outlier: 8.792A pdb=" N CYS F 258 " --> pdb=" O PHE F 227 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA F 228 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE F 296 " --> pdb=" O ALA F 228 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL F 230 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N THR F 298 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ALA F 232 " --> pdb=" O THR F 298 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 163 through 164 removed outlier: 4.009A pdb=" N ARG F 340 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 183 through 184 removed outlier: 4.361A pdb=" N ILE F 183 " --> pdb=" O ILE F 170 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 353 through 355 removed outlier: 6.541A pdb=" N ILE F 191 " --> pdb=" O LEU F 354 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR F 378 " --> pdb=" O PRO F 396 " (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: 6.588A pdb=" N ALA L 9 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASN L 67 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ILE L 11 " --> pdb=" O ASN L 67 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE L 64 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE L 91 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE L 66 " --> pdb=" O ILE L 91 " (cutoff:3.500A) 2083 hydrogen bonds defined for protein. 6024 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: 7.24 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13020 1.34 - 1.46: 7642 1.46 - 1.58: 18786 1.58 - 1.70: 3 1.70 - 1.81: 376 Bond restraints: 39827 Sorted by residual: bond pdb=" C4 ADP A 701 " pdb=" C5 ADP A 701 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" CG1 ILE L 61 " pdb=" CD1 ILE L 61 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.61e+00 bond pdb=" CA ILE K 152 " pdb=" CB ILE K 152 " ideal model delta sigma weight residual 1.539 1.532 0.007 5.40e-03 3.43e+04 1.51e+00 bond pdb=" N ASN B 397 " pdb=" CA ASN B 397 " ideal model delta sigma weight residual 1.462 1.452 0.010 8.50e-03 1.38e+04 1.35e+00 bond pdb=" CA ILE D 495 " pdb=" CB ILE D 495 " ideal model delta sigma weight residual 1.537 1.524 0.014 1.29e-02 6.01e+03 1.13e+00 ... (remaining 39822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 52018 1.25 - 2.51: 1406 2.51 - 3.76: 279 3.76 - 5.02: 80 5.02 - 6.27: 7 Bond angle restraints: 53790 Sorted by residual: angle pdb=" N ILE E 177 " pdb=" CA ILE E 177 " pdb=" C ILE E 177 " ideal model delta sigma weight residual 111.56 108.53 3.03 8.60e-01 1.35e+00 1.24e+01 angle pdb=" N ILE A 428 " pdb=" CA ILE A 428 " pdb=" C ILE A 428 " ideal model delta sigma weight residual 111.62 109.11 2.51 7.90e-01 1.60e+00 1.01e+01 angle pdb=" N ILE B 428 " pdb=" CA ILE B 428 " pdb=" C ILE B 428 " ideal model delta sigma weight residual 111.62 109.32 2.30 7.90e-01 1.60e+00 8.49e+00 angle pdb=" N ILE A 55 " pdb=" CA ILE A 55 " pdb=" C ILE A 55 " ideal model delta sigma weight residual 113.53 110.89 2.64 9.80e-01 1.04e+00 7.24e+00 angle pdb=" CA MET J 54 " pdb=" CB MET J 54 " pdb=" CG MET J 54 " ideal model delta sigma weight residual 114.10 119.21 -5.11 2.00e+00 2.50e-01 6.53e+00 ... (remaining 53785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.66: 21904 18.66 - 37.31: 2031 37.31 - 55.97: 440 55.97 - 74.62: 105 74.62 - 93.28: 43 Dihedral angle restraints: 24523 sinusoidal: 10100 harmonic: 14423 Sorted by residual: dihedral pdb=" O2A ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PA ADP A 701 " pdb=" PB ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 33.28 -93.28 1 2.00e+01 2.50e-03 2.54e+01 dihedral pdb=" O1B ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PB ADP A 701 " pdb=" PA ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 24.06 -84.06 1 2.00e+01 2.50e-03 2.15e+01 dihedral pdb=" CA PHE A 18 " pdb=" C PHE A 18 " pdb=" N GLY A 19 " pdb=" CA GLY A 19 " ideal model delta harmonic sigma weight residual 180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 24520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3648 0.028 - 0.057: 1570 0.057 - 0.085: 454 0.085 - 0.113: 303 0.113 - 0.142: 92 Chirality restraints: 6067 Sorted by residual: chirality pdb=" CA ILE H 94 " pdb=" N ILE H 94 " pdb=" C ILE H 94 " pdb=" CB ILE H 94 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE A 64 " pdb=" N ILE A 64 " pdb=" C ILE A 64 " pdb=" CB ILE A 64 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE C 118 " pdb=" N ILE C 118 " pdb=" C ILE C 118 " pdb=" CB ILE C 118 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 6064 not shown) Planarity restraints: 6962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN J 194 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.53e+00 pdb=" C ASN J 194 " 0.041 2.00e-02 2.50e+03 pdb=" O ASN J 194 " -0.015 2.00e-02 2.50e+03 pdb=" N THR J 195 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN K 194 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C ASN K 194 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN K 194 " 0.014 2.00e-02 2.50e+03 pdb=" N THR K 195 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN I 194 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C ASN I 194 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN I 194 " 0.013 2.00e-02 2.50e+03 pdb=" N THR I 195 " 0.012 2.00e-02 2.50e+03 ... (remaining 6959 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 350 2.58 - 3.16: 34421 3.16 - 3.74: 62398 3.74 - 4.32: 88119 4.32 - 4.90: 150987 Nonbonded interactions: 336275 Sorted by model distance: nonbonded pdb=" O GLY D 55 " pdb=" OG1 THR D 102 " model vdw 2.004 3.040 nonbonded pdb=" O LEU Q 121 " pdb=" OG SER Q 124 " model vdw 2.026 3.040 nonbonded pdb=" O LEU A 42 " pdb=" OG1 THR A 82 " model vdw 2.026 3.040 nonbonded pdb=" OH TYR C 274 " pdb=" OD1 ASP C 349 " model vdw 2.070 3.040 nonbonded pdb=" OD2 ASP A 151 " pdb=" ND2 ASN A 397 " model vdw 2.082 3.120 ... (remaining 336270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 616) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'I' and resid 56 through 226) selection = (chain 'J' and resid 56 through 226) selection = chain 'K' } ncs_group { reference = chain 'M' selection = (chain 'O' and resid 70 through 116) } ncs_group { reference = (chain 'Q' and resid 12 through 274) selection = (chain 'R' and resid 12 through 274) selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 34.550 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 39827 Z= 0.159 Angle : 0.532 6.269 53790 Z= 0.289 Chirality : 0.040 0.142 6067 Planarity : 0.004 0.069 6962 Dihedral : 15.635 93.281 15237 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.84 % Allowed : 11.32 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.12), residues: 4924 helix: 1.81 (0.11), residues: 2457 sheet: -1.53 (0.19), residues: 616 loop : -0.47 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 364 TYR 0.014 0.001 TYR R 112 PHE 0.023 0.001 PHE B 612 TRP 0.011 0.001 TRP B 450 HIS 0.005 0.001 HIS M 111 Details of bonding type rmsd covalent geometry : bond 0.00360 (39827) covalent geometry : angle 0.53219 (53790) hydrogen bonds : bond 0.10288 ( 2083) hydrogen bonds : angle 5.66002 ( 6024) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 519 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.7196 (mtt) cc_final: 0.6710 (mtt) REVERT: B 112 GLN cc_start: 0.8483 (tt0) cc_final: 0.8137 (tt0) REVERT: B 161 LEU cc_start: 0.8825 (mp) cc_final: 0.8481 (mp) REVERT: B 442 ARG cc_start: 0.7981 (mpt180) cc_final: 0.7726 (mpt180) REVERT: B 459 ARG cc_start: 0.7963 (tmm160) cc_final: 0.7667 (tmt170) REVERT: B 485 