Starting phenix.real_space_refine on Tue Apr 7 15:22:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21ak_67448/04_2026/21ak_67448_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/21ak_67448/04_2026/21ak_67448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21ak_67448/04_2026/21ak_67448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21ak_67448/04_2026/21ak_67448.map" model { file = "/net/cci-nas-00/data/ceres_data/21ak_67448/04_2026/21ak_67448_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21ak_67448/04_2026/21ak_67448_neut.cif" } resolution = 3.23 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= 0.004 sd= 0.040 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 18337 2.51 5 N 5015 2.21 5 O 5132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28592 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2080 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 257} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2091 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 258} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2082 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 2077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2077 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 258} Chain breaks: 3 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2078 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 256} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2091 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 258} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2666 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 16, 'TRANS': 308} Chain breaks: 1 Chain: "H" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2681 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Chain: "I" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2693 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 16, 'TRANS': 312} Chain breaks: 1 Chain: "J" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2685 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 16, 'TRANS': 311} Chain breaks: 2 Chain: "K" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2681 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Chain: "L" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2687 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Time building chain proxies: 6.55, per 1000 atoms: 0.23 Number of scatterers: 28592 At special positions: 0 Unit cell: (171.6, 154.7, 113.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 5132 8.00 N 5015 7.00 C 18337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.2 seconds 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6708 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 43 sheets defined 44.5% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 8 through 22 Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.958A pdb=" N LEU A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN A 123 " --> pdb=" O TRP A 119 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 177 removed outlier: 4.844A pdb=" N GLU A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLN A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 213 through 225 removed outlier: 3.609A pdb=" N LEU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 297 removed outlier: 4.362A pdb=" N LEU A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 22 Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 64 through 75 Processing helix chain 'B' and resid 89 through 96 removed outlier: 3.599A pdb=" N LEU B 93 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.642A pdb=" N TRP B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 182 removed outlier: 3.709A pdb=" N GLN B 175 " --> pdb=" O GLN B 171 " (cutoff:3.500A) Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 213 through 225 removed outlier: 3.654A pdb=" N LEU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 297 removed outlier: 4.291A pdb=" N LEU B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 44 through 52 Processing helix chain 'C' and resid 64 through 75 Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 115 through 123 removed outlier: 4.011A pdb=" N LEU C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN C 123 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 182 removed outlier: 4.217A pdb=" N GLN C 175 " --> pdb=" O GLN C 171 " (cutoff:3.500A) Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 213 through 224 Processing helix chain 'C' and resid 289 through 297 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 44 through 53 removed outlier: 3.801A pdb=" N LEU D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 75 Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 115 through 121 Processing helix chain 'D' and resid 157 through 183 removed outlier: 4.224A pdb=" N GLN D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 213 through 224 Processing helix chain 'D' and resid 288 through 297 removed outlier: 3.813A pdb=" N LEU D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 23 Processing helix chain 'E' and resid 44 through 53 removed outlier: 4.207A pdb=" N LEU E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 89 through 94 Processing helix chain 'E' and resid 115 through 123 removed outlier: 4.090A pdb=" N TRP E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN E 123 " --> pdb=" O TRP E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 183 removed outlier: 4.358A pdb=" N GLN E 175 " --> pdb=" O GLN E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 213 through 225 removed outlier: 3.552A pdb=" N LEU E 217 " --> pdb=" O PRO E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 297 removed outlier: 4.084A pdb=" N LEU E 292 " --> pdb=" O GLN E 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 22 Processing helix chain 'F' and resid 44 through 53 Processing helix chain 'F' and resid 64 through 75 Processing helix chain 'F' and resid 89 through 94 Processing helix chain 'F' and resid 115 through 124 removed outlier: 3.878A pdb=" N ASN F 123 " --> pdb=" O TRP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 183 removed outlier: 3.964A pdb=" N GLN F 175 " --> pdb=" O GLN F 171 " (cutoff:3.500A) Proline residue: F 178 - end of helix Processing helix chain 'F' and resid 213 through 224 removed outlier: 3.728A pdb=" N VAL F 224 " --> pdb=" O MET F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 297 Processing helix chain 'G' and resid 325 through 337 removed outlier: 3.821A pdb=" N ARG G 337 " --> pdb=" O GLU G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 358 removed outlier: 4.566A pdb=" N ASN G 358 " --> pdb=" O SER G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 383 Processing helix chain 'G' and resid 394 through 401 removed outlier: 3.762A pdb=" N TYR G 398 " --> pdb=" O THR G 394 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR G 399 " --> pdb=" O PRO G 395 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG G 400 " --> pdb=" O ILE G 396 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN G 401 " --> pdb=" O GLU G 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 394 through 401' Processing helix chain 'G' and resid 401 through 423 removed outlier: 4.669A pdb=" N GLU G 412 " --> pdb=" O LEU G 408 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN G 413 " --> pdb=" O ASP G 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 482 removed outlier: 3.612A pdb=" N GLU G 479 " --> pdb=" O TRP G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 509 through 522 Processing helix chain 'G' and resid 528 through 531 Processing helix chain 'G' and resid 540 through 553 Processing helix chain 'G' and resid 574 through 588 removed outlier: 3.656A pdb=" N LYS G 587 " --> pdb=" O ALA G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 590 through 594 removed outlier: 3.915A pdb=" N HIS G 593 " --> pdb=" O LEU G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 623 through 631 Processing helix chain 'G' and resid 637 through 652 removed outlier: 3.850A pdb=" N THR G 641 " --> pdb=" O ASP G 637 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 338 removed outlier: 3.727A pdb=" N ARG H 337 " --> pdb=" O GLU H 333 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU H 338 " --> pdb=" O ARG H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 357 removed outlier: 3.646A pdb=" N LEU H 357 " --> pdb=" O SER H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 373 through 383 Processing helix chain 'H' and resid 394 through 401 removed outlier: 4.119A pdb=" N TYR H 398 " --> pdb=" O THR H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 424 removed outlier: 4.569A pdb=" N GLU H 412 " --> pdb=" O LEU H 408 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASN H 413 " --> pdb=" O ASP H 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 436 removed outlier: 3.963A pdb=" N VAL H 435 " --> pdb=" O THR H 432 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR H 436 " --> pdb=" O SER H 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 432 through 436' Processing helix chain 'H' and resid 461 through 482 removed outlier: 3.985A pdb=" N GLN H 468 " --> pdb=" O SER H 464 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY H 478 " --> pdb=" O ILE H 474 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU H 479 " --> pdb=" O TRP H 475 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS H 480 " --> pdb=" O ALA H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 509 through 522 Processing helix chain 'H' and resid 530 through 532 No H-bonds generated for 'chain 'H' and resid 530 through 532' Processing helix chain 'H' and resid 539 through 553 removed outlier: 4.056A pdb=" N GLY H 543 " --> pdb=" O ASP H 539 " (cutoff:3.500A) Processing helix chain 'H' and resid 554 through 557 Processing helix chain 'H' and resid 574 through 586 Processing helix chain 'H' and resid 587 through 594 removed outlier: 5.913A pdb=" N LEU H 590 " --> pdb=" O LYS H 587 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS H 592 " --> pdb=" O PRO H 589 " (cutoff:3.500A) Processing helix chain 'H' and resid 623 through 631 Processing helix chain 'H' and resid 637 through 652 removed outlier: 4.230A pdb=" N THR H 641 " --> pdb=" O ASP H 637 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 337 removed outlier: 4.459A pdb=" N ARG I 337 " --> pdb=" O GLU I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 353 through 357 removed outlier: 3.668A pdb=" N LEU I 357 " --> pdb=" O SER I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 383 Processing helix chain 'I' and resid 394 through 401 removed outlier: 3.688A pdb=" N THR I 399 " --> pdb=" O PRO I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 401 through 410 Processing helix chain 'I' and resid 410 through 424 Processing helix chain 'I' and resid 432 through 436 removed outlier: 3.796A pdb=" N VAL I 435 " --> pdb=" O THR I 432 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR I 436 " --> pdb=" O SER I 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 432 through 436' Processing helix chain 'I' and resid 462 through 482 removed outlier: 3.557A pdb=" N GLN I 468 " --> pdb=" O SER I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 509 through 522 Processing helix chain 'I' and resid 527 through 532 removed outlier: 4.204A pdb=" N LYS I 532 " --> pdb=" O ASP I 529 " (cutoff:3.500A) Processing helix chain 'I' and resid 540 through 553 Processing helix chain 'I' and resid 554 through 557 removed outlier: 3.576A pdb=" N ARG I 557 " --> pdb=" O ALA I 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 554 through 557' Processing helix chain 'I' and resid 574 through 586 Processing helix chain 'I' and resid 590 through 594 removed outlier: 4.307A pdb=" N HIS I 593 " --> pdb=" O LEU I 590 " (cutoff:3.500A) Processing helix chain 'I' and resid 623 through 630 Processing helix chain 'I' and resid 637 through 652 removed outlier: 3.863A pdb=" N THR I 641 " --> pdb=" O ASP I 637 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 336 Processing helix chain 'J' and resid 373 through 383 Processing helix chain 'J' and resid 396 through 401 Processing helix chain 'J' and resid 401 through 410 Processing helix chain 'J' and resid 410 through 424 Processing helix chain 'J' and resid 432 through 436 removed outlier: 3.604A pdb=" N VAL J 435 " --> pdb=" O THR J 432 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR J 436 " --> pdb=" O SER J 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 432 through 436' Processing helix chain 'J' and resid 460 through 482 removed outlier: 4.603A pdb=" N SER J 464 " --> pdb=" O ARG J 460 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER J 466 " --> pdb=" O ILE J 462 " (cutoff:3.500A) Processing helix chain 'J' and resid 509 through 522 Processing helix chain 'J' and resid 539 through 553 removed outlier: 3.842A pdb=" N GLY J 543 " --> pdb=" O ASP