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6393 (mt-10) REVERT: B 540 MET cc_start: 0.7971 (mtp) cc_final: 0.7454 (mtp) REVERT: C 284 MET cc_start: 0.8632 (tpp) cc_final: 0.8247 (tpp) REVERT: C 532 CYS cc_start: 0.8726 (t) cc_final: 0.8136 (t) REVERT: D 238 MET cc_start: 0.8844 (tpp) cc_final: 0.8549 (tpp) REVERT: D 382 GLN cc_start: 0.8284 (mp-120) cc_final: 0.8037 (mm110) REVERT: E 156 GLN cc_start: 0.8464 (tt0) cc_final: 0.7994 (mt0) REVERT: E 360 ASP cc_start: 0.8506 (t0) cc_final: 0.8206 (t0) REVERT: F 45 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8232 (mt) REVERT: F 133 ASN cc_start: 0.8914 (p0) cc_final: 0.8627 (p0) REVERT: F 226 ASN cc_start: 0.7459 (p0) cc_final: 0.6816 (m-40) REVERT: F 234 MET cc_start: 0.9390 (mtm) cc_final: 0.9011 (mtt) REVERT: F 329 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7631 (m) REVERT: H 58 MET cc_start: 0.7029 (ttp) cc_final: 0.6646 (tmm) REVERT: H 206 GLN cc_start: 0.8089 (mt0) cc_final: 0.7725 (mt0) REVERT: I 66 GLN cc_start: 0.7484 (tt0) cc_final: 0.6701 (mm-40) REVERT: J 54 MET cc_start: 0.4499 (mmp) cc_final: 0.3819 (tpt) REVERT: J 68 LYS cc_start: 0.7646 (tppp) cc_final: 0.7356 (tptm) REVERT: J 133 ILE cc_start: 0.9123 (mt) cc_final: 0.8828 (mp) REVERT: J 194 ASN cc_start: 0.8954 (t0) cc_final: 0.8715 (t0) REVERT: J 197 GLU cc_start: 0.8616 (mp0) cc_final: 0.8297 (mp0) REVERT: N 69 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5532 (mt) REVERT: Q 37 ASP cc_start: 0.7553 (t0) cc_final: 0.7075 (t0) REVERT: Q 109 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7232 (mm-30) REVERT: Q 255 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7745 (tt) REVERT: R 34 GLN cc_start: 0.7599 (tp40) cc_final: 0.6645 (tm-30) REVERT: R 50 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7185 (mm-40) REVERT: R 118 HIS cc_start: 0.8234 (t-90) cc_final: 0.8022 (t-90) REVERT: R 162 GLN cc_start: 0.6917 (mm110) cc_final: 0.6030 (mt0) REVERT: R 229 MET cc_start: 0.4296 (mmm) cc_final: 0.3652 (mmm) REVERT: R 234 MET cc_start: 0.6119 (tmm) cc_final: 0.4860 (mmm) REVERT: S 20 SER cc_start: 0.8506 (t) cc_final: 0.7953 (p) REVERT: S 31 ARG cc_start: 0.8571 (mtm-85) cc_final: 0.8336 (mtm110) REVERT: S 123 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8041 (mtpp) REVERT: S 168 ILE cc_start: 0.7996 (pt) cc_final: 0.7728 (pt) REVERT: S 173 GLU cc_start: 0.7529 (mp0) cc_final: 0.7202 (mp0) REVERT: S 188 MET cc_start: 0.8243 (ttm) cc_final: 0.7859 (ttm) outliers start: 36 outliers final: 29 residues processed: 544 average time/residue: 0.2599 time to fit residues: 229.8717 Evaluate side-chains 525 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 492 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 91 ASN Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 76 ASN Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 254 VAL Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 175 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 30.0000 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 521 GLN C 523 ASN D 54 ASN D 393 ASN E 363 HIS E 415 HIS E 497 GLN L 67 ASN N 91 ASN O 98 GLN ** Q 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 207 GLN Q 270 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.151987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111552 restraints weight = 45517.088| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.65 r_work: 0.3187 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 39827 Z= 0.298 Angle : 0.646 9.560 53790 Z= 0.331 Chirality : 0.047 0.242 6067 Planarity : 0.005 0.045 6962 Dihedral : 5.973 95.414 5483 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.61 % Allowed : 11.79 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.12), residues: 4924 helix: 1.73 (0.10), residues: 2454 sheet: -1.57 (0.19), residues: 600 loop : -0.65 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 400 TYR 0.018 0.002 TYR J 125 PHE 0.024 0.002 PHE C 472 TRP 0.016 0.002 TRP Q 122 HIS 0.008 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00738 (39827) covalent geometry : angle 0.64587 (53790) hydrogen bonds : bond 0.04444 ( 2083) hydrogen bonds : angle 4.78107 ( 6024) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 537 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.8124 (m-30) cc_final: 0.7769 (m-30) REVERT: A 371 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7796 (t0) REVERT: A 399 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7299 (mp0) REVERT: A 466 ASP cc_start: 0.7834 (p0) cc_final: 0.7400 (m-30) REVERT: A 521 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8485 (tt0) REVERT: A 574 MET cc_start: 0.7582 (mtt) cc_final: 0.7238 (mtt) REVERT: B 112 GLN cc_start: 0.8611 (tt0) cc_final: 0.8294 (tt0) REVERT: B 161 LEU cc_start: 0.8870 (mp) cc_final: 0.8558 (mt) REVERT: B 195 GLU cc_start: 0.8364 (tt0) cc_final: 0.8049 (pt0) REVERT: B 459 ARG cc_start: 0.8145 (tmm160) cc_final: 0.7806 (tmt170) REVERT: B 485 GLU cc_start: 0.7522 (mm-30) cc_final: 0.6760 (mt-10) REVERT: C 171 ARG cc_start: 0.7632 (ptp-110) cc_final: 0.7324 (ptp-170) REVERT: C 284 MET cc_start: 0.8754 (tpp) cc_final: 0.8232 (tpp) REVERT: C 532 CYS cc_start: 0.8908 (t) cc_final: 0.8491 (t) REVERT: D 39 TYR cc_start: 0.7569 (p90) cc_final: 0.7310 (p90) REVERT: D 435 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8505 (tmm) REVERT: E 156 GLN cc_start: 0.8631 (tt0) cc_final: 0.8242 (mt0) REVERT: F 45 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8407 (mp) REVERT: F 180 MET cc_start: 0.9069 (mmm) cc_final: 0.8865 (mmm) REVERT: F 226 ASN cc_start: 0.7800 (p0) cc_final: 0.7111 (m-40) REVERT: F 359 ASP cc_start: 0.8425 (m-30) cc_final: 0.8201 (m-30) REVERT: H 48 LEU cc_start: 0.8154 (tp) cc_final: 0.7675 (tt) REVERT: H 97 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7562 (ttmm) REVERT: H 206 GLN cc_start: 0.8445 (mt0) cc_final: 0.8102 (mt0) REVERT: I 66 GLN cc_start: 0.7537 (tt0) cc_final: 0.6743 (mm-40) REVERT: I 97 GLU cc_start: 0.8375 (tp30) cc_final: 0.8134 (tt0) REVERT: J 56 TYR cc_start: 0.6285 (OUTLIER) cc_final: 0.5850 (t80) REVERT: J 72 MET cc_start: 0.7993 (tpp) cc_final: 0.7396 (tpp) REVERT: J 197 GLU cc_start: 0.8897 (mp0) cc_final: 0.8528 (mp0) REVERT: Q 37 ASP cc_start: 0.7962 (t0) cc_final: 0.7556 (t0) REVERT: Q 109 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7448 (mm-30) REVERT: Q 176 ASN cc_start: 0.7675 (m-40) cc_final: 0.7463 (m110) REVERT: Q 255 LEU cc_start: 0.7730 (mp) cc_final: 0.7448 (tt) REVERT: R 34 GLN cc_start: 0.7830 (tp40) cc_final: 0.6875 (tm-30) REVERT: R 37 ASP cc_start: 0.7888 (t0) cc_final: 0.7150 (t0) REVERT: R 50 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7148 (mm110) REVERT: R 104 LYS cc_start: 0.8094 (tppt) cc_final: 0.7284 (mtmt) REVERT: R 162 GLN cc_start: 0.6895 (mm110) cc_final: 0.6055 (mt0) REVERT: R 229 MET cc_start: 0.4356 (mmm) cc_final: 0.3824 (mmm) REVERT: R 234 MET cc_start: 0.5916 (tmm) cc_final: 0.4667 (tpp) REVERT: S 118 HIS cc_start: 0.8293 (t-90) cc_final: 0.8046 (t-90) REVERT: S 123 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8277 (mtpp) REVERT: S 173 GLU cc_start: 0.7601 (mp0) cc_final: 0.7272 (mp0) REVERT: S 188 MET cc_start: 0.8381 (ttm) cc_final: 0.7991 (ttm) outliers start: 112 outliers final: 64 residues processed: 616 average time/residue: 0.2596 time to fit residues: 260.8828 Evaluate side-chains 562 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 491 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 482 GLN Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain O residue 105 ASP Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 