J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 554 through 557 removed outlier: 3.603A pdb=" N ARG J 557 " --> pdb=" O ALA J 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 554 through 557' Processing helix chain 'J' and resid 574 through 587 removed outlier: 3.697A pdb=" N LYS J 587 " --> pdb=" O ALA J 583 " (cutoff:3.500A) Processing helix chain 'J' and resid 623 through 631 Processing helix chain 'J' and resid 637 through 652 removed outlier: 3.955A pdb=" N THR J 641 " --> pdb=" O ASP J 637 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 336 Processing helix chain 'K' and resid 350 through 354 removed outlier: 3.710A pdb=" N SER K 354 " --> pdb=" O ASP K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 373 through 383 Processing helix chain 'K' and resid 394 through 401 removed outlier: 3.831A pdb=" N TYR K 398 " --> pdb=" O THR K 394 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR K 399 " --> pdb=" O PRO K 395 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN K 401 " --> pdb=" O GLU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 401 through 423 removed outlier: 3.849A pdb=" N GLU K 412 " --> pdb=" O LEU K 408 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN K 413 " --> pdb=" O ASP K 409 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR K 423 " --> pdb=" O TYR K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 458 through 460 No H-bonds generated for 'chain 'K' and resid 458 through 460' Processing helix chain 'K' and resid 461 through 482 removed outlier: 4.362A pdb=" N VAL K 465 " --> pdb=" O TRP K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 509 through 522 Processing helix chain 'K' and resid 528 through 532 removed outlier: 4.541A pdb=" N LYS K 532 " --> pdb=" O ASP K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 540 through 552 Processing helix chain 'K' and resid 553 through 557 removed outlier: 3.581A pdb=" N ASN K 556 " --> pdb=" O ASN K 553 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG K 557 " --> pdb=" O ALA K 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 553 through 557' Processing helix chain 'K' and resid 567 through 569 No H-bonds generated for 'chain 'K' and resid 567 through 569' Processing helix chain 'K' and resid 574 through 586 Processing helix chain 'K' and resid 588 through 594 removed outlier: 3.882A pdb=" N ARG K 591 " --> pdb=" O HIS K 588 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N HIS K 592 " --> pdb=" O PRO K 589 " (cutoff:3.500A) Processing helix chain 'K' and resid 623 through 631 Processing helix chain 'K' and resid 637 through 652 removed outlier: 4.343A pdb=" N THR K 641 " --> pdb=" O ASP K 637 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 337 removed outlier: 3.793A pdb=" N ARG L 337 " --> pdb=" O GLU L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 357 removed outlier: 3.533A pdb=" N LEU L 357 " --> pdb=" O SER L 354 " (cutoff:3.500A) Processing helix chain 'L' and resid 373 through 383 Processing helix chain 'L' and resid 394 through 401 removed outlier: 3.902A pdb=" N TYR L 398 " --> pdb=" O THR L 394 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR L 399 " --> pdb=" O PRO L 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 423 removed outlier: 3.772A pdb=" N VAL L 405 " --> pdb=" O ASN L 401 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU L 411 " --> pdb=" O GLU L 407 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU L 412 " --> pdb=" O LEU L 408 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 481 removed outlier: 4.325A pdb=" N SER L 464 " --> pdb=" O ARG L 460 " (cutoff:3.500A) Processing helix chain 'L' and resid 509 through 522 Processing helix chain 'L' and resid 528 through 532 removed outlier: 3.885A pdb=" N LYS L 532 " --> pdb=" O ASP L 529 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 553 Processing helix chain 'L' and resid 554 through 557 removed outlier: 4.012A pdb=" N ARG L 557 " --> pdb=" O ALA L 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 554 through 557' Processing helix chain 'L' and resid 574 through 586 Processing helix chain 'L' and resid 588 through 594 removed outlier: 4.239A pdb=" N HIS L 592 " --> pdb=" O PRO L 589 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS L 593 " --> pdb=" O LEU L 590 " (cutoff:3.500A) Processing helix chain 'L' and resid 623 through 630 removed outlier: 3.546A pdb=" N HIS L 627 " --> pdb=" O ILE L 623 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 652 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 7.628A pdb=" N THR A 3 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE A 29 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL A 5 " --> pdb=" O ILE A 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 82 removed outlier: 6.553A pdb=" N ILE A 79 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N LEU A 103 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N SER A 81 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU A 132 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 145 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 235 removed outlier: 6.552A pdb=" N THR A 278 " --> pdb=" O TRP A 243 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER A 245 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE A 276 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL A 247 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU A 274 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 25 through 29 removed outlier: 7.951A pdb=" N THR B 3 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE B 29 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL B 5 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL B 78 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL B 4 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE B 80 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ARG B 134 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE B 144 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.832A pdb=" N ALA B 231 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR B 278 " --> pdb=" O TRP B 243 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N SER B 245 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 276 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL B 247 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU B 274 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.809A pdb=" N THR C 3 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N PHE C 30 " --> pdb=" O THR C 3 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL C 5 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 80 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 103 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN C 102 " --> pdb=" O HIS C 133 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ARG C 134 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE C 144 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 231 through 235 removed outlier: 3.974A pdb=" N ALA C 231 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C 280 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR C 278 " --> pdb=" O TRP C 243 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER C 245 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE C 276 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 247 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C 274 " --> pdb=" O VAL C 247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 231 through 235 removed outlier: 3.974A pdb=" N ALA C 231 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C 280 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR C 278 " --> pdb=" O TRP C 243 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER C 245 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE C 276 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 247 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C 274 " --> pdb=" O VAL C 247 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 25 through 29 removed outlier: 3.959A pdb=" N SER D 27 " --> pdb=" O THR D 3 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N VAL D 5 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE D 29 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA D 7 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ARG D 134 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE D 144 " --> pdb=" O ARG D 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 231 through 235 removed outlier: 7.409A pdb=" N THR D 278 " --> pdb=" O TRP D 243 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N SER D 245 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE D 276 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL D 247 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU D 274 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER D 261 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA D 268 " --> pdb=" O VAL D 259 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D 259 " --> pdb=" O ALA D 268 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 5 removed outlier: 7.012A pdb=" N THR E 3 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N PHE E 30 " --> pdb=" O THR E 3 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL E 5 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N TYR E 57 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE E 29 " --> pdb=" O TYR E 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 79 through 82 removed outlier: 6.084A pdb=" N ILE E 79 " --> pdb=" O PHE E 101 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU E 103 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER E 81 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU E 132 " --> pdb=" O VAL E 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 231 through 235 removed outlier: 4.272A pdb=" N ALA E 231 " --> pdb=" O VAL E 242 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 244 through 248 removed outlier: 3.815A pdb=" N THR E 278 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG E 246 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ILE E 276 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS E 248 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU E 274 " --> pdb=" O HIS E 248 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU E 266 " --> pdb=" O ILE E 260 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 26 through 29 removed outlier: 8.132A pdb=" N THR F 3 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE F 29 " --> pdb=" O THR F 3 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL F 5 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N PHE F 80 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE F 82 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE F 79 " --> pdb=" O PHE F 101 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEU F 103 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N SER F 81 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA F 146 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ARG F 134 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE F 144 " --> pdb=" O ARG F 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 231 through 235 removed outlier: 3.755A pdb=" N ALA F 231 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL F 242 " --> pdb=" O GLY F 279 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY F 279 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N SER F 244 " --> pdb=" O VAL F 277 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 231 through 235 removed outlier: 3.755A pdb=" N ALA F 231 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL F 242 " --> pdb=" O GLY F 279 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY F 279 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N SER F 244 " --> pdb=" O VAL F 277 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY F 279 " --> pdb=" O MET F 287 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 343 through 346 removed outlier: 6.301A pdb=" N VAL G 318 " --> pdb=" O TYR G 344 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU G 346 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE G 320 " --> pdb=" O LEU G 346 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 451 through 452 removed outlier: 3.595A pdb=" N LEU K 451 " --> pdb=" O LEU G 451 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 488 through 489 Processing sheet with id=AC3, first strand: chain 'G' and resid 525 through 527 removed outlier: 4.020A pdb=" N ARG G 601 " --> pdb=" O ILE G 525 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU G 527 " --> pdb=" O ARG G 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 534 through 535 Processing sheet with id=AC5, first strand: chain 'H' and resid 318 through 321 Processing sheet with id=AC6, first strand: chain 'H' and resid 346 through 347 removed outlier: 3.560A pdb=" N ASP H 347 " --> pdb=" O VAL H 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'H' and resid 451 through 453 removed outlier: 3.551A pdb=" N VAL H 453 " --> pdb=" O LEU J 451 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU J 451 " --> pdb=" O VAL H 453 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 486 through 489 removed outlier: 6.054A pdb=" N LEU H 487 " --> pdb=" O ILE H 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'H' and resid 525 through 528 removed outlier: 5.647A pdb=" N ILE H 525 " --> pdb=" O ARG H 601 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL H 603 " --> pdb=" O ILE H 525 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU H 527 " --> pdb=" O VAL H 603 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'H' and resid 534 through 535 Processing sheet with id=AD2, first strand: chain 'I' and resid 362 through 366 removed outlier: 6.188A pdb=" N VAL I 318 " --> pdb=" O TYR I 344 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU I 346 " --> pdb=" O VAL I 318 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE I 320 " --> pdb=" O LEU I 346 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE I 427 " --> pdb=" O THR I 486 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE I 488 " --> pdb=" O ILE I 427 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE I 429 " --> pdb=" O PHE I 488 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE I 485 " --> pdb=" O GLU I 561 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE I 563 " --> pdb=" O PHE I 485 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU I 487 " --> pdb=" O ILE I 563 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE I 565 " --> pdb=" O LEU I 487 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG I 489 " --> pdb=" O ILE I 565 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 493 through 494 Processing sheet with id=AD4, first strand: chain 'I' and resid 534 through 535 Processing sheet with id=AD5, first strand: chain 'J' and resid 318 through 321 removed outlier: 6.500A pdb=" N LEU J 319 " --> pdb=" O LEU J 387 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE J 488 " --> pdb=" O PHE J 429 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE J 485 " --> pdb=" O GLU J 561 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE J 563 " --> pdb=" O PHE J 485 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU J 487 " --> pdb=" O ILE J 563 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE J 565 " --> pdb=" O LEU J 487 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG J 489 " --> pdb=" O ILE J 565 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 526 through 528 Processing sheet with id=AD7, first strand: chain 'J' and resid 534 through 535 Processing sheet with id=AD8, first strand: chain 'K' and resid 362 through 366 removed outlier: 3.711A pdb=" N GLY K 345 " --> pdb=" O HIS K 363 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL K 318 " --> pdb=" O TYR K 344 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU K 346 " --> pdb=" O VAL K 318 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE K 320 " --> pdb=" O LEU K 346 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU K 321 " --> pdb=" O LEU K 387 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 486 through 490 removed outlier: 5.979A pdb=" N LEU K 487 " --> pdb=" O ILE K 563 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE K 565 " --> pdb=" O LEU K 487 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG K 489 " --> pdb=" O ILE K 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'K' and resid 525 through 527 removed outlier: 3.521A pdb=" N ARG K 601 " --> pdb=" O ILE K 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 534 through 536 Processing sheet with id=AE3, first strand: chain 'L' and resid 362 through 366 removed outlier: 6.676A pdb=" N VAL L 343 " --> pdb=" O HIS L 363 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL L 365 " --> pdb=" O VAL L 343 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY L 345 " --> pdb=" O VAL L 365 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL L 318 " --> pdb=" O TYR L 344 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LEU L 346 " --> pdb=" O VAL L 318 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE L 320 " --> pdb=" O LEU L 346 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 486 through 489 removed outlier: 6.407A pdb=" N LEU L 487 " --> pdb=" O ILE L 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'L' and resid 493 through 494 Processing sheet with id=AE6, first strand: chain 'L' and resid 525 through 526 removed outlier: 6.922A pdb=" N ILE L 525 " --> pdb=" O ARG L 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'L' and resid 534 through 535 removed outlier: 3.631A pdb=" N ALA L 572 " --> pdb=" O ARG L 535 " (cutoff:3.500A) 1163 hydrogen bonds defined for protein. 3333 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.80 Time building geometry restraints manager: 3.09 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: 9421 1.34 - 1.46: 5547 1.46 - 1.58: 14173 1.58 - 1.70: 0 1.70 - 1.82: 162 Bond restraints: 29303 Sorted by residual: bond pdb=" C ALA A 115 " pdb=" O ALA A 115 " ideal model delta sigma weight residual 1.235 1.246 -0.011 4.70e-03 4.53e+04 5.58e+00 bond pdb=" CB ASN J 570 " pdb=" CG ASN J 570 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.67e+00 bond pdb=" CA ASP L 637 " pdb=" CB ASP L 637 " ideal model delta sigma weight residual 1.527 1.551 -0.024 1.49e-02 4.50e+03 2.53e+00 bond pdb=" CB ARG D 85 " pdb=" CG ARG D 85 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.23e+00 bond pdb=" CA PRO L 595 " pdb=" C PRO L 595 " ideal model delta sigma weight residual 1.517 1.527 -0.010 6.70e-03 2.23e+04 2.07e+00 ... (remaining 29298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 39415 2.92 - 5.84: 324 5.84 - 8.77: 48 8.77 - 11.69: 11 11.69 - 14.61: 2 Bond angle restraints: 39800 Sorted by residual: angle pdb=" CA ARG H 424 " pdb=" CB ARG H 424 " pdb=" CG ARG H 424 " ideal model delta sigma weight residual 114.10 123.30 -9.20 2.00e+00 2.50e-01 2.12e+01 angle pdb=" N ASP L 637 " pdb=" CA ASP L 637 " pdb=" C ASP L 637 " ideal model delta sigma weight residual 109.86 102.95 6.91 1.55e+00 4.16e-01 1.99e+01 angle pdb=" CB MET G 638 " pdb=" CG MET G 638 " pdb=" SD MET G 638 " ideal model delta sigma weight residual 112.70 126.06 -13.36 3.00e+00 1.11e-01 1.98e+01 angle pdb=" CA LEU I 547 " pdb=" CB LEU I 547 " pdb=" CG LEU I 547 " ideal model delta sigma weight residual 116.30 130.91 -14.61 3.50e+00 8.16e-02 1.74e+01 angle pdb=" CA ASP L 637 " pdb=" CB ASP L 637 " pdb=" CG ASP L 637 " ideal model delta sigma weight residual 112.60 116.63 -4.03 1.00e+00 1.00e+00 1.62e+01 ... (remaining 39795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14826 17.98 - 35.96: 1895 35.96 - 53.94: 513 53.94 - 71.92: 73 71.92 - 89.90: 19 Dihedral angle restraints: 17326 sinusoidal: 6923 harmonic: 10403 Sorted by residual: dihedral pdb=" CA GLN B 73 " pdb=" C GLN B 73 " pdb=" N LEU B 74 " pdb=" CA LEU B 74 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ARG C 114 " pdb=" C ARG C 114 " pdb=" N ALA C 115 " pdb=" CA ALA C 115 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA HIS C 250 " pdb=" C HIS C 250 " pdb=" N ALA C 251 " pdb=" CA ALA C 251 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 17323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3654 0.060 - 0.121: 709 0.121 - 0.181: 35 0.181 - 0.242: 1 0.242 - 0.302: 2 Chirality restraints: 4401 Sorted by residual: chirality pdb=" CB ILE I 565 " pdb=" CA ILE I 565 " pdb=" CG1 ILE I 565 " pdb=" CG2 ILE I 565 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CG LEU C 173 " pdb=" CB LEU C 173 " pdb=" CD1 LEU C 173 " pdb=" CD2 LEU C 173 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CG LEU G 581 " pdb=" CB LEU G 581 " pdb=" CD1 LEU G 581 " pdb=" CD2 LEU G 581 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.92e-01 ... (remaining 4398 not shown) Planarity restraints: 5147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 375 " 0.029 2.00e-02 2.50e+03 1.91e-02 9.12e+00 pdb=" CG TRP I 375 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP I 375 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP I 375 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 375 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP I 375 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP I 375 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 375 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 375 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP I 375 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 67 " 0.022 2.00e-02 2.50e+03 1.81e-02 8.16e+00 pdb=" CG TRP E 67 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP E 67 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP E 67 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 67 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 67 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 67 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 67 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 67 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP E 67 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN J 570 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.66e+00 pdb=" C ASN J 570 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN J 570 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU J 571 " 0.016 2.00e-02 2.50e+03 ... (remaining 5144 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 10184 2.87 - 3.38: 28274 3.38 - 3.88: 47045 3.88 - 4.39: 50812 4.39 - 4.90: 83338 Nonbonded interactions: 219653 Sorted by model distance: nonbonded pdb=" OD1 ASP L 637 " pdb=" N MET L 638 " model vdw 2.360 3.120 nonbonded pdb=" O ASN J 570 " pdb=" OD1 ASN J 570 " model vdw 2.397 3.040 nonbonded pdb=" N ASP L 637 " pdb=" O ASP L 637 " model vdw 2.481 2.496 nonbonded pdb=" N MET C 1 " pdb=" N LYS C 2 " model vdw 2.487 2.560 nonbonded pdb=" N GLN G 533 " pdb=" OE1 GLN G 533 " model vdw 2.488 3.120 ... (remaining 219648 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 94 or resid 96 through 113 or (resid 114 through \ 115 and (name N or name CA or name C or name O or name CB )) or resid 116 throu \ gh 118 or (resid 119 and (name N or name CA or name C or name O or name CB )) or \ resid 120 through 183 or (resid 202 and (name N or name CA or name C or name O \ or name CB )) or resid 203 through 300)) selection = (chain 'B' and (resid 1 through 94 or resid 96 through 113 or (resid 114 through \ 115 and (name N or name CA or name C or name O or name CB )) or resid 116 throu \ gh 118 or (resid 119 and (name N or name CA or name C or name O or name CB )) or \ resid 120 through 183 or (resid 202 and (name N or name CA or name C or name O \ or name CB )) or resid 203 through 300)) selection = (chain 'C' and (resid 1 through 94 or resid 96 through 113 or (resid 114 through \ 115 and (name N or name CA or name C or name O or name CB )) or resid 116 throu \ gh 183 or (resid 202 and (name N or name CA or name C or name O or name CB )) or \ resid 203 through 249 or resid 253 through 300)) selection = (chain 'D' and (resid 1 through 94 or resid 96 through 118 or (resid 119 and (na \ me N or name CA or name C or name O or name CB )) or resid 120 through 183 or re \ sid 202 through 300)) selection = (chain 'E' and (resid 1 through 113 or (resid 114 through 115 and (name N or nam \ e CA or name C or name O or name CB )) or resid 116 through 118 or (resid 119 an \ d (name N or name CA or name C or name O or name CB )) or resid 120 through 183 \ or (resid 202 and (name N or name CA or name C or name O or name CB )) or resid \ 203 through 300)) selection = (chain 'F' and (resid 1 through 94 or resid 96 through 113 or (resid 114 through \ 115 and (name N or name CA or name C or name O or name CB )) or resid 116 throu \ gh 118 or (resid 119 and (name N or name CA or name C or name O or name CB )) or \ resid 120 through 183 or (resid 202 and (name N or name CA or name C or name O \ or name CB )) or resid 203 through 300)) } ncs_group { reference = (chain 'G' and (resid 317 through 589 or resid 591 through 653)) selection = (chain 'H' and (resid 317 through 589 or resid 591 through 603 or resid 616 thro \ ugh 653)) selection = (chain 'I' and (resid 317 through 589 or resid 591 through 603 or resid 616 thro \ ugh 653)) selection = (chain 'J' and (resid 317 through 603 or resid 616 through 653)) selection = (chain 'K' and (resid 317 through 589 or resid 591 through 603 or resid 616 thro \ ugh 653)) selection = (chain 'L' and (resid 317 through 589 or resid 591 through 603 or resid 616 thro \ ugh 653)) } 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.590 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29303 Z= 0.138 Angle : 0.715 14.612 39800 Z= 0.365 Chirality : 0.045 0.302 4401 Planarity : 0.005 0.057 5147 Dihedral : 16.963 89.897 10618 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.07 % Rotamer: Outliers : 3.86 % Allowed : 29.22 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.57 (0.14), residues: 3538 helix: 0.23 (0.14), residues: 1405 sheet: -0.24 (0.25), residues: 450 loop : -0.86 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 624 TYR 0.020 0.001 TYR A 8 PHE 0.026 0.001 PHE K 326 TRP 0.051 0.002 TRP I 375 HIS 0.010 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00287 (29303) covalent geometry : angle 0.71481 (39800) hydrogen bonds : bond 0.13468 ( 1146) hydrogen bonds : angle 6.85305 ( 3333) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 570 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 THR cc_start: 0.6694 (OUTLIER) cc_final: 0.6349 (t) REVERT: A 205 ASP cc_start: 0.6625 (OUTLIER) cc_final: 0.6056 (m-30) REVERT: A 287 MET cc_start: -0.0125 (tpt) cc_final: -0.0555 (tpt) REVERT: A 298 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5614 (mm) REVERT: B 85 ARG cc_start: 0.3131 (OUTLIER) cc_final: 0.1211 (ptp90) REVERT: B 132 LEU cc_start: 0.3976 (OUTLIER) cc_final: 0.3566 (mt) REVERT: B 147 GLN cc_start: 0.1147 (OUTLIER) cc_final: 0.0895 (tm130) REVERT: B 220 MET cc_start: 0.5501 (tpt) cc_final: 0.4947 (mmp) REVERT: B 241 THR cc_start: 0.7673 (p) cc_final: 0.7099 (t) REVERT: B 287 MET cc_start: 0.2668 (tmm) cc_final: 0.0669 (tmm) REVERT: B 291 GLN cc_start: 0.7308 (pp30) cc_final: 0.6529 (pp30) REVERT: C 220 MET cc_start: 0.6424 (tpt) cc_final: 0.5986 (tpp) REVERT: C 287 MET cc_start: -0.0898 (tpp) cc_final: -0.1206 (tpt) REVERT: D 11 MET cc_start: 0.6497 (mpp) cc_final: 0.5497 (mpp) REVERT: D 82 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5370 (t80) REVERT: D 220 MET cc_start: 0.5597 (mmm) cc_final: 0.4794 (mmm) REVERT: E 3 THR cc_start: 0.4591 (OUTLIER) cc_final: 0.4262 (t) REVERT: E 287 MET cc_start: 0.1892 (tpt) cc_final: 0.1493 (tpt) REVERT: F 161 LEU cc_start: 0.2493 (OUTLIER) cc_final: 0.1851 (tt) REVERT: F 220 MET cc_start: 0.5946 (mmp) cc_final: 0.5611 (mmp) REVERT: G 477 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6754 (m-80) REVERT: G 587 LYS cc_start: 0.6172 (tmtt) cc_final: 0.5947 (tmtt) REVERT: G 637 ASP cc_start: 0.7862 (t70) cc_final: 0.7342 (t0) REVERT: G 640 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6681 (pm20) REVERT: H 356 PHE cc_start: 0.7448 (m-10) cc_final: 0.7153 (m-80) REVERT: H 474 ILE cc_start: 0.8498 (tt) cc_final: 0.8142 (tt) REVERT: H 558 CYS cc_start: 0.7379 (m) cc_final: 0.7004 (m) REVERT: I 333 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7152 (pp20) REVERT: I 396 ILE cc_start: 0.6283 (OUTLIER) cc_final: 0.6008 (pp) REVERT: I 461 TRP cc_start: 0.4473 (p-90) cc_final: 0.2418 (p-90) REVERT: I 481 GLU cc_start: 0.6208 (tp30) cc_final: 0.5397 (mm-30) REVERT: I 491 PHE cc_start: 0.6661 (m-10) cc_final: 0.6419 (m-10) REVERT: I 577 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7859 (tt) REVERT: I 633 GLU cc_start: 0.5969 (pp20) cc_final: 0.5215 (pp20) REVERT: J 324 ASN cc_start: 0.7535 (t0) cc_final: 0.7323 (t0) REVERT: J 453 VAL cc_start: 0.8297 (OUTLIER) cc_final: 0.8090 (m) REVERT: J 477 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6106 (t80) REVERT: J 514 GLN cc_start: 0.7668 (tp40) cc_final: 0.6984 (tp40) REVERT: K 417 ILE cc_start: 0.8174 (mt) cc_final: 0.7745 (tt) REVERT: K 461 TRP cc_start: 0.5291 (m100) cc_final: 0.4697 (t-100) REVERT: K 537 PHE cc_start: 0.6564 (m-10) cc_final: 0.6290 (m-10) REVERT: K 549 ARG cc_start: 0.7380 (ptp-170) cc_final: 0.7043 (mtt180) REVERT: K 585 PHE cc_start: 0.6925 (t80) cc_final: 0.6491 (t80) REVERT: K 624 ARG cc_start: 0.7457 (mtm180) cc_final: 0.7166 (mtm110) REVERT: K 638 MET cc_start: 0.5985 (pmm) cc_final: 0.5240 (ppp) REVERT: L 337 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7282 (ptt-90) REVERT: L 359 HIS cc_start: 0.7666 (t-90) cc_final: 0.7290 (t70) REVERT: L 477 TYR cc_start: 0.7172 (OUTLIER) cc_final: 0.6169 (m-80) outliers start: 117 outliers final: 88 residues processed: 643 average time/residue: 0.1821 time to fit residues: 184.9437 Evaluate side-chains 673 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 567 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 133 HIS Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain G residue 477 TYR Chi-restraints excluded: chain G residue 480 LYS Chi-restraints excluded: chain G residue 486 THR Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 557 ARG Chi-restraints excluded: chain G residue 640 GLU Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 461 TRP Chi-restraints excluded: chain H residue 538 THR Chi-restraints excluded: chain H residue 577 LEU Chi-restraints excluded: chain H residue 627 HIS Chi-restraints excluded: chain I residue 333 GLU Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 396 ILE Chi-restraints excluded: chain I residue 434 GLU Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 523 SER Chi-restraints excluded: chain I residue 577 LEU Chi-restraints excluded: chain I residue 585 PHE Chi-restraints excluded: chain I residue 602 VAL Chi-restraints excluded: chain I residue 627 HIS Chi-restraints excluded: chain I residue 653 VAL Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 424 ARG Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 464 SER Chi-restraints excluded: chain J residue 465 VAL Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 577 LEU Chi-restraints excluded: chain K residue 356 PHE Chi-restraints excluded: chain K residue 423 TYR Chi-restraints excluded: chain K residue 499 ASP Chi-restraints excluded: chain K residue 506 ILE Chi-restraints excluded: chain K residue 540 ILE Chi-restraints excluded: chain K residue 563 ILE Chi-restraints excluded: chain K residue 591 ARG Chi-restraints excluded: chain K residue 603 VAL Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 336 LEU Chi-restraints excluded: chain L residue 337 ARG Chi-restraints excluded: chain L residue 376 ILE Chi-restraints excluded: chain L residue 477 TYR Chi-restraints excluded: chain L residue 486 THR Chi-restraints excluded: chain L residue 544 ILE Chi-restraints excluded: chain L residue 641 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.0020 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN C 280 GLN D 133 HIS D 147 GLN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 HIS ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 GLN G 329 ASN I 363 HIS ** J 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 514 GLN ** K 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 ASN ** L 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.250050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.208855 restraints weight = 53573.214| |-----------------------------------------------------------------------------| r_work (start): 0.4510 rms_B_bonded: 3.98 r_work: 0.4345 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29303 Z= 0.141 Angle : 0.618 10.425 39800 Z= 0.309 Chirality : 0.045 0.178 4401 Planarity : 0.004 0.046 5147 Dihedral : 7.599 84.855 4115 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.64 % Favored : 95.31 % Rotamer: Outliers : 5.77 % Allowed : 26.29 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 3538 helix: 0.29 (0.14), residues: 1422 sheet: -0.50 (0.24), residues: 472 loop : -0.89 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 624 TYR 0.014 0.001 TYR G 436 PHE 0.022 0.002 PHE J 444 TRP 0.036 0.002 TRP E 67 HIS 0.010 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00318 (29303) covalent geometry : angle 0.61781 (39800) hydrogen bonds : bond 0.03812 ( 1146) hydrogen bonds : angle 5.53738 ( 3333) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 607 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7258 (mm) cc_final: 0.7036 (mm) REVERT: A 205 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6346 (m-30) REVERT: B 287 MET cc_start: 0.3477 (tmm) cc_final: 0.1588 (tmm) REVERT: B 291 GLN cc_start: 0.7320 (pp30) cc_final: 0.7027 (pp30) REVERT: C 11 MET cc_start: 0.7055 (mmt) cc_final: 0.6608 (ptt) REVERT: C 220 MET cc_start: 0.6384 (tpt) cc_final: 0.5942 (tpp) REVERT: C 287 MET cc_start: -0.2023 (tpp) cc_final: -0.2270 (tpt) REVERT: D 11 MET cc_start: 0.6517 (mpp) cc_final: 0.5437 (mpp) REVERT: D 82 PHE cc_start: 0.5923 (OUTLIER) cc_final: 0.5297 (t80) REVERT: D 220 MET cc_start: 0.5623 (mmm) cc_final: 0.4782 (mmm) REVERT: E 57 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.6818 (t80) REVERT: E 287 MET cc_start: 0.1783 (tpt) cc_final: 0.1482 (tpt) REVERT: F 220 MET cc_start: 0.5926 (mmp) cc_final: 0.5601 (mmp) REVERT: G 333 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8060 (tm-30) REVERT: G 336 LEU cc_start: 0.8095 (mt) cc_final: 0.7870 (mt) REVERT: G 422 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6703 (ptmt) REVERT: G 472 ARG cc_start: 0.8563 (mtt-85) cc_final: 0.8233 (mtp85) REVERT: G 491 PHE cc_start: 0.5519 (m-10) cc_final: 0.5023 (m-10) REVERT: G 637 ASP cc_start: 0.7834 (t70) cc_final: 0.6757 (t0) REVERT: G 639 GLN cc_start: 0.7935 (pm20) cc_final: 0.6214 (pm20) REVERT: G 640 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: H 337 ARG cc_start: 0.7378 (mmm160) cc_final: 0.6986 (mmm160) REVERT: H 356 PHE cc_start: 0.7552 (m-80) cc_final: 0.7259 (m-80) REVERT: H 415 ARG cc_start: 0.7429 (ptm160) cc_final: 0.7037 (mtp-110) REVERT: H 424 ARG cc_start: 0.7296 (tpm170) cc_final: 0.6980 (tpm170) REVERT: H 434 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7554 (mm-30) REVERT: H 438 MET cc_start: 0.7268 (pmm) cc_final: 0.6900 (ptp) REVERT: H 474 ILE cc_start: 0.8531 (tt) cc_final: 0.8184 (tt) REVERT: H 553 ASN cc_start: 0.5716 (t0) cc_final: 0.5245 (t0) REVERT: H 632 TRP cc_start: 0.7023 (t60) cc_final: 0.6348 (t60) REVERT: I 351 ASP cc_start: 0.7402 (p0) cc_final: 0.7170 (p0) REVERT: I 385 VAL cc_start: 0.8027 (OUTLIER) cc_final: 0.7790 (p) REVERT: I 446 GLU cc_start: 0.2900 (OUTLIER) cc_final: -0.1968 (pt0) REVERT: I 461 TRP cc_start: 0.4660 (p-90) cc_final: 0.2885 (p-90) REVERT: I 477 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.6691 (m-80) REVERT: I 491 PHE cc_start: 0.6776 (m-10) cc_final: 0.6551 (m-10) REVERT: I 627 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7467 (t-90) REVERT: I 633 GLU cc_start: 0.6051 (pp20) cc_final: 0.5283 (pp20) REVERT: J 324 ASN cc_start: 0.7672 (t0) cc_final: 0.7292 (t0) REVERT: J 337 ARG cc_start: 0.7457 (mtm180) cc_final: 0.7251 (mtp180) REVERT: J 369 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7784 (mt) REVERT: J 453 VAL cc_start: 0.8241 (OUTLIER) cc_final: 0.7994 (m) REVERT: J 477 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.6406 (t80) REVERT: K 417 ILE cc_start: 0.8175 (mt) cc_final: 0.7794 (tt) REVERT: K 461 TRP cc_start: 0.5545 (m100) cc_final: 0.4810 (t-100) REVERT: K 514 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7124 (tm130) REVERT: K 527 LEU cc_start: 0.7318 (tp) cc_final: 0.6976 (tp) REVERT: K 549 ARG cc_start: 0.7654 (ptp-170) cc_final: 0.7335 (mtt180) REVERT: K 585 PHE cc_start: 0.6955 (t80) cc_final: 0.6554 (t80) REVERT: K 597 PHE cc_start: 0.7823 (t80) cc_final: 0.7516 (t80) REVERT: K 624 ARG cc_start: 0.7464 (mtm180) cc_final: 0.7194 (mtm110) REVERT: K 638 MET cc_start: 0.6078 (pmm) cc_final: 0.5224 (ppp) REVERT: K 642 ILE cc_start: 0.5936 (pt) cc_final: 0.5539 (pt) REVERT: L 417 ILE cc_start: 0.8017 (mt) cc_final: 0.7796 (mm) REVERT: L 422 LYS cc_start: 0.7500 (ptmt) cc_final: 0.7243 (ptmm) REVERT: L 423 TYR cc_start: 0.8372 (m-10) cc_final: 0.7626 (m-80) REVERT: L 451 LEU cc_start: 0.1833 (OUTLIER) cc_final: 0.1431 (mp) REVERT: L 453 VAL cc_start: -0.0425 (OUTLIER) cc_final: -0.0888 (m) REVERT: L 477 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.6436 (m-80) REVERT: L 479 GLU cc_start: 0.5633 (OUTLIER) cc_final: 0.4843 (tm-30) REVERT: L 633 GLU cc_start: 0.6307 (tm-30) cc_final: 0.6018 (pp20) outliers start: 175 outliers final: 97 residues processed: 719 average time/residue: 0.1840 time to fit residues: 208.1992 Evaluate side-chains 694 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 580 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 119 TRP Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 67 TRP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 422 LYS Chi-restraints excluded: chain G residue 461 TRP Chi-restraints excluded: chain G residue 477 TYR Chi-restraints excluded: chain G residue 486 THR Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 557 ARG Chi-restraints excluded: chain G residue 571 GLU Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 640 GLU Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 461 TRP Chi-restraints excluded: chain H residue 602 VAL Chi-restraints excluded: chain H residue 627 HIS Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 332 THR Chi-restraints excluded: chain I residue 333 GLU Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 446 GLU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 465 VAL Chi-restraints excluded: chain I residue 477 TYR Chi-restraints excluded: chain I residue 479 GLU Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 585 PHE Chi-restraints excluded: chain I residue 602 VAL Chi-restraints excluded: chain I residue 627 HIS Chi-restraints excluded: chain I residue 639 GLN Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 368 ASP Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 465 VAL Chi-restraints excluded: chain J residue 474 ILE Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain J residue 512 ILE Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 577 LEU Chi-restraints excluded: chain J residue 584 SER Chi-restraints excluded: chain K residue 346 LEU Chi-restraints excluded: chain K residue 356 PHE Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 423 TYR Chi-restraints excluded: chain K residue 438 MET Chi-restraints excluded: chain K residue 514 GLN Chi-restraints excluded: chain K residue 540 ILE Chi-restraints excluded: chain K residue 591 ARG Chi-restraints excluded: chain K residue 603 VAL Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 336 LEU Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain L residue 439 CYS Chi-restraints excluded: chain L residue 451 LEU Chi-restraints excluded: chain L residue 453 VAL Chi-restraints excluded: chain L residue 477 TYR Chi-restraints excluded: chain L residue 479 GLU Chi-restraints excluded: chain L residue 486 THR Chi-restraints excluded: chain L residue 557 ARG Chi-restraints excluded: chain L residue 627 HIS Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 649 PHE Chi-restraints excluded: chain L residue 653 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 141 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 chunk 240 optimal weight: 0.2980 chunk 47 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 350 optimal weight: 1.9990 chunk 316 optimal weight: 0.7980 chunk 253 optimal weight: 0.0000 chunk 70 optimal weight: 1.9990 chunk 192 optimal weight: 0.4980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS C 280 GLN ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 484 GLN K 468 GLN ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.250088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.208659 restraints weight = 53824.824| |-----------------------------------------------------------------------------| r_work (start): 0.4507 rms_B_bonded: 4.31 r_work: 0.4357 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29303 Z= 0.112 Angle : 0.600 11.191 39800 Z= 0.296 Chirality : 0.043 0.196 4401 Planarity : 0.004 0.057 5147 Dihedral : 6.589 59.303 4025 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 5.44 % Allowed : 27.18 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.45 (0.14), residues: 3538 helix: 0.44 (0.14), residues: 1420 sheet: -0.42 (0.25), residues: 465 loop : -0.84 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 337 TYR 0.014 0.001 TYR I 463 PHE 0.023 0.001 PHE L 364 TRP 0.037 0.001 TRP E 67 HIS 0.010 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00250 (29303) covalent geometry : angle 0.59973 (39800) hydrogen bonds : bond 0.03480 ( 1146) hydrogen bonds : angle 5.25933 ( 3333) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 592 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7321 (mm) cc_final: 0.7062 (mm) REVERT: A 152 ILE cc_start: 0.1941 (OUTLIER) cc_final: 0.1681 (tt) REVERT: A 205 ASP cc_start: 0.6850 (t0) cc_final: 0.6262 (m-30) REVERT: A 277 VAL cc_start: 0.5695 (t) cc_final: 0.5427 (p) REVERT: B 159 ILE cc_start: 0.5674 (OUTLIER) cc_final: 0.5418 (mp) REVERT: B 220 MET cc_start: 0.5336 (tpt) cc_final: 0.4833 (mmp) REVERT: B 241 THR cc_start: 0.7622 (p) cc_final: 0.6951 (t) REVERT: B 287 MET cc_start: 0.3507 (tmm) cc_final: 0.3145 (ttp) REVERT: C 11 MET cc_start: 0.6989 (mmt) cc_final: 0.6609 (ptt) REVERT: C 220 MET cc_start: 0.6374 (tpt) cc_final: 0.6092 (tpp) REVERT: C 241 THR cc_start: 0.5690 (OUTLIER) cc_final: 0.5414 (t) REVERT: D 11 MET cc_start: 0.6559 (mpp) cc_final: 0.5468 (mpp) REVERT: D 82 PHE cc_start: 0.5768 (OUTLIER) cc_final: 0.5082 (t80) REVERT: D 220 MET cc_start: 0.5677 (mmm) cc_final: 0.4797 (mmm) REVERT: D 285 ILE cc_start: 0.7125 (pt) cc_final: 0.6760 (mp) REVERT: E 3 THR cc_start: 0.4728 (OUTLIER) cc_final: 0.4448 (t) REVERT: F 66 LEU cc_start: 0.7080 (tp) cc_final: 0.6791 (pp) REVERT: F 220 MET cc_start: 0.5919 (mmp) cc_final: 0.5653 (mmp) REVERT: F 287 MET cc_start: -0.1577 (tpt) cc_final: -0.2317 (tpp) REVERT: G 333 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8042 (tm-30) REVERT: G 422 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6605 (ptmt) REVERT: G 456 VAL cc_start: 0.3291 (OUTLIER) cc_final: 0.2456 (p) REVERT: G 472 ARG cc_start: 0.8499 (mtt-85) cc_final: 0.8222 (mtp85) REVERT: G 491 PHE cc_start: 0.5539 (OUTLIER) cc_final: 0.5058 (m-10) REVERT: G 527 LEU cc_start: 0.8279 (mp) cc_final: 0.8069 (mp) REVERT: G 637 ASP cc_start: 0.7884 (t70) cc_final: 0.7415 (t70) REVERT: G 640 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6801 (pm20) REVERT: H 319 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7356 (tp) REVERT: H 337 ARG cc_start: 0.7325 (mmm160) cc_final: 0.6995 (mmm160) REVERT: H 356 PHE cc_start: 0.7601 (m-80) cc_final: 0.7302 (m-80) REVERT: H 415 ARG cc_start: 0.7458 (ptm160) cc_final: 0.7214 (ptm-80) REVERT: H 438 MET cc_start: 0.7284 (pmm) cc_final: 0.6902 (ptp) REVERT: H 474 ILE cc_start: 0.8468 (tt) cc_final: 0.8150 (tt) REVERT: H 540 ILE cc_start: 0.6808 (mm) cc_final: 0.6177 (mt) REVERT: H 553 ASN cc_start: 0.5324 (t0) cc_final: 0.4837 (t0) REVERT: H 561 GLU cc_start: 0.7077 (pm20) cc_final: 0.5960 (pt0) REVERT: I 385 VAL cc_start: 0.7986 (OUTLIER) cc_final: 0.7745 (p) REVERT: I 446 GLU cc_start: 0.3014 (OUTLIER) cc_final: -0.1822 (mt-10) REVERT: I 461 TRP cc_start: 0.4352 (p-90) cc_final: 0.2333 (p-90) REVERT: I 477 TYR cc_start: 0.7051 (m-80) cc_final: 0.6647 (m-80) REVERT: I 627 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7516 (t-90) REVERT: J 369 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7757 (mt) REVERT: J 453 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7897 (m) REVERT: J 477 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.6372 (t80) REVERT: J 514 GLN cc_start: 0.7687 (tp-100) cc_final: 0.6993 (tp-100) REVERT: K 461 TRP cc_start: 0.5562 (m100) cc_final: 0.4856 (t-100) REVERT: K 549 ARG cc_start: 0.7586 (ptp-170) cc_final: 0.7294 (mtt180) REVERT: K 585 PHE cc_start: 0.6963 (t80) cc_final: 0.6532 (t80) REVERT: K 624 ARG cc_start: 0.7617 (mtm180) cc_final: 0.7341 (mtm110) REVERT: L 422 LYS cc_start: 0.7573 (ptmt) cc_final: 0.7268 (ptmm) REVERT: L 423 TYR cc_start: 0.8297 (m-10) cc_final: 0.7433 (m-80) REVERT: L 451 LEU cc_start: 0.2164 (OUTLIER) cc_final: 0.1622 (mp) REVERT: L 453 VAL cc_start: -0.0045 (OUTLIER) cc_final: -0.0655 (m) REVERT: L 477 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6210 (m-80) REVERT: L 479 GLU cc_start: 0.5459 (OUTLIER) cc_final: 0.4742 (tm-30) outliers start: 165 outliers final: 109 residues processed: 697 average time/residue: 0.1841 time to fit residues: 203.3897 Evaluate side-chains 708 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 579 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 119 TRP Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 422 LYS Chi-restraints excluded: chain G residue 434 GLU Chi-restraints excluded: chain G residue 449 SER Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 461 TRP Chi-restraints excluded: chain G residue 477 TYR Chi-restraints excluded: chain G residue 486 THR Chi-restraints excluded: chain G residue 491 PHE Chi-restraints excluded: chain G residue 494 MET Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 571 GLU Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 640 GLU Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 423 TYR Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 461 TRP Chi-restraints excluded: chain H residue 494 MET Chi-restraints excluded: chain H residue 499 ASP Chi-restraints excluded: chain H residue 558 CYS Chi-restraints excluded: chain H residue 602 VAL Chi-restraints excluded: chain H residue 627 HIS Chi-restraints excluded: chain I residue 333 GLU Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 446 GLU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 534 LYS Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 585 PHE Chi-restraints excluded: chain I residue 602 VAL Chi-restraints excluded: chain I residue 627 HIS Chi-restraints excluded: chain I residue 639 GLN Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 369 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 444 PHE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 465 VAL Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain J residue 484 GLN Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 577 LEU Chi-restraints excluded: chain J residue 584 SER Chi-restraints excluded: chain K residue 346 LEU Chi-restraints excluded: chain K residue 356 PHE Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 468 GLN Chi-restraints excluded: chain K residue 486 THR Chi-restraints excluded: chain K residue 540 ILE Chi-restraints excluded: chain K residue 563 ILE Chi-restraints excluded: chain K residue 603 VAL Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 336 LEU Chi-restraints excluded: chain L residue 346 LEU Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 432 THR Chi-restraints excluded: chain L residue 451 LEU Chi-restraints excluded: chain L residue 453 VAL Chi-restraints excluded: chain L residue 477 TYR Chi-restraints excluded: chain L residue 479 GLU Chi-restraints excluded: chain L residue 486 THR Chi-restraints excluded: chain L residue 523 SER Chi-restraints excluded: chain L residue 538 THR Chi-restraints excluded: chain L residue 540 ILE Chi-restraints excluded: chain L residue 557 ARG Chi-restraints excluded: chain L residue 627 HIS Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 649 PHE Chi-restraints excluded: chain L residue 653 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 52 optimal weight: 0.3980 chunk 209 optimal weight: 0.6980 chunk 255 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 285 optimal weight: 0.0050 chunk 344 optimal weight: 0.6980 chunk 300 optimal weight: 0.5980 chunk 325 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 252 optimal weight: 0.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS B 73 GLN ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 HIS ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 372 HIS ** H 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 593 HIS J 330 HIS ** J 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 484 GLN ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 564 ASN L 324 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.250257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.208976 restraints weight = 53358.669| |-----------------------------------------------------------------------------| r_work (start): 0.4522 rms_B_bonded: 3.92 r_work: 0.4364 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29303 Z= 0.108 Angle : 0.594 10.076 39800 Z= 0.291 Chirality : 0.043 0.201 4401 Planarity : 0.004 0.061 5147 Dihedral : 6.382 59.134 4009 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.68 % Rotamer: Outliers : 5.80 % Allowed : 26.52 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.40 (0.14), residues: 3538 helix: 0.49 (0.14), residues: 1420 sheet: -0.47 (0.24), residues: 484 loop : -0.79 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 70 TYR 0.031 0.001 TYR A 89 PHE 0.032 0.001 PHE L 326 TRP 0.036 0.001 TRP E 67 HIS 0.017 0.001 HIS E 9 Details of bonding type rmsd covalent geometry : bond 0.00240 (29303) covalent geometry : angle 0.59412 (39800) hydrogen bonds : bond 0.03290 ( 1146) hydrogen bonds : angle 5.10148 ( 3333) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 606 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7320 (mm) cc_final: 0.7053 (mm) REVERT: A 152 ILE cc_start: 0.1809 (OUTLIER) cc_final: 0.1540 (tt) REVERT: A 202 THR cc_start: 0.7171 (OUTLIER) cc_final: 0.6805 (t) REVERT: A 205 ASP cc_start: 0.7034 (t0) cc_final: 0.6642 (m-30) REVERT: A 277 VAL cc_start: 0.5755 (t) cc_final: 0.5527 (p) REVERT: B 135 MET cc_start: 0.3888 (tpt) cc_final: 0.3678 (tpp) REVERT: B 159 ILE cc_start: 0.5643 (OUTLIER) cc_final: 0.5365 (mp) REVERT: B 220 MET cc_start: 0.5326 (tpt) cc_final: 0.4837 (mmp) REVERT: B 241 THR cc_start: 0.7611 (p) cc_final: 0.6931 (t) REVERT: B 287 MET cc_start: 0.3377 (tmm) cc_final: 0.2913 (ttp) REVERT: C 11 MET cc_start: 0.6984 (mmt) cc_final: 0.6636 (ptp) REVERT: C 220 MET cc_start: 0.6418 (tpt) cc_final: 0.6125 (tpp) REVERT: C 233 SER cc_start: 0.6022 (p) cc_final: 0.5716 (p) REVERT: D 11 MET cc_start: 0.6560 (mpp) cc_final: 0.5464 (mpp) REVERT: D 82 PHE cc_start: 0.5750 (OUTLIER) cc_final: 0.5098 (t80) REVERT: D 220 MET cc_start: 0.5696 (mmm) cc_final: 0.4848 (mmm) REVERT: D 285 ILE cc_start: 0.7130 (pt) cc_final: 0.6759 (mp) REVERT: E 3 THR cc_start: 0.4559 (OUTLIER) cc_final: 0.4258 (t) REVERT: F 66 LEU cc_start: 0.7223 (tp) cc_final: 0.6923 (pp) REVERT: F 220 MET cc_start: 0.5929 (mmp) cc_final: 0.5606 (mmp) REVERT: G 333 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7796 (tm-30) REVERT: G 422 LYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6506 (ptmt) REVERT: G 456 VAL cc_start: 0.3345 (OUTLIER) cc_final: 0.2473 (p) REVERT: G 491 PHE cc_start: 0.5619 (OUTLIER) cc_final: 0.4969 (m-10) REVERT: G 637 ASP cc_start: 0.7958 (t70) cc_final: 0.6889 (t70) REVERT: G 638 MET cc_start: 0.7873 (ppp) cc_final: 0.7578 (ppp) REVERT: G 639 GLN cc_start: 0.8019 (pm20) cc_final: 0.6281 (pm20) REVERT: G 640 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6675 (pm20) REVERT: H 319 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7348 (tp) REVERT: H 337 ARG cc_start: 0.7288 (mmm160) cc_final: 0.6965 (mmm160) REVERT: H 415 ARG cc_start: 0.7398 (ptm160) cc_final: 0.7183 (ptm-80) REVERT: H 438 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.7019 (ptp) REVERT: H 474 ILE cc_start: 0.8444 (tt) cc_final: 0.8152 (tt) REVERT: H 477 TYR cc_start: 0.7962 (m-80) cc_final: 0.7375 (m-80) REVERT: H 540 ILE cc_start: 0.6878 (mm) cc_final: 0.6537 (mt) REVERT: H 553 ASN cc_start: 0.5119 (t0) cc_final: 0.4691 (t0) REVERT: I 351 ASP cc_start: 0.7193 (p0) cc_final: 0.6953 (p0) REVERT: I 385 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7809 (p) REVERT: I 446 GLU cc_start: 0.2936 (OUTLIER) cc_final: -0.1184 (pt0) REVERT: I 461 TRP cc_start: 0.4487 (p-90) cc_final: 0.3864 (p-90) REVERT: I 477 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.6487 (m-80) REVERT: I 623 ILE cc_start: 0.6627 (mm) cc_final: 0.6421 (mm) REVERT: I 633 GLU cc_start: 0.5946 (pp20) cc_final: 0.5283 (pp20) REVERT: I 639 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7240 (pm20) REVERT: J 324 ASN cc_start: 0.7744 (t0) cc_final: 0.7496 (t0) REVERT: J 453 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7823 (m) REVERT: J 477 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.6369 (t80) REVERT: K 417 ILE cc_start: 0.8156 (mt) cc_final: 0.7880 (tt) REVERT: K 423 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: K 461 TRP cc_start: 0.5540 (m100) cc_final: 0.4912 (t-100) REVERT: K 549 ARG cc_start: 0.7554 (ptp-170) cc_final: 0.7300 (mtt180) REVERT: K 624 ARG cc_start: 0.7577 (mtm180) cc_final: 0.7314 (mtm110) REVERT: L 422 LYS cc_start: 0.7572 (ptmt) cc_final: 0.7277 (ptmm) REVERT: L 423 TYR cc_start: 0.8270 (m-10) cc_final: 0.7436 (m-80) REVERT: L 470 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8322 (tp) REVERT: L 477 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6144 (m-80) REVERT: L 479 GLU cc_start: 0.5509 (OUTLIER) cc_final: 0.4841 (tm-30) REVERT: L 480 LYS cc_start: 0.6928 (pptt) cc_final: 0.6449 (tmmt) REVERT: L 591 ARG cc_start: 0.6273 (ttt180) cc_final: 0.5994 (ttt-90) outliers start: 176 outliers final: 112 residues processed: 717 average time/residue: 0.1902 time to fit residues: 214.3520 Evaluate side-chains 730 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 597 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 119 TRP Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 67 TRP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 422 LYS Chi-restraints excluded: chain G residue 449 SER Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 461 TRP Chi-restraints excluded: chain G residue 477 TYR Chi-restraints excluded: chain G residue 486 THR Chi-restraints excluded: chain G residue 491 PHE Chi-restraints excluded: chain G residue 494 MET Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 551 ILE Chi-restraints excluded: chain G residue 571 GLU Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 640 GLU Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 423 TYR Chi-restraints excluded: chain H residue 438 MET Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 461 TRP Chi-restraints excluded: chain H residue 494 MET Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain H residue 602 VAL Chi-restraints excluded: chain H residue 627 HIS Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 446 GLU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 465 VAL Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 477 TYR Chi-restraints excluded: chain I residue 534 LYS Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 585 PHE Chi-restraints excluded: chain I residue 602 VAL Chi-restraints excluded: chain I residue 639 GLN Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 444 PHE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 465 VAL Chi-restraints excluded: chain J residue 470 LEU Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain J residue 484 GLN Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 539 ASP Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 577 LEU Chi-restraints excluded: chain J residue 584 SER Chi-restraints excluded: chain K residue 346 LEU Chi-restraints excluded: chain K residue 356 PHE Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 423 TYR Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 THR Chi-restraints excluded: chain K residue 540 ILE Chi-restraints excluded: chain K residue 563 ILE Chi-restraints excluded: chain K residue 564 ASN Chi-restraints excluded: chain K residue 603 VAL Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 336 LEU Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 432 THR Chi-restraints excluded: chain L residue 453 VAL Chi-restraints excluded: chain L residue 470 LEU Chi-restraints excluded: chain L residue 477 TYR Chi-restraints excluded: chain L residue 479 GLU Chi-restraints excluded: chain L residue 486 THR Chi-restraints excluded: chain L residue 523 SER Chi-restraints excluded: chain L residue 538 THR Chi-restraints excluded: chain L residue 557 ARG Chi-restraints excluded: chain L residue 627 HIS Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 649 PHE Chi-restraints excluded: chain L residue 653 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 324 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 326 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 191 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 241 optimal weight: 0.9990 chunk 140 optimal weight: 20.0000 chunk 290 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS E 9 HIS E 64 HIS ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 372 HIS ** I 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 ASN L 492 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.244590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.201723 restraints weight = 52001.509| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 3.83 r_work: 0.4273 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 29303 Z= 0.174 Angle : 0.652 12.225 39800 Z= 0.327 Chirality : 0.045 0.233 4401 Planarity : 0.004 0.065 5147 Dihedral : 6.358 57.358 4001 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 6.73 % Allowed : 26.19 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.57 (0.14), residues: 3538 helix: 0.34 (0.14), residues: 1414 sheet: -0.55 (0.25), residues: 456 loop : -0.87 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 337 TYR 0.026 0.001 TYR I 423 PHE 0.029 0.002 PHE L 326 TRP 0.042 0.002 TRP E 67 HIS 0.012 0.001 HIS E 9 Details of bonding type rmsd covalent geometry : bond 0.00394 (29303) covalent geometry : angle 0.65225 (39800) hydrogen bonds : bond 0.03801 ( 1146) hydrogen bonds : angle 5.08890 ( 3333) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 630 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7325 (mm) cc_final: 0.7002 (mm) REVERT: A 152 ILE cc_start: 0.2072 (OUTLIER) cc_final: 0.1825 (tt) REVERT: A 202 THR cc_start: 0.7147 (OUTLIER) cc_final: 0.6783 (t) REVERT: A 205 ASP cc_start: 0.7073 (t0) cc_final: 0.6673 (m-30) REVERT: A 226 ASP cc_start: 0.5232 (OUTLIER) cc_final: 0.4919 (t70) REVERT: A 277 VAL cc_start: 0.5945 (t) cc_final: 0.5719 (p) REVERT: B 159 ILE cc_start: 0.5598 (OUTLIER) cc_final: 0.5351 (mp) REVERT: B 220 MET cc_start: 0.5377 (tpt) cc_final: 0.4872 (mmp) REVERT: B 287 MET cc_start: 0.3448 (tmm) cc_final: 0.1754 (tmm) REVERT: B 291 GLN cc_start: 0.7185 (pp30) cc_final: 0.6422 (pp30) REVERT: C 11 MET cc_start: 0.6942 (mmt) cc_final: 0.6634 (ptp) REVERT: C 161 LEU cc_start: 0.2633 (OUTLIER) cc_final: 0.1668 (tp) REVERT: C 233 SER cc_start: 0.6256 (p) cc_final: 0.5938 (p) REVERT: D 11 MET cc_start: 0.6522 (mpp) cc_final: 0.5449 (mpp) REVERT: D 82 PHE cc_start: 0.6255 (OUTLIER) cc_final: 0.5322 (t80) REVERT: D 220 MET cc_start: 0.5827 (mmm) cc_final: 0.5030 (mmm) REVERT: E 3 THR cc_start: 0.4189 (OUTLIER) cc_final: 0.3862 (t) REVERT: E 57 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6735 (t80) REVERT: E 92 ILE cc_start: 0.2407 (OUTLIER) cc_final: 0.2148 (mp) REVERT: F 32 HIS cc_start: 0.3915 (m170) cc_final: 0.3154 (m170) REVERT: F 161 LEU cc_start: 0.2422 (OUTLIER) cc_final: 0.2063 (tt) REVERT: F 220 MET cc_start: 0.5839 (mmp) cc_final: 0.5531 (mmp) REVERT: G 317 ARG cc_start: 0.4960 (mtp180) cc_final: 0.4719 (mtp180) REVERT: G 333 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7489 (tm-30) REVERT: G 422 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7124 (ptmt) REVERT: G 456 VAL cc_start: 0.3574 (OUTLIER) cc_final: 0.3179 (m) REVERT: G 491 PHE cc_start: 0.6414 (OUTLIER) cc_final: 0.5870 (m-10) REVERT: G 536 CYS cc_start: 0.7789 (p) cc_final: 0.7578 (p) REVERT: G 625 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7554 (m-40) REVERT: G 637 ASP cc_start: 0.8107 (t70) cc_final: 0.6975 (t70) REVERT: G 638 MET cc_start: 0.7985 (ppp) cc_final: 0.7724 (ppp) REVERT: G 639 GLN cc_start: 0.8078 (pm20) cc_final: 0.6573 (pm20) REVERT: G 640 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6745 (pm20) REVERT: H 337 ARG cc_start: 0.7463 (mmm160) cc_final: 0.7132 (mmm160) REVERT: H 415 ARG cc_start: 0.7740 (ptm160) cc_final: 0.7454 (ptm-80) REVERT: H 474 ILE cc_start: 0.8542 (tt) cc_final: 0.8250 (tt) REVERT: H 477 TYR cc_start: 0.8206 (m-80) cc_final: 0.7857 (m-80) REVERT: H 540 ILE cc_start: 0.7781 (mm) cc_final: 0.7279 (mt) REVERT: H 553 ASN cc_start: 0.6042 (t0) cc_final: 0.5809 (t0) REVERT: I 351 ASP cc_start: 0.7564 (p0) cc_final: 0.7346 (p0) REVERT: I 385 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.8043 (p) REVERT: I 407 GLU cc_start: 0.7796 (pp20) cc_final: 0.7430 (pp20) REVERT: I 446 GLU cc_start: 0.2818 (OUTLIER) cc_final: -0.0869 (pt0) REVERT: I 461 TRP cc_start: 0.5219 (p-90) cc_final: 0.3278 (p-90) REVERT: I 477 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7570 (m-80) REVERT: I 623 ILE cc_start: 0.7337 (mm) cc_final: 0.6880 (mt) REVERT: I 633 GLU cc_start: 0.6452 (pp20) cc_final: 0.5785 (pp20) REVERT: I 637 ASP cc_start: 0.7501 (t0) cc_final: 0.7108 (t0) REVERT: I 639 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: J 324 ASN cc_start: 0.7802 (t0) cc_final: 0.7594 (t0) REVERT: J 329 ASN cc_start: 0.8342 (t0) cc_final: 0.8094 (t0) REVERT: J 337 ARG cc_start: 0.7656 (mtp180) cc_final: 0.7450 (mtp180) REVERT: J 477 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.6477 (t80) REVERT: J 632 TRP cc_start: 0.7773 (t60) cc_final: 0.7264 (t60) REVERT: K 353 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7463 (tp) REVERT: K 355 ARG cc_start: 0.7290 (ttp80) cc_final: 0.6574 (ttp80) REVERT: K 461 TRP cc_start: 0.5864 (m100) cc_final: 0.4681 (t-100) REVERT: K 464 SER cc_start: 0.8542 (p) cc_final: 0.8269 (p) REVERT: K 477 TYR cc_start: 0.7897 (m-80) cc_final: 0.7508 (m-80) REVERT: K 514 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7187 (tm130) REVERT: K 549 ARG cc_start: 0.7914 (ptp-170) cc_final: 0.7593 (mtt180) REVERT: K 597 PHE cc_start: 0.7964 (t80) cc_final: 0.7487 (t80) REVERT: K 624 ARG cc_start: 0.7741 (mtm180) cc_final: 0.7489 (mtm110) REVERT: K 649 PHE cc_start: 0.6198 (OUTLIER) cc_final: 0.5925 (m-80) REVERT: L 382 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7149 (tttt) REVERT: L 422 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7435 (ptmm) REVERT: L 423 TYR cc_start: 0.8584 (m-10) cc_final: 0.7858 (m-80) REVERT: L 477 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.7001 (m-80) REVERT: L 479 GLU cc_start: 0.5506 (OUTLIER) cc_final: 0.5107 (tm-30) REVERT: L 480 LYS cc_start: 0.7071 (pptt) cc_final: 0.6736 (tmmt) REVERT: L 574 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8627 (tp) outliers start: 204 outliers final: 121 residues processed: 751 average time/residue: 0.1992 time to fit residues: 234.1642 Evaluate side-chains 756 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 607 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 67 TRP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 HIS Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 422 LYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 461 TRP Chi-restraints excluded: chain G residue 477 TYR Chi-restraints excluded: chain G residue 486 THR Chi-restraints excluded: chain G residue 491 PHE Chi-restraints excluded: chain G residue 494 MET Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 551 ILE Chi-restraints excluded: chain G residue 557 ARG Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 625 ASN Chi-restraints excluded: chain G residue 640 GLU Chi-restraints excluded: chain G residue 641 THR Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 423 TYR Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 461 TRP Chi-restraints excluded: chain H residue 494 MET Chi-restraints excluded: chain H residue 523 SER Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain H residue 558 CYS Chi-restraints excluded: chain H residue 577 LEU Chi-restraints excluded: chain H residue 627 HIS Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 446 GLU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 465 VAL Chi-restraints excluded: chain I residue 477 TYR Chi-restraints excluded: chain I residue 534 LYS Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 585 PHE Chi-restraints excluded: chain I residue 602 VAL Chi-restraints excluded: chain I residue 639 GLN Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 368 ASP Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 444 PHE Chi-restraints excluded: chain J residue 465 VAL Chi-restraints excluded: chain J residue 470 LEU Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain J residue 484 GLN Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 584 SER Chi-restraints excluded: chain J residue 624 ARG Chi-restraints excluded: chain K residue 346 LEU Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 385 VAL Chi-restraints excluded: chain K residue 439 CYS Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 THR Chi-restraints excluded: chain K residue 514 GLN Chi-restraints excluded: chain K residue 540 ILE Chi-restraints excluded: chain K residue 603 VAL Chi-restraints excluded: chain K residue 649 PHE Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 382 LYS Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 422 LYS Chi-restraints excluded: chain L residue 432 THR Chi-restraints excluded: chain L residue 438 MET Chi-restraints excluded: chain L residue 453 VAL Chi-restraints excluded: chain L residue 477 TYR Chi-restraints excluded: chain L residue 479 GLU Chi-restraints excluded: chain L residue 486 THR Chi-restraints excluded: chain L residue 499 ASP Chi-restraints excluded: chain L residue 523 SER Chi-restraints excluded: chain L residue 557 ARG Chi-restraints excluded: chain L residue 574 ILE Chi-restraints excluded: chain L residue 627 HIS Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 649 PHE Chi-restraints excluded: chain L residue 653 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 167 optimal weight: 0.2980 chunk 256 optimal weight: 5.9990 chunk 270 optimal weight: 0.6980 chunk 332 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 HIS ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN ** C 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS E 9 HIS E 86 HIS E 94 GLN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN H 556 ASN ** H 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 HIS I 340 HIS ** I 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 324 ASN J 450 ASN ** J 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 ASN ** L 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.237702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.194041 restraints weight = 51360.427| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 4.12 r_work: 0.4139 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 29303 Z= 0.243 Angle : 0.750 13.872 39800 Z= 0.383 Chirality : 0.049 0.272 4401 Planarity : 0.005 0.058 5147 Dihedral : 6.705 59.189 3992 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 7.03 % Allowed : 26.78 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3538 helix: -0.06 (0.14), residues: 1416 sheet: -0.89 (0.25), residues: 431 loop : -1.08 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 355 TYR 0.026 0.002 TYR I 463 PHE 0.035 0.002 PHE G 444 TRP 0.043 0.003 TRP K 375 HIS 0.018 0.002 HIS E 9 Details of bonding type rmsd covalent geometry : bond 0.00544 (29303) covalent geometry : angle 0.75021 (39800) hydrogen bonds : bond 0.04596 ( 1146) hydrogen bonds : angle 5.26436 ( 3333) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 697 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7284 (mm) cc_final: 0.6885 (mm) REVERT: A 56 VAL cc_start: 0.3679 (OUTLIER) cc_final: 0.2938 (t) REVERT: A 79 ILE cc_start: 0.1060 (mp) cc_final: 0.0802 (mt) REVERT: A 220 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.5857 (tpp) REVERT: B 159 ILE cc_start: 0.5730 (OUTLIER) cc_final: 0.5509 (mp) REVERT: B 276 ILE cc_start: 0.4519 (OUTLIER) cc_final: 0.4266 (tt) REVERT: B 285 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6470 (mp) REVERT: B 287 MET cc_start: 0.3713 (tmm) cc_final: 0.3329 (ttp) REVERT: C 11 MET cc_start: 0.6942 (mmt) cc_final: 0.6648 (ptp) REVERT: C 161 LEU cc_start: 0.2421 (OUTLIER) cc_final: 0.2160 (tp) REVERT: C 233 SER cc_start: 0.6189 (p) cc_final: 0.5856 (p) REVERT: D 11 MET cc_start: 0.6488 (mpp) cc_final: 0.5386 (mpp) REVERT: D 82 PHE cc_start: 0.6583 (OUTLIER) cc_final: 0.5556 (t80) REVERT: D 220 MET cc_start: 0.5694 (mmm) cc_final: 0.4990 (mmm) REVERT: E 3 THR cc_start: 0.4717 (OUTLIER) cc_final: 0.4427 (t) REVERT: E 20 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.5919 (pp) REVERT: F 66 LEU cc_start: 0.7166 (tp) cc_final: 0.6764 (pp) REVERT: F 220 MET cc_start: 0.6031 (mmp) cc_final: 0.5747 (mmp) REVERT: G 438 MET cc_start: 0.7768 (pmm) cc_final: 0.7496 (pmm) REVERT: G 456 VAL cc_start: 0.3364 (OUTLIER) cc_final: 0.2959 (m) REVERT: G 461 TRP cc_start: 0.7540 (OUTLIER) cc_final: 0.7154 (m100) REVERT: G 491 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7310 (m-10) REVERT: G 514 GLN cc_start: 0.7902 (mt0) cc_final: 0.7326 (mt0) REVERT: G 534 LYS cc_start: 0.7066 (mmmt) cc_final: 0.6659 (mmmt) REVERT: G 536 CYS cc_start: 0.7910 (p) cc_final: 0.7591 (p) REVERT: G 537 PHE cc_start: 0.7077 (m-10) cc_final: 0.6555 (m-10) REVERT: G 541 ARG cc_start: 0.8530 (mpt-90) cc_final: 0.8314 (mtm-85) REVERT: G 637 ASP cc_start: 0.8367 (t70) cc_final: 0.7766 (t70) REVERT: G 639 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: H 326 PHE cc_start: 0.7378 (t80) cc_final: 0.6995 (t80) REVERT: H 336 LEU cc_start: 0.8355 (mt) cc_final: 0.7774 (mm) REVERT: H 337 ARG cc_start: 0.7729 (mmm160) cc_final: 0.7405 (mmm160) REVERT: H 415 ARG cc_start: 0.7810 (ptm160) cc_final: 0.7555 (ptm-80) REVERT: H 424 ARG cc_start: 0.7153 (tpm170) cc_final: 0.6814 (tpm170) REVERT: H 461 TRP cc_start: 0.7853 (OUTLIER) cc_final: 0.5482 (m-10) REVERT: H 463 TYR cc_start: 0.7852 (t80) cc_final: 0.7261 (t80) REVERT: H 472 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8553 (mtt-85) REVERT: H 474 ILE cc_start: 0.8597 (tt) cc_final: 0.8293 (tt) REVERT: H 477 TYR cc_start: 0.8309 (m-80) cc_final: 0.7886 (m-80) REVERT: H 526 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.6102 (mtmt) REVERT: H 558 CYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8198 (m) REVERT: H 624 ARG cc_start: 0.7886 (mtm110) cc_final: 0.7681 (mtm110) REVERT: I 355 ARG cc_start: 0.7930 (tmm160) cc_final: 0.7632 (tmm160) REVERT: I 407 GLU cc_start: 0.7960 (pp20) cc_final: 0.7618 (pp20) REVERT: I 446 GLU cc_start: 0.3102 (OUTLIER) cc_final: -0.0432 (pt0) REVERT: I 461 TRP cc_start: 0.5804 (p-90) cc_final: 0.2857 (p-90) REVERT: I 471 ASP cc_start: 0.8480 (t0) cc_final: 0.8268 (t0) REVERT: I 477 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7780 (m-80) REVERT: I 563 ILE cc_start: 0.8741 (mp) cc_final: 0.8517 (mt) REVERT: I 633 GLU cc_start: 0.7225 (pp20) cc_final: 0.6684 (pp20) REVERT: I 637 ASP cc_start: 0.7802 (t0) cc_final: 0.7218 (t0) REVERT: I 638 MET cc_start: 0.7998 (tmm) cc_final: 0.7428 (tpp) REVERT: I 639 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: J 323 VAL cc_start: 0.8943 (p) cc_final: 0.8714 (t) REVERT: J 324 ASN cc_start: 0.7796 (t160) cc_final: 0.7565 (t0) REVERT: J 355 ARG cc_start: 0.8070 (mmp80) cc_final: 0.7609 (mmp80) REVERT: J 365 VAL cc_start: 0.6816 (OUTLIER) cc_final: 0.6538 (p) REVERT: J 477 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.6530 (t80) REVERT: J 553 ASN cc_start: 0.7029 (t0) cc_final: 0.6721 (t0) REVERT: J 577 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7509 (tt) REVERT: J 624 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7868 (mtm110) REVERT: J 632 TRP cc_start: 0.8264 (t60) cc_final: 0.7413 (t60) REVERT: K 355 ARG cc_start: 0.7586 (ttp80) cc_final: 0.7384 (ttp80) REVERT: K 356 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6939 (m-10) REVERT: K 403 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7169 (mp) REVERT: K 415 ARG cc_start: 0.7804 (ptm-80) cc_final: 0.7567 (ptm-80) REVERT: K 461 TRP cc_start: 0.5321 (m100) cc_final: 0.4395 (t-100) REVERT: K 477 TYR cc_start: 0.8053 (m-80) cc_final: 0.7231 (m-80) REVERT: K 514 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7305 (tm130) REVERT: K 549 ARG cc_start: 0.8177 (ptp-170) cc_final: 0.7831 (mtt180) REVERT: K 565 ILE cc_start: 0.8312 (mp) cc_final: 0.8073 (mp) REVERT: K 597 PHE cc_start: 0.8127 (t80) cc_final: 0.7773 (t80) REVERT: K 624 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7702 (mtm110) REVERT: K 628 ARG cc_start: 0.8164 (tmm-80) cc_final: 0.7759 (mtm110) REVERT: K 649 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.6328 (m-10) REVERT: L 382 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7277 (tttt) REVERT: L 422 LYS cc_start: 0.7771 (ptmt) cc_final: 0.7457 (ptmm) REVERT: L 423 TYR cc_start: 0.8676 (m-10) cc_final: 0.7970 (m-80) REVERT: L 480 LYS cc_start: 0.7514 (pptt) cc_final: 0.7005 (ttpp) outliers start: 213 outliers final: 121 residues processed: 817 average time/residue: 0.2058 time to fit residues: 258.7735 Evaluate side-chains 813 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 663 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 67 TRP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 461 TRP Chi-restraints excluded: chain G residue 477 TYR Chi-restraints excluded: chain G residue 486 THR Chi-restraints excluded: chain G residue 491 PHE Chi-restraints excluded: chain G residue 494 MET Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 551 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 639 GLN Chi-restraints excluded: chain G residue 641 THR Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 438 MET Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 461 TRP Chi-restraints excluded: chain H residue 472 ARG Chi-restraints excluded: chain H residue 526 LYS Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain H residue 558 CYS Chi-restraints excluded: chain H residue 636 ILE Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 446 GLU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 465 VAL Chi-restraints excluded: chain I residue 477 TYR Chi-restraints excluded: chain I residue 551 ILE Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 585 PHE Chi-restraints excluded: chain I residue 602 VAL Chi-restraints excluded: chain I residue 639 GLN Chi-restraints excluded: chain J residue 343 VAL Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 368 ASP Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 444 PHE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 464 SER Chi-restraints excluded: chain J residue 465 VAL Chi-restraints excluded: chain J residue 470 LEU Chi-restraints excluded: chain J residue 474 ILE Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 577 LEU Chi-restraints excluded: chain J residue 584 SER Chi-restraints excluded: chain J residue 624 ARG Chi-restraints excluded: chain J residue 641 THR Chi-restraints excluded: chain K residue 346 LEU Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 356 PHE Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 385 VAL Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 403 LEU Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 439 CYS Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 486 THR Chi-restraints excluded: chain K residue 514 GLN Chi-restraints excluded: chain K residue 551 ILE Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain K residue 603 VAL Chi-restraints excluded: chain K residue 649 PHE Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 382 LYS Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 438 MET Chi-restraints excluded: chain L residue 439 CYS Chi-restraints excluded: chain L residue 453 VAL Chi-restraints excluded: chain L residue 486 THR Chi-restraints excluded: chain L residue 499 ASP Chi-restraints excluded: chain L residue 523 SER Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain L residue 557 ARG Chi-restraints excluded: chain L residue 597 PHE Chi-restraints excluded: chain L residue 627 HIS Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 653 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 150 optimal weight: 4.9990 chunk 159 optimal weight: 0.0050 chunk 289 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 286 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 272 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 overall best weight: 2.