254 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 184 HIS Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain S residue 14 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 169 optimal weight: 5.9990 chunk 459 optimal weight: 30.0000 chunk 413 optimal weight: 8.9990 chunk 376 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 241 optimal weight: 4.9990 chunk 265 optimal weight: 0.9990 chunk 302 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 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 261 GLN A 521 GLN B 231 GLN D 415 HIS E 497 GLN M 85 GLN ** Q 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.161135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.122009 restraints weight = 44243.552| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.57 r_work: 0.2909 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39827 Z= 0.122 Angle : 0.506 8.379 53790 Z= 0.262 Chirality : 0.041 0.159 6067 Planarity : 0.004 0.050 6962 Dihedral : 5.320 91.443 5452 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.77 % Allowed : 12.75 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: 0.94 (0.12), residues: 4924 helix: 2.07 (0.10), residues: 2453 sheet: -1.61 (0.20), residues: 589 loop : -0.52 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 44 TYR 0.018 0.001 TYR J 125 PHE 0.016 0.001 PHE L 52 TRP 0.013 0.001 TRP A 567 HIS 0.005 0.001 HIS H 111 Details of bonding type rmsd covalent geometry : bond 0.00277 (39827) covalent geometry : angle 0.50553 (53790) hydrogen bonds : bond 0.03770 ( 2083) hydrogen bonds : angle 4.43900 ( 6024) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 550 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8107 (tttp) cc_final: 0.7677 (tppt) REVERT: A 286 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: A 399 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7198 (mp0) REVERT: A 466 ASP cc_start: 0.7526 (p0) cc_final: 0.7268 (m-30) REVERT: A 574 MET cc_start: 0.7161 (mtt) cc_final: 0.6907 (mtt) REVERT: B 112 GLN cc_start: 0.8509 (tt0) cc_final: 0.8228 (mt0) REVERT: B 161 LEU cc_start: 0.8785 (mp) cc_final: 0.8561 (mt) REVERT: B 195 GLU cc_start: 0.8091 (tt0) cc_final: 0.7855 (pt0) REVERT: B 356 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7283 (tp30) REVERT: B 442 ARG cc_start: 0.8095 (mpt180) cc_final: 0.7711 (mpt180) REVERT: B 459 ARG cc_start: 0.8146 (tmm160) cc_final: 0.7746 (tmt170) REVERT: B 485 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6350 (mt-10) REVERT: C 284 MET cc_start: 0.8490 (tpp) cc_final: 0.7961 (tpp) REVERT: C 529 ASP cc_start: 0.6804 (p0) cc_final: 0.6571 (p0) REVERT: C 532 CYS cc_start: 0.8750 (t) cc_final: 0.8157 (t) REVERT: D 39 TYR cc_start: 0.7206 (p90) cc_final: 0.6892 (p90) REVERT: D 435 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8195 (tmm) REVERT: E 156 GLN cc_start: 0.8486 (tt0) cc_final: 0.8107 (mt0) REVERT: E 161 GLN cc_start: 0.8440 (tp40) cc_final: 0.7482 (tm-30) REVERT: F 226 ASN cc_start: 0.7522 (p0) cc_final: 0.6751 (m-40) REVERT: H 48 LEU cc_start: 0.7796 (tp) cc_final: 0.7400 (tt) REVERT: H 58 MET cc_start: 0.7117 (ttp) cc_final: 0.6817 (tmm) REVERT: H 206 GLN cc_start: 0.8154 (mt0) cc_final: 0.7770 (mt0) REVERT: J 56 TYR cc_start: 0.5996 (OUTLIER) cc_final: 0.5594 (t80) REVERT: J 71 GLN cc_start: 0.7042 (tp40) cc_final: 0.6834 (tp40) REVERT: J 72 MET cc_start: 0.7696 (tpp) cc_final: 0.7141 (tpp) REVERT: J 133 ILE cc_start: 0.8963 (mt) cc_final: 0.8633 (mp) REVERT: J 194 ASN cc_start: 0.9342 (t0) cc_final: 0.9112 (t0) REVERT: K 185 ASN cc_start: 0.8718 (p0) cc_final: 0.8479 (p0) REVERT: N 102 MET cc_start: 0.8584 (mtm) cc_final: 0.8245 (mtm) REVERT: Q 37 ASP cc_start: 0.7519 (t0) cc_final: 0.7091 (t0) REVERT: Q 55 TRP cc_start: 0.8616 (m100) cc_final: 0.8202 (m100) REVERT: Q 109 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7132 (mm-30) REVERT: R 34 GLN cc_start: 0.7458 (tp40) cc_final: 0.6539 (tm-30) REVERT: R 37 ASP cc_start: 0.7571 (t0) cc_final: 0.6837 (t0) REVERT: R 50 GLN cc_start: 0.7876 (tm-30) cc_final: 0.6751 (tp40) REVERT: R 104 LYS cc_start: 0.7994 (tppt) cc_final: 0.7110 (mppt) REVERT: R 118 HIS cc_start: 0.8305 (t-90) cc_final: 0.7639 (t-90) REVERT: R 162 GLN cc_start: 0.6736 (mm110) cc_final: 0.5834 (mt0) REVERT: R 229 MET cc_start: 0.4307 (mmm) cc_final: 0.3810 (mmm) REVERT: R 234 MET cc_start: 0.5901 (tmm) cc_final: 0.4573 (tpp) REVERT: S 107 LEU cc_start: 0.8043 (tp) cc_final: 0.7836 (tp) REVERT: S 118 HIS cc_start: 0.8258 (t-90) cc_final: 0.7910 (t-90) REVERT: S 123 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8033 (mtpp) REVERT: S 173 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: S 188 MET cc_start: 0.8010 (ttm) cc_final: 0.7481 (ttm) outliers start: 76 outliers final: 46 residues processed: 594 average time/residue: 0.2608 time to fit residues: 253.8120 Evaluate side-chains 557 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 506 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 482 GLN Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 171 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 109 GLN Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 254 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 184 HIS Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain S residue 61 ARG Chi-restraints excluded: chain S residue 74 CYS Chi-restraints excluded: chain S residue 173 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 423 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 371 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 264 optimal weight: 9.9990 chunk 322 optimal weight: 6.9990 chunk 359 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 385 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 261 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 HIS D 54 ASN E 497 GLN ** Q 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 207 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.153372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113078 restraints weight = 45224.036| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.63 r_work: 0.2963 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 39827 Z= 0.208 Angle : 0.556 8.008 53790 Z= 0.284 Chirality : 0.044 0.178 6067 Planarity : 0.004 0.050 6962 Dihedral : 5.344 93.412 5445 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.66 % Allowed : 12.79 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: 0.85 (0.12), residues: 4924 helix: 2.03 (0.10), residues: 2449 sheet: -1.63 (0.19), residues: 620 loop : -0.59 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 142 TYR 0.018 0.002 TYR J 125 PHE 0.021 0.002 PHE C 472 TRP 0.013 0.002 TRP A 567 HIS 0.006 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00512 (39827) covalent geometry : angle 0.55596 (53790) hydrogen bonds : bond 0.03934 ( 2083) hydrogen bonds : angle 4.44758 ( 6024) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 519 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8599 (p0) REVERT: A 371 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7553 (t0) REVERT: A 399 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7279 (mp0) REVERT: A 466 ASP cc_start: 0.7639 (p0) cc_final: 0.7333 (m-30) REVERT: A 574 MET cc_start: 0.7401 (mtt) cc_final: 0.7160 (mtt) REVERT: B 112 GLN cc_start: 0.8555 (tt0) cc_final: 0.8223 (tt0) REVERT: B 195 GLU cc_start: 0.8193 (tt0) cc_final: 0.7974 (pt0) REVERT: B 442 ARG cc_start: 0.8374 (mpt180) cc_final: 0.7971 (mpt180) REVERT: B 459 ARG cc_start: 0.8150 (tmm160) cc_final: 0.7705 (tmt170) REVERT: B 485 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6487 (mt-10) REVERT: B 604 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7000 (tt) REVERT: C 142 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7567 (mtm-85) REVERT: C 171 ARG cc_start: 0.7476 (ptp-110) cc_final: 0.7148 (ptp-170) REVERT: C 284 MET cc_start: 0.8682 (tpp) cc_final: 0.8135 (tpp) REVERT: C 532 CYS cc_start: 0.8835 (t) cc_final: 0.8337 (t) REVERT: D 39 TYR cc_start: 0.7397 (p90) cc_final: 0.7131 (p90) REVERT: D 135 SER cc_start: 0.8810 (t) cc_final: 0.8379 (m) REVERT: D 174 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8486 (mm) REVERT: D 188 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8129 (mtmm) REVERT: D 435 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8271 (tmm) REVERT: E 156 GLN cc_start: 0.8492 (tt0) cc_final: 0.8121 (mt0) REVERT: F 125 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: F 226 ASN cc_start: 0.7745 (p0) cc_final: 0.7037 (m-40) REVERT: F 413 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8207 (ptmt) REVERT: H 48 LEU cc_start: 0.7991 (tp) cc_final: 0.7634 (tt) REVERT: H 58 MET cc_start: 0.7234 (ttp) cc_final: 0.6958 (tmm) REVERT: H 145 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.5592 (mp) REVERT: H 206 GLN cc_start: 0.8286 (mt0) cc_final: 0.7892 (mt0) REVERT: I 97 GLU cc_start: 0.8200 (tp30) cc_final: 0.7888 (tt0) REVERT: J 56 TYR cc_start: 0.6107 (OUTLIER) cc_final: 0.5728 (t80) REVERT: J 62 LYS cc_start: 0.7220 (mmtm) cc_final: 0.7004 (mmtm) REVERT: J 71 GLN cc_start: 0.7112 (tp40) cc_final: 0.6892 (tp40) REVERT: K 185 ASN cc_start: 0.8857 (p0) cc_final: 0.8597 (p0) REVERT: N 102 MET cc_start: 0.8813 (mtm) cc_final: 0.8459 (mtm) REVERT: Q 37 ASP cc_start: 0.7742 (t0) cc_final: 0.7286 (t0) REVERT: Q 109 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7238 (mm-30) REVERT: Q 255 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7462 (tt) REVERT: R 34 GLN cc_start: 0.7589 (tp40) cc_final: 0.6667 (tm-30) REVERT: R 37 ASP cc_start: 0.7789 (t0) cc_final: 0.7116 (t0) REVERT: R 50 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7041 (mm110) REVERT: R 104 LYS cc_start: 0.8074 (tppt) cc_final: 0.7805 (tppt) REVERT: R 118 HIS cc_start: 0.8375 (t-90) cc_final: 0.7879 (t-90) REVERT: R 162 GLN cc_start: 0.6821 (mm110) cc_final: 0.5905 (mt0) REVERT: R 229 MET cc_start: 0.4456 (mmm) cc_final: 0.3835 (mmm) REVERT: R 234 MET cc_start: 0.6013 (tmm) cc_final: 0.5122 (tpt) REVERT: S 107 LEU cc_start: 0.8108 (tp) cc_final: 0.7877 (tp) REVERT: S 118 HIS cc_start: 0.8258 (t-90) cc_final: 0.8026 (t-90) REVERT: S 123 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8069 (mtpp) REVERT: S 173 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: S 188 MET cc_start: 0.8171 (ttm) cc_final: 0.7643 (ttm) REVERT: S 201 LYS cc_start: 0.6774 (ttmt) cc_final: 0.6230 (mtmm) outliers start: 114 outliers final: 83 residues processed: 598 average time/residue: 0.2589 time to fit residues: 253.0807 Evaluate side-chains 593 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 497 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 482 GLN Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 406 ILE Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 171 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 254 VAL Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 184 HIS Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain S residue 61 ARG Chi-restraints excluded: chain S residue 74 CYS Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 173 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 176 optimal weight: 0.7980 chunk 383 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 361 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 424 optimal weight: 9.9990 chunk 430 optimal weight: 4.9990 chunk 197 optimal weight: 0.6980 chunk 486 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN E 497 GLN K 78 GLN Q 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.155370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115172 restraints weight = 45113.234| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.62 r_work: 0.3206 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 39827 Z= 0.138 Angle : 0.500 7.087 53790 Z= 0.257 Chirality : 0.041 0.213 6067 Planarity : 0.004 0.049 6962 Dihedral : 5.161 91.337 5444 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.61 % Allowed : 13.49 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 4924 helix: 2.18 (0.10), residues: 2449 sheet: -1.62 (0.20), residues: 594 loop : -0.56 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 107 TYR 0.017 0.001 TYR J 125 PHE 0.016 0.001 PHE L 52 TRP 0.013 0.001 TRP A 567 HIS 0.011 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00327 (39827) covalent geometry : angle 0.50045 (53790) hydrogen bonds : bond 0.03651 ( 2083) hydrogen bonds : angle 4.32099 ( 6024) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 512 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.7843 (mtt180) cc_final: 0.7345 (mtt180) REVERT: A 399 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7247 (mp0) REVERT: A 466 ASP cc_start: 0.7658 (p0) cc_final: 0.7423 (m-30) REVERT: B 112 GLN cc_start: 0.8585 (tt0) cc_final: 0.8298 (mt0) REVERT: B 161 LEU cc_start: 0.8753 (mp) cc_final: 0.8492 (mt) REVERT: B 275 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8876 (m) REVERT: B 283 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: B 356 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7581 (tp30) REVERT: B 442 ARG cc_start: 0.8334 (mpt180) cc_final: 0.7905 (mpt180) REVERT: B 459 ARG cc_start: 0.8173 (tmm160) cc_final: 0.7727 (tmt170) REVERT: B 485 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6681 (mt-10) REVERT: B 508 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7353 (t) REVERT: B 604 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7336 (tt) REVERT: C 68 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8640 (mt-10) REVERT: C 279 GLU cc_start: 0.8577 (mm-30) cc_final: 0.7908 (mt-10) REVERT: C 285 SER cc_start: 0.8929 (t) cc_final: 0.8629 (p) REVERT: C 318 MET cc_start: 0.9034 (mmm) cc_final: 0.8788 (mmm) REVERT: C 529 ASP cc_start: 0.7158 (p0) cc_final: 0.6834 (p0) REVERT: C 532 CYS cc_start: 0.8918 (t) cc_final: 0.8488 (t) REVERT: D 39 TYR cc_start: 0.7455 (p90) cc_final: 0.7234 (p90) REVERT: D 135 SER cc_start: 0.8714 (t) cc_final: 0.8392 (m) REVERT: D 188 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8088 (mtmm) REVERT: E 156 GLN cc_start: 0.8570 (tt0) cc_final: 0.8196 (mt0) REVERT: E 161 GLN cc_start: 0.8486 (tp40) cc_final: 0.7687 (tm-30) REVERT: F 125 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: F 226 ASN cc_start: 0.7713 (p0) cc_final: 0.7041 (m-40) REVERT: H 48 LEU cc_start: 0.8214 (tp) cc_final: 0.7826 (tt) REVERT: H 58 MET cc_start: 0.7269 (ttp) cc_final: 0.7044 (tmm) REVERT: H 97 LYS cc_start: 0.7851 (ttmt) cc_final: 0.7637 (ttpt) REVERT: H 206 GLN cc_start: 0.8349 (mt0) cc_final: 0.7960 (mt0) REVERT: I 97 GLU cc_start: 0.8354 (tp30) cc_final: 0.8044 (tt0) REVERT: J 56 TYR cc_start: 0.6210 (OUTLIER) cc_final: 0.5782 (t80) REVERT: J 62 LYS cc_start: 0.7468 (mmtm) cc_final: 0.7215 (mmtm) REVERT: J 71 GLN cc_start: 0.7059 (tp40) cc_final: 0.6838 (tp40) REVERT: K 185 ASN cc_start: 0.8874 (p0) cc_final: 0.8603 (p0) REVERT: N 102 MET cc_start: 0.8795 (mtm) cc_final: 0.8516 (mtm) REVERT: Q 37 ASP cc_start: 0.7797 (t0) cc_final: 0.7376 (t0) REVERT: Q 109 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: Q 225 LEU cc_start: 0.8096 (mp) cc_final: 0.7846 (mp) REVERT: Q 255 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7365 (tt) REVERT: R 34 GLN cc_start: 0.7706 (tp40) cc_final: 0.6812 (tm-30) REVERT: R 37 ASP cc_start: 0.7889 (t0) cc_final: 0.7365 (t0) REVERT: R 50 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7131 (mm-40) REVERT: R 118 HIS cc_start: 0.8463 (t-90) cc_final: 0.7890 (t-90) REVERT: R 138 ASP cc_start: 0.8279 (m-30) cc_final: 0.8015 (m-30) REVERT: R 229 MET cc_start: 0.4507 (mmm) cc_final: 0.3863 (mmm) REVERT: R 234 MET cc_start: 0.6046 (tmm) cc_final: 0.5172 (tpt) REVERT: S 118 HIS cc_start: 0.8274 (t-90) cc_final: 0.7981 (t-90) REVERT: S 123 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8079 (mtpp) REVERT: S 165 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: S 173 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: S 188 MET cc_start: 0.8283 (ttm) cc_final: 0.7776 (ttm) outliers start: 112 outliers final: 73 residues processed: 588 average time/residue: 0.2396 time to fit residues: 231.7460 Evaluate side-chains 580 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 495 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 482 GLN Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 171 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 254 VAL Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 184 HIS Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 61 ARG Chi-restraints excluded: chain S residue 74 CYS Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 165 GLN Chi-restraints excluded: chain S residue 173 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 487 optimal weight: 20.0000 chunk 371 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 274 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 476 optimal weight: 0.9990 chunk 206 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 ASN D 54 ASN E 497 GLN Q 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.151836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111280 restraints weight = 45506.043| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.64 r_work: 0.3164 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 39827 Z= 0.279 Angle : 0.596 7.708 53790 Z= 0.304 Chirality : 0.045 0.222 6067 Planarity : 0.005 0.048 6962 Dihedral : 5.396 94.495 5442 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.22 % Allowed : 13.87 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: 0.73 (0.12), residues: 4924 helix: 1.94 (0.10), residues: 2449 sheet: -1.64 (0.19), residues: 649 loop : -0.68 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 459 TYR 0.021 0.002 TYR J 125 PHE 0.024 0.002 PHE C 472 TRP 0.013 0.002 TRP S 55 HIS 0.008 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00691 (39827) covalent geometry : angle 0.59593 (53790) hydrogen bonds : bond 0.04062 ( 2083) hydrogen bonds : angle 4.48404 ( 6024) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 499 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7369 (mp0) REVERT: A 458 MET cc_start: 0.8809 (mtt) cc_final: 0.8562 (mtt) REVERT: A 466 ASP cc_start: 0.7697 (p0) cc_final: 0.7433 (m-30) REVERT: B 112 GLN cc_start: 0.8556 (tt0) cc_final: 0.8191 (tt0) REVERT: B 161 LEU cc_start: 0.8908 (mp) cc_final: 0.8653 (mt) REVERT: B 283 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: B 442 ARG cc_start: 0.8552 (mpt180) cc_final: 0.8220 (mpt180) REVERT: B 485 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6699 (mt-10) REVERT: B 604 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7492 (tt) REVERT: C 68 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8608 (mt-10) REVERT: C 171 ARG cc_start: 0.7508 (ptp-110) cc_final: 0.7250 (ptp-170) REVERT: C 279 GLU cc_start: 0.8625 (mm-30) cc_final: 0.7968 (mt-10) REVERT: C 284 MET cc_start: 0.8777 (tpp) cc_final: 0.8185 (tpt) REVERT: C 285 SER cc_start: 0.8926 (t) cc_final: 0.8589 (p) REVERT: C 532 CYS cc_start: 0.8972 (t) cc_final: 0.8641 (t) REVERT: D 174 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8695 (mm) REVERT: D 188 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8241 (mtmm) REVERT: E 156 GLN cc_start: 0.8564 (tt0) cc_final: 0.8186 (mt0) REVERT: F 45 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8451 (mp) REVERT: F 125 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: F 168 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: F 226 ASN cc_start: 0.7870 (p0) cc_final: 0.7195 (m-40) REVERT: F 359 ASP cc_start: 0.8346 (m-30) cc_final: 0.8107 (m-30) REVERT: H 48 LEU cc_start: 0.8220 (tp) cc_final: 0.7879 (tt) REVERT: H 58 MET cc_start: 0.7376 (ttp) cc_final: 0.7139 (tmm) REVERT: H 206 GLN cc_start: 0.8391 (mt0) cc_final: 0.7998 (mt0) REVERT: J 56 TYR cc_start: 0.6306 (OUTLIER) cc_final: 0.5880 (t80) REVERT: J 71 GLN cc_start: 0.7138 (tp40) cc_final: 0.6936 (tp40) REVERT: K 185 ASN cc_start: 0.9046 (p0) cc_final: 0.8716 (p0) REVERT: L 27 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6170 (pt0) REVERT: N 102 MET cc_start: 0.8876 (mtm) cc_final: 0.8573 (mtm) REVERT: Q 37 ASP cc_start: 0.7987 (t0) cc_final: 0.7483 (t0) REVERT: Q 109 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7462 (mm-30) REVERT: Q 225 LEU cc_start: 0.8134 (mp) cc_final: 0.7858 (mp) REVERT: Q 255 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7350 (tt) REVERT: R 34 GLN cc_start: 0.7851 (tp40) cc_final: 0.6857 (tm-30) REVERT: R 37 ASP cc_start: 0.7979 (t0) cc_final: 0.7452 (t0) REVERT: R 50 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7234 (mm-40) REVERT: R 118 HIS cc_start: 0.8492 (t-90) cc_final: 0.8099 (t-90) REVERT: R 229 MET cc_start: 0.4418 (mmm) cc_final: 0.3835 (mmm) REVERT: R 234 MET cc_start: 0.6190 (tmm) cc_final: 0.5279 (tpt) REVERT: S 118 HIS cc_start: 0.8284 (t-90) cc_final: 0.8074 (t-90) REVERT: S 123 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8245 (mmtt) REVERT: S 165 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: S 173 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: S 188 MET cc_start: 0.8349 (ttm) cc_final: 0.7917 (ttm) outliers start: 138 outliers final: 98 residues processed: 597 average time/residue: 0.2595 time to fit residues: 254.6107 Evaluate side-chains 597 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 485 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 482 GLN Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 171 GLN Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain O residue 89 GLN Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 254 VAL Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 184 HIS Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 61 ARG Chi-restraints excluded: chain S residue 74 CYS Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 165 GLN Chi-restraints excluded: chain S residue 173 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 126 optimal weight: 1.9990 chunk 449 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 303 optimal weight: 0.9980 chunk 360 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 327 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 389 optimal weight: 20.0000 chunk 158 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 HIS A 521 GLN D 54 ASN E 497 GLN Q 134 ASN R 17 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120556 restraints weight = 44331.356| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.56 r_work: 0.2867 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 39827 Z= 0.141 Angle : 0.505 7.524 53790 Z= 0.259 Chirality : 0.042 0.206 6067 Planarity : 0.004 0.046 6962 Dihedral : 5.185 91.800 5442 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.71 % Allowed : 14.45 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: 0.93 (0.12), residues: 4924 helix: 2.14 (0.10), residues: 2452 sheet: -1.71 (0.20), residues: 593 loop : -0.61 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 173 TYR 0.012 0.001 TYR A 535 PHE 0.017 0.001 PHE L 52 TRP 0.012 0.001 TRP Q 122 HIS 0.004 0.001 HIS M 111 Details of bonding type rmsd covalent geometry : bond 0.00338 (39827) covalent geometry : angle 0.50469 (53790) hydrogen bonds : bond 0.03632 ( 2083) hydrogen bonds : angle 4.32807 ( 6024) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 514 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8379 (mt-10) REVERT: A 171 ARG cc_start: 0.7901 (mtt180) cc_final: 0.7428 (mtt180) REVERT: A 399 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7387 (mp0) REVERT: A 466 ASP cc_start: 0.7610 (p0) cc_final: 0.7342 (m-30) REVERT: B 112 GLN cc_start: 0.8484 (tt0) cc_final: 0.8202 (mt0) REVERT: B 275 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8814 (m) REVERT: B 283 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: B 356 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7376 (tp30) REVERT: B 442 ARG cc_start: 0.8261 (mpt180) cc_final: 0.7789 (mpt180) REVERT: B 485 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6457 (mt-10) REVERT: B 508 THR cc_start: 0.7404 (OUTLIER) cc_final: 0.7062 (t) REVERT: B 604 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7031 (tt) REVERT: B 612 PHE cc_start: 0.7626 (m-10) cc_final: 0.7379 (m-80) REVERT: C 68 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8553 (mt-10) REVERT: C 279 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7627 (mt-10) REVERT: C 284 MET cc_start: 0.8636 (tpp) cc_final: 0.8341 (tpt) REVERT: C 285 SER cc_start: 0.8817 (t) cc_final: 0.8525 (p) REVERT: C 318 MET cc_start: 0.8969 (mmm) cc_final: 0.8747 (mmm) REVERT: D 135 SER cc_start: 0.8756 (m) cc_final: 0.8455 (m) REVERT: D 174 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8438 (mm) REVERT: D 188 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8076 (mtmm) REVERT: E 161 GLN cc_start: 0.8471 (tp40) cc_final: 0.7513 (tm-30) REVERT: F 125 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: F 168 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: F 226 ASN cc_start: 0.7608 (p0) cc_final: 0.6904 (m-40) REVERT: F 359 ASP cc_start: 0.8332 (m-30) cc_final: 0.8082 (m-30) REVERT: H 48 LEU cc_start: 0.7925 (tp) cc_final: 0.7624 (tt) REVERT: H 58 MET cc_start: 0.7246 (ttp) cc_final: 0.7028 (tmm) REVERT: H 206 GLN cc_start: 0.8268 (mt0) cc_final: 0.7872 (mt0) REVERT: J 56 TYR cc_start: 0.6174 (OUTLIER) cc_final: 0.5833 (t80) REVERT: J 71 GLN cc_start: 0.6964 (tp40) cc_final: 0.6724 (tp40) REVERT: K 103 SER cc_start: 0.8367 (t) cc_final: 0.7916 (m) REVERT: K 185 ASN cc_start: 0.8765 (p0) cc_final: 0.8528 (p0) REVERT: N 102 MET cc_start: 0.8694 (mtm) cc_final: 0.8373 (mtm) REVERT: Q 33 MET cc_start: 0.8784 (tpt) cc_final: 0.8557 (tpp) REVERT: Q 37 ASP cc_start: 0.7678 (t0) cc_final: 0.7135 (t0) REVERT: Q 109 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: R 34 GLN cc_start: 0.7569 (tp40) cc_final: 0.6599 (tm-30) REVERT: R 35 THR cc_start: 0.8069 (m) cc_final: 0.7353 (p) REVERT: R 37 ASP cc_start: 0.7700 (t0) cc_final: 0.7156 (t0) REVERT: R 50 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7021 (mm-40) REVERT: R 118 HIS cc_start: 0.8377 (t-90) cc_final: 0.7783 (t-90) REVERT: R 229 MET cc_start: 0.4443 (mmm) cc_final: 0.3856 (mmm) REVERT: R 234 MET cc_start: 0.6149 (tmm) cc_final: 0.5223 (tpt) REVERT: S 115 MET cc_start: 0.8136 (mtt) cc_final: 0.7850 (mtt) REVERT: S 118 HIS cc_start: 0.8252 (t-90) cc_final: 0.8020 (t-90) REVERT: S 123 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8001 (mtpp) REVERT: S 165 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: S 173 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: S 188 MET cc_start: 0.8048 (ttm) cc_final: 0.7606 (ttm) outliers start: 116 outliers final: 82 residues processed: 592 average time/residue: 0.2498 time to fit residues: 244.5442 Evaluate side-chains 588 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 492 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 482 GLN Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 171 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 272 ILE Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain Q residue 74 CYS Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 254 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 184 HIS Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 74 CYS Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 165 GLN Chi-restraints excluded: chain S residue 173 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 425 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 451 optimal weight: 7.9990 chunk 440 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 396 optimal weight: 5.9990 chunk 259 optimal weight: 0.0970 chunk 437 optimal weight: 5.9990 chunk 418 optimal weight: 0.9980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN E 497 GLN M 111 HIS Q 134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.154090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113841 restraints weight = 45133.170| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.63 r_work: 0.3194 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 39827 Z= 0.185 Angle : 0.536 11.195 53790 Z= 0.273 Chirality : 0.043 0.193 6067 Planarity : 0.004 0.048 6962 Dihedral : 5.224 93.455 5442 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.80 % Allowed : 14.68 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: 0.91 (0.12), residues: 4924 helix: 2.11 (0.10), residues: 2452 sheet: -1.65 (0.19), residues: 643 loop : -0.58 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 142 TYR 0.015 0.001 TYR F 389 PHE 0.019 0.001 PHE C 472 TRP 0.011 0.001 TRP A 567 HIS 0.005 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00454 (39827) covalent geometry : angle 0.53643 (53790) hydrogen bonds : bond 0.03743 ( 2083) hydrogen bonds : angle 4.35317 ( 6024) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 499 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8541 (mt-10) REVERT: A 171 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7520 (mtt180) REVERT: A 399 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7394 (mp0) REVERT: A 458 MET cc_start: 0.8790 (mtt) cc_final: 0.8557 (mtt) REVERT: A 466 ASP cc_start: 0.7750 (p0) cc_final: 0.7464 (m-30) REVERT: B 112 GLN cc_start: 0.8557 (tt0) cc_final: 0.8284 (mt0) REVERT: B 275 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8917 (m) REVERT: B 283 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: B 356 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7631 (tp30) REVERT: B 442 ARG cc_start: 0.8492 (mpt180) cc_final: 0.8049 (mpt180) REVERT: B 485 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6750 (mt-10) REVERT: B 604 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7485 (tt) REVERT: B 612 PHE cc_start: 0.7933 (m-10) cc_final: 0.7630 (m-80) REVERT: C 68 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8648 (mt-10) REVERT: C 95 MET cc_start: 0.9261 (mmp) cc_final: 0.8657 (mmp) REVERT: C 279 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7864 (mt-10) REVERT: C 284 MET cc_start: 0.8783 (tpp) cc_final: 0.8460 (tpt) REVERT: C 285 SER cc_start: 0.8930 (t) cc_final: 0.8626 (p) REVERT: C 318 MET cc_start: 0.9040 (mmm) cc_final: 0.8830 (mmm) REVERT: D 135 SER cc_start: 0.8818 (m) cc_final: 0.8563 (m) REVERT: D 174 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8653 (mm) REVERT: D 188 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8170 (mtmm) REVERT: E 161 GLN cc_start: 0.8526 (tp40) cc_final: 0.7681 (tm-30) REVERT: F 45 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8400 (mp) REVERT: F 125 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8445 (tt0) REVERT: F 168 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8240 (mt-10) REVERT: F 226 ASN cc_start: 0.7840 (p0) cc_final: 0.7185 (m-40) REVERT: F 359 ASP cc_start: 0.8338 (m-30) cc_final: 0.8123 (m-30) REVERT: H 48 LEU cc_start: 0.8231 (tp) cc_final: 0.7892 (tt) REVERT: H 206 GLN cc_start: 0.8389 (mt0) cc_final: 0.7994 (mt0) REVERT: J 54 MET cc_start: 0.5226 (mmm) cc_final: 0.4051 (tpp) REVERT: J 56 TYR cc_start: 0.6240 (OUTLIER) cc_final: 0.5835 (t80) REVERT: J 71 GLN cc_start: 0.7108 (tp40) cc_final: 0.6875 (tp40) REVERT: K 103 SER cc_start: 0.8588 (t) cc_final: 0.8166 (m) REVERT: K 185 ASN cc_start: 0.8926 (p0) cc_final: 0.8675 (p0) REVERT: N 102 MET cc_start: 0.8885 (mtm) cc_final: 0.8584 (mtm) REVERT: Q 37 ASP cc_start: 0.7897 (t0) cc_final: 0.7390 (t0) REVERT: Q 109 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: R 34 GLN cc_start: 0.7811 (tp40) cc_final: 0.6846 (tm-30) REVERT: R 35 THR cc_start: 0.8127 (m) cc_final: 0.7461 (p) REVERT: R 37 ASP cc_start: 0.7935 (t0) cc_final: 0.7418 (t0) REVERT: R 50 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7236 (mm-40) REVERT: R 118 HIS cc_start: 0.8497 (t-90) cc_final: 0.8066 (t-90) REVERT: R 229 MET cc_start: 0.4432 (mmm) cc_final: 0.3852 (mmm) REVERT: R 234 MET cc_start: 0.6216 (tmm) cc_final: 0.5331 (tpt) REVERT: S 115 MET cc_start: 0.8394 (mtt) cc_final: 0.8089 (mtt) REVERT: S 123 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8079 (mtpp) REVERT: S 165 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: S 173 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: S 188 MET cc_start: 0.8289 (ttm) cc_final: 0.7869 (ttm) outliers start: 120 outliers final: 90 residues processed: 581 average time/residue: 0.2515 time to fit residues: 241.0994 Evaluate side-chains 591 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 487 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 482 GLN Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 171 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 254 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 184 HIS Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 74 CYS Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 165 GLN Chi-restraints excluded: chain S residue 173 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 133 optimal weight: 7.9990 chunk 301 optimal weight: 0.7980 chunk 312 optimal weight: 1.9990 chunk 360 optimal weight: 5.9990 chunk 252 optimal weight: 0.4980 chunk 319 optimal weight: 2.9990 chunk 450 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 356 optimal weight: 2.9990 chunk 85 optimal weight: 0.0980 chunk 112 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN Q 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.160004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120952 restraints weight = 44416.522| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.55 r_work: 0.2875 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39827 Z= 0.141 Angle : 0.511 10.030 53790 Z= 0.261 Chirality : 0.042 0.297 6067 Planarity : 0.004 0.046 6962 Dihedral : 5.045 92.234 5441 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.54 % Allowed : 15.01 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.12), residues: 4924 helix: 2.20 (0.10), residues: 2455 sheet: -1.68 (0.20), residues: 586 loop : -0.56 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 173 TYR 0.012 0.001 TYR F 389 PHE 0.015 0.001 PHE L 52 TRP 0.011 0.001 TRP Q 122 HIS 0.005 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00335 (39827) covalent geometry : angle 0.51088 (53790) hydrogen bonds : bond 0.03581 ( 2083) hydrogen bonds : angle 4.29065 ( 6024) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 517 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: A 399 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7390 (mp0) REVERT: A 466 ASP cc_start: 0.7556 (p0) cc_final: 0.7299 (m-30) REVERT: A 574 MET cc_start: 0.7096 (mmm) cc_final: 0.6712 (mtt) REVERT: B 112 GLN cc_start: 0.8494 (tt0) cc_final: 0.8190 (mt0) REVERT: B 275 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8815 (m) REVERT: B 283 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: B 356 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7348 (tp30) REVERT: B 442 ARG cc_start: 0.8267 (mpt180) cc_final: 0.7797 (mpt180) REVERT: B 485 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6449 (mt-10) REVERT: B 604 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7029 (tt) REVERT: C 68 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8565 (mt-10) REVERT: C 279 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7559 (mt-10) REVERT: C 284 MET cc_start: 0.8614 (tpp) cc_final: 0.8320 (tpt) REVERT: C 285 SER cc_start: 0.8828 (t) cc_final: 0.8552 (p) REVERT: C 318 MET cc_start: 0.8959 (mmm) cc_final: 0.8743 (mmm) REVERT: D 135 SER cc_start: 0.8772 (m) cc_final: 0.8508 (m) REVERT: D 154 MET cc_start: 0.8664 (mmm) cc_final: 0.7762 (ttt) REVERT: D 188 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8060 (mtmm) REVERT: E 161 GLN cc_start: 0.8457 (tp40) cc_final: 0.7477 (tm-30) REVERT: E 255 ASP cc_start: 0.8334 (t70) cc_final: 0.8109 (t70) REVERT: F 45 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8213 (mp) REVERT: F 125 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: F 226 ASN cc_start: 0.7596 (p0) cc_final: 0.6888 (m-40) REVERT: H 48 LEU cc_start: 0.7873 (tp) cc_final: 0.7582 (tt) REVERT: H 206 GLN cc_start: 0.8199 (mt0) cc_final: 0.7798 (mt0) REVERT: J 54 MET cc_start: 0.5464 (mmm) cc_final: 0.4100 (tpp) REVERT: J 56 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.5784 (t80) REVERT: J 71 GLN cc_start: 0.6930 (tp40) cc_final: 0.6628 (tp40) REVERT: J 183 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8040 (mm) REVERT: K 103 SER cc_start: 0.8348 (t) cc_final: 0.7895 (m) REVERT: K 185 ASN cc_start: 0.8718 (p0) cc_final: 0.8439 (p0) REVERT: Q 37 ASP cc_start: 0.7663 (t0) cc_final: 0.7170 (t0) REVERT: Q 109 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7235 (mm-30) REVERT: R 34 GLN cc_start: 0.7541 (tp40) cc_final: 0.6582 (tm-30) REVERT: R 35 THR cc_start: 0.7952 (m) cc_final: 0.7300 (p) REVERT: R 37 ASP cc_start: 0.7689 (t0) cc_final: 0.7023 (t70) REVERT: R 50 GLN cc_start: 0.7908 (tm-30) cc_final: 0.6953 (mm-40) REVERT: R 118 HIS cc_start: 0.8385 (t-90) cc_final: 0.7832 (t-90) REVERT: R 229 MET cc_start: 0.4336 (mmm) cc_final: 0.3807 (mmm) REVERT: R 234 MET cc_start: 0.6181 (tmm) cc_final: 0.5281 (tpt) REVERT: S 55 TRP cc_start: 0.8866 (m100) cc_final: 0.8558 (m100) REVERT: S 115 MET cc_start: 0.8142 (mtt) cc_final: 0.7890 (mtt) REVERT: S 123 LYS cc_start: 0.8480 (mmtt) cc_final: 0.7944 (mtpp) REVERT: S 165 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: S 173 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: S 188 MET cc_start: 0.7978 (ttm) cc_final: 0.7508 (ttm) outliers start: 109 outliers final: 86 residues processed: 590 average time/residue: 0.2566 time to fit residues: 248.3809 Evaluate side-chains 598 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 499 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 482 GLN Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 171 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 84 MET Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 254 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 184 