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS A 167 HIS ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 HIS D 133 HIS D 288 GLN ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 GLN ** H 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 324 ASN I 340 HIS ** I 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 450 ASN ** J 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 468 GLN L 324 ASN ** L 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.235395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.190569 restraints weight = 50422.955| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 3.90 r_work: 0.4137 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 29303 Z= 0.205 Angle : 0.730 14.927 39800 Z= 0.367 Chirality : 0.048 0.267 4401 Planarity : 0.005 0.078 5147 Dihedral : 6.429 59.266 3978 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.66 % Rotamer: Outliers : 5.87 % Allowed : 28.30 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 3538 helix: -0.08 (0.14), residues: 1423 sheet: -1.11 (0.25), residues: 447 loop : -1.19 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 355 TYR 0.024 0.002 TYR H 378 PHE 0.037 0.002 PHE G 444 TRP 0.044 0.003 TRP E 67 HIS 0.028 0.001 HIS K 379 Details of bonding type rmsd covalent geometry : bond 0.00467 (29303) covalent geometry : angle 0.73041 (39800) hydrogen bonds : bond 0.04128 ( 1146) hydrogen bonds : angle 5.16997 ( 3333) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 682 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7338 (mm) cc_final: 0.6913 (mm) REVERT: A 220 MET cc_start: 0.6198 (OUTLIER) cc_final: 0.5689 (tpp) REVERT: A 287 MET cc_start: 0.0371 (tpt) cc_final: 0.0097 (tpt) REVERT: B 159 ILE cc_start: 0.5736 (OUTLIER) cc_final: 0.5510 (mp) REVERT: B 220 MET cc_start: 0.5420 (tpt) cc_final: 0.4922 (mmp) REVERT: B 287 MET cc_start: 0.3866 (tmm) cc_final: 0.2293 (tmm) REVERT: B 291 GLN cc_start: 0.7191 (pp30) cc_final: 0.6640 (pp30) REVERT: C 11 MET cc_start: 0.7191 (mmt) cc_final: 0.6832 (ptp) REVERT: C 161 LEU cc_start: 0.2667 (OUTLIER) cc_final: 0.2289 (tp) REVERT: C 233 SER cc_start: 0.6330 (p) cc_final: 0.6031 (p) REVERT: D 11 MET cc_start: 0.6498 (mpp) cc_final: 0.5376 (mpp) REVERT: D 82 PHE cc_start: 0.6248 (OUTLIER) cc_final: 0.5332 (t80) REVERT: D 220 MET cc_start: 0.5871 (mmm) cc_final: 0.5174 (mmm) REVERT: D 222 ARG cc_start: 0.4357 (OUTLIER) cc_final: 0.3587 (mtt-85) REVERT: E 3 THR cc_start: 0.4817 (OUTLIER) cc_final: 0.4595 (t) REVERT: E 20 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.5825 (pp) REVERT: E 57 TYR cc_start: 0.7018 (t80) cc_final: 0.6815 (t80) REVERT: F 220 MET cc_start: 0.5904 (mmp) cc_final: 0.5600 (mmp) REVERT: F 298 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.5922 (mm) REVERT: G 456 VAL cc_start: 0.3306 (OUTLIER) cc_final: 0.2919 (m) REVERT: G 514 GLN cc_start: 0.7872 (mt0) cc_final: 0.7271 (mt0) REVERT: G 536 CYS cc_start: 0.7849 (p) cc_final: 0.7537 (p) REVERT: G 537 PHE cc_start: 0.7090 (m-10) cc_final: 0.6614 (m-10) REVERT: G 567 ASN cc_start: 0.7981 (p0) cc_final: 0.7659 (p0) REVERT: G 637 ASP cc_start: 0.8474 (t70) cc_final: 0.8080 (t70) REVERT: G 639 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7049 (pm20) REVERT: H 326 PHE cc_start: 0.7383 (t80) cc_final: 0.7039 (t80) REVERT: H 336 LEU cc_start: 0.8331 (mt) cc_final: 0.7666 (mm) REVERT: H 337 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7295 (mmm160) REVERT: H 415 ARG cc_start: 0.7860 (ptm160) cc_final: 0.7612 (ptm-80) REVERT: H 461 TRP cc_start: 0.7992 (OUTLIER) cc_final: 0.6635 (m-10) REVERT: H 472 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8383 (mtt-85) REVERT: H 474 ILE cc_start: 0.8571 (tt) cc_final: 0.8242 (tt) REVERT: H 480 LYS cc_start: 0.7640 (mmtm) cc_final: 0.7305 (tppt) REVERT: H 638 MET cc_start: 0.7987 (tmm) cc_final: 0.7302 (tmm) REVERT: I 356 PHE cc_start: 0.7792 (m-80) cc_final: 0.7330 (m-80) REVERT: I 407 GLU cc_start: 0.7989 (pp20) cc_final: 0.7671 (pp20) REVERT: I 423 TYR cc_start: 0.6062 (m-80) cc_final: 0.5798 (m-80) REVERT: I 446 GLU cc_start: 0.3365 (OUTLIER) cc_final: -0.0413 (pt0) REVERT: I 456 VAL cc_start: 0.1466 (OUTLIER) cc_final: -0.0266 (m) REVERT: I 461 TRP cc_start: 0.5599 (p-90) cc_final: 0.3057 (p-90) REVERT: I 472 ARG cc_start: 0.8533 (mtt-85) cc_final: 0.7947 (mtt90) REVERT: I 477 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: I 561 GLU cc_start: 0.7659 (tt0) cc_final: 0.7314 (tt0) REVERT: I 563 ILE cc_start: 0.8787 (mp) cc_final: 0.8565 (mt) REVERT: I 633 GLU cc_start: 0.7240 (pp20) cc_final: 0.6810 (pm20) REVERT: I 639 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7459 (pm20) REVERT: J 323 VAL cc_start: 0.9003 (p) cc_final: 0.8718 (t) REVERT: J 365 VAL cc_start: 0.6777 (OUTLIER) cc_final: 0.6485 (p) REVERT: J 415 ARG cc_start: 0.7689 (ptm160) cc_final: 0.7469 (ptm-80) REVERT: J 460 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7847 (ttp80) REVERT: J 477 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.6495 (t80) REVERT: J 479 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7439 (tm-30) REVERT: J 480 LYS cc_start: 0.8353 (mmmt) cc_final: 0.7823 (tppt) REVERT: J 481 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6899 (tp30) REVERT: J 534 LYS cc_start: 0.7774 (mtmm) cc_final: 0.7540 (mtmt) REVERT: J 624 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7741 (mtm110) REVERT: K 355 ARG cc_start: 0.7442 (ttp80) cc_final: 0.7226 (ttp80) REVERT: K 461 TRP cc_start: 0.5176 (m100) cc_final: 0.4354 (t-100) REVERT: K 477 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: K 514 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7295 (tm130) REVERT: K 548 TYR cc_start: 0.8571 (t80) cc_final: 0.8039 (t80) REVERT: K 549 ARG cc_start: 0.8178 (ptp-170) cc_final: 0.7827 (mtt180) REVERT: K 556 ASN cc_start: 0.8011 (t0) cc_final: 0.7555 (t0) REVERT: K 561 GLU cc_start: 0.7722 (tt0) cc_final: 0.7461 (tt0) REVERT: K 628 ARG cc_start: 0.8185 (tmm-80) cc_final: 0.7917 (ptm-80) REVERT: K 633 GLU cc_start: 0.6982 (pm20) cc_final: 0.6749 (pp20) REVERT: K 635 LYS cc_start: 0.7592 (mmtm) cc_final: 0.7291 (mmtm) REVERT: L 382 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7262 (tttt) REVERT: L 422 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7415 (ptmm) REVERT: L 423 TYR cc_start: 0.8572 (m-10) cc_final: 0.7833 (m-80) REVERT: L 477 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7225 (m-80) REVERT: L 480 LYS cc_start: 0.7587 (pptt) cc_final: 0.7259 (ttpp) REVERT: L 638 MET cc_start: 0.7992 (tmm) cc_final: 0.7721 (tpp) outliers start: 178 outliers final: 122 residues processed: 784 average time/residue: 0.2043 time to fit residues: 246.8016 Evaluate side-chains 798 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 652 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 67 TRP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 HIS Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 341 TYR Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 477 TYR Chi-restraints excluded: chain G residue 486 THR Chi-restraints excluded: chain G residue 491 PHE Chi-restraints excluded: chain G residue 494 MET Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 551 ILE Chi-restraints excluded: chain G residue 557 ARG Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 639 GLN Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 355 ARG Chi-restraints excluded: chain H residue 356 PHE Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 423 TYR Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 461 TRP Chi-restraints excluded: chain H residue 472 ARG Chi-restraints excluded: chain H residue 499 ASP Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 340 HIS Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 446 GLU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 465 VAL Chi-restraints excluded: chain I residue 477 TYR Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 585 PHE Chi-restraints excluded: chain I residue 602 VAL Chi-restraints excluded: chain I residue 639 GLN Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 444 PHE Chi-restraints excluded: chain J residue 458 LYS Chi-restraints excluded: chain J residue 465 VAL Chi-restraints excluded: chain J residue 470 LEU Chi-restraints excluded: chain J residue 474 ILE Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 584 SER Chi-restraints excluded: chain J residue 624 ARG Chi-restraints excluded: chain J residue 638 MET Chi-restraints excluded: chain J residue 641 THR Chi-restraints excluded: chain K residue 346 LEU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 385 VAL Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 468 GLN Chi-restraints excluded: chain K residue 477 TYR Chi-restraints excluded: chain K residue 486 THR Chi-restraints excluded: chain K residue 514 GLN Chi-restraints excluded: chain K residue 603 VAL Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 382 LYS Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 407 GLU Chi-restraints excluded: chain L residue 422 LYS Chi-restraints excluded: chain L residue 434 GLU Chi-restraints excluded: chain L residue 439 CYS Chi-restraints excluded: chain L residue 477 TYR Chi-restraints excluded: chain L residue 486 THR Chi-restraints excluded: chain L residue 499 ASP Chi-restraints excluded: chain L residue 516 ILE Chi-restraints excluded: chain L residue 523 SER Chi-restraints excluded: chain L residue 557 ARG Chi-restraints excluded: chain L residue 574 ILE Chi-restraints excluded: chain L residue 597 PHE Chi-restraints excluded: chain L residue 627 HIS Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 653 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 140 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 340 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 chunk 321 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 313 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 chunk 214 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 133 HIS A 163 HIS B 73 GLN ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 ASN G 492 ASN ** G 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 457 ASN ** H 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 HIS ** I 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 484 GLN K 324 ASN ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 ASN L 330 HIS L 448 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.237216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.193239 restraints weight = 50981.686| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 3.74 r_work: 0.4194 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29303 Z= 0.133 Angle : 0.698 13.049 39800 Z= 0.344 Chirality : 0.045 0.245 4401 Planarity : 0.005 0.069 5147 Dihedral : 6.166 59.569 3975 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 4.85 % Allowed : 30.41 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 3538 helix: 0.03 (0.14), residues: 1433 sheet: -0.95 (0.25), residues: 443 loop : -1.10 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 549 TYR 0.025 0.001 TYR G 548 PHE 0.043 0.002 PHE L 326 TRP 0.052 0.002 TRP K 375 HIS 0.028 0.001 HIS I 340 Details of bonding type rmsd covalent geometry : bond 0.00305 (29303) covalent geometry : angle 0.69754 (39800) hydrogen bonds : bond 0.03611 ( 1146) hydrogen bonds : angle 5.09255 ( 3333) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 655 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7341 (mm) cc_final: 0.6914 (mm) REVERT: A 135 MET cc_start: 0.5649 (mmm) cc_final: 0.4706 (tpt) REVERT: A 152 ILE cc_start: 0.2144 (OUTLIER) cc_final: 0.1879 (tt) REVERT: A 220 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.4895 (mmm) REVERT: B 159 ILE cc_start: 0.5708 (OUTLIER) cc_final: 0.5471 (mp) REVERT: B 220 MET cc_start: 0.5194 (tpt) cc_final: 0.4760 (mmp) REVERT: B 285 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6542 (mp) REVERT: B 287 MET cc_start: 0.3948 (tmm) cc_final: 0.3448 (ttp) REVERT: C 11 MET cc_start: 0.7185 (mmt) cc_final: 0.6855 (ptp) REVERT: C 161 LEU cc_start: 0.2353 (OUTLIER) cc_final: 0.2097 (tp) REVERT: C 233 SER cc_start: 0.6334 (p) cc_final: 0.6000 (p) REVERT: D 11 MET cc_start: 0.6425 (mpp) cc_final: 0.5244 (mpp) REVERT: D 57 TYR cc_start: 0.6707 (m-80) cc_final: 0.6452 (m-80) REVERT: D 82 PHE cc_start: 0.6050 (OUTLIER) cc_final: 0.5269 (t80) REVERT: D 220 MET cc_start: 0.5841 (mmm) cc_final: 0.5099 (mmm) REVERT: D 222 ARG cc_start: 0.4447 (OUTLIER) cc_final: 0.3499 (mtt-85) REVERT: E 287 MET cc_start: 0.2316 (tpt) cc_final: 0.1700 (tpp) REVERT: F 66 LEU cc_