HIS Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain S residue 74 CYS Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 165 GLN Chi-restraints excluded: chain S residue 173 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 220 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 325 optimal weight: 7.9990 chunk 355 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 284 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 ASN D 54 ASN E 497 GLN Q 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.158817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119689 restraints weight = 44446.853| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.58 r_work: 0.3214 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 39827 Z= 0.182 Angle : 0.542 12.874 53790 Z= 0.274 Chirality : 0.043 0.249 6067 Planarity : 0.004 0.049 6962 Dihedral : 5.052 93.319 5439 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.47 % Allowed : 15.22 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: 0.94 (0.12), residues: 4924 helix: 2.14 (0.10), residues: 2456 sheet: -1.72 (0.19), residues: 628 loop : -0.56 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 142 TYR 0.015 0.001 TYR F 389 PHE 0.018 0.001 PHE C 472 TRP 0.010 0.001 TRP B 567 HIS 0.005 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00445 (39827) covalent geometry : angle 0.54168 (53790) hydrogen bonds : bond 0.03690 ( 2083) hydrogen bonds : angle 4.33350 ( 6024) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9848 Ramachandran restraints generated. 4924 Oldfield, 0 Emsley, 4924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 508 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8358 (mt-10) REVERT: A 171 ARG cc_start: 0.7895 (mtt180) cc_final: 0.7414 (mtt180) REVERT: A 399 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7444 (mp0) REVERT: A 458 MET cc_start: 0.8688 (mtt) cc_final: 0.8453 (mtt) REVERT: A 466 ASP cc_start: 0.7602 (p0) cc_final: 0.7358 (m-30) REVERT: B 112 GLN cc_start: 0.8458 (tt0) cc_final: 0.8176 (mt0) REVERT: B 275 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8825 (m) REVERT: B 283 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: B 356 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7344 (tp30) REVERT: B 442 ARG cc_start: 0.8362 (mpt180) cc_final: 0.7890 (mpt180) REVERT: B 485 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6461 (mt-10) REVERT: B 604 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7191 (tt) REVERT: C 68 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8561 (mt-10) REVERT: C 95 MET cc_start: 0.9151 (mmp) cc_final: 0.8502 (mmp) REVERT: C 279 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7647 (mt-10) REVERT: C 284 MET cc_start: 0.8672 (tpp) cc_final: 0.8382 (tpt) REVERT: C 285 SER cc_start: 0.8831 (t) cc_final: 0.8531 (p) REVERT: C 318 MET cc_start: 0.9000 (mmm) cc_final: 0.8783 (mmm) REVERT: C 399 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7788 (mm-30) REVERT: D 135 SER cc_start: 0.8859 (m) cc_final: 0.8603 (m) REVERT: D 174 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8507 (mm) REVERT: D 188 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8113 (mtmm) REVERT: E 161 GLN cc_start: 0.8431 (tp40) cc_final: 0.7475 (tm-30) REVERT: F 45 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8314 (mp) REVERT: F 125 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: F 226 ASN cc_start: 0.7635 (p0) cc_final: 0.6971 (m-40) REVERT: F 359 ASP cc_start: 0.8343 (m-30) cc_final: 0.8112 (m-30) REVERT: H 48 LEU cc_start: 0.7929 (tp) cc_final: 0.7626 (tt) REVERT: H 206 GLN cc_start: 0.8258 (mt0) cc_final: 0.7859 (mt0) REVERT: J 54 MET cc_start: 0.5462 (mmm) cc_final: 0.4047 (tpp) REVERT: J 56 TYR cc_start: 0.6128 (OUTLIER) cc_final: 0.5803 (t80) REVERT: J 183 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8134 (mm) REVERT: K 103 SER cc_start: 0.8411 (t) cc_final: 0.7979 (m) REVERT: K 185 ASN cc_start: 0.8783 (p0) cc_final: 0.8503 (p0) REVERT: Q 37 ASP cc_start: 0.7822 (t0) cc_final: 0.7333 (t0) REVERT: Q 109 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7247 (mm-30) REVERT: R 34 GLN cc_start: 0.7630 (tp40) cc_final: 0.6661 (tm-30) REVERT: R 35 THR cc_start: 0.7995 (m) cc_final: 0.7339 (p) REVERT: R 37 ASP cc_start: 0.7802 (t0) cc_final: 0.7153 (t70) REVERT: R 50 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7072 (mm110) REVERT: R 118 HIS cc_start: 0.8409 (t-90) cc_final: 0.7951 (t-90) REVERT: R 234 MET cc_start: 0.6246 (tmm) cc_final: 0.5354 (tpt) REVERT: S 55 TRP cc_start: 0.8895 (m100) cc_final: 0.8617 (m100) REVERT: S 115 MET cc_start: 0.8230 (mtt) cc_final: 0.7957 (mtt) REVERT: S 118 HIS cc_start: 0.8070 (t-90) cc_final: 0.7614 (t-90) REVERT: S 123 LYS cc_start: 0.8503 (mmtt) cc_final: 0.7976 (mtpp) REVERT: S 165 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: S 173 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: S 188 MET cc_start: 0.8047 (ttm) cc_final: 0.7584 (ttm) outliers start: 106 outliers final: 88 residues processed: 581 average time/residue: 0.2510 time to fit residues: 240.2016 Evaluate side-chains 596 residues out of total 4305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 494 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 596 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 360 ASP Chi-restraints excluded: chain D residue 482 GLN Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 171 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 435 MET Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain J residue 56 TYR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 193 SER Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 84 MET Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 254 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 23 VAL Chi-restraints excluded: chain R residue 156 THR Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 184 HIS Chi-restraints excluded: chain R residue 188 MET Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 74 CYS Chi-restraints excluded: chain S residue 106 ASP Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 165 GLN Chi-restraints excluded: chain S residue 173 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 455 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 375 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 423 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 329 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN E 497 GLN Q 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.159246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120149 restraints weight = 44552.115| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.58 r_work: 0.2859 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 39827 Z= 0.164 Angle : 0.532 14.013 53790 Z= 0.268 Chirality : 0.042 0.201 6067 Planarity : 0.004 0.049 6962 Dihedral : 5.002 93.004 5439 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.50 % Allowed : 15.15 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: 0.97 (0.12), residues: 4924 helix: 2.16 (0.10), residues: 2454 sheet: -1.70 (0.19), residues: 628 loop : -0.54 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 107 TYR 0.014 0.001 TYR F 389 PHE 0.019 0.001 PHE B 612 TRP 0.011 0.001 TRP B 567 HIS 0.005 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00398 (39827) covalent geometry : angle 0.53196 (53790) hydrogen bonds : bond 0.03634 ( 2083) hydrogen bonds : angle 4.31662 ( 6024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12639.77 seconds wall clock time: 216 minutes 17.05 seconds (12977.05 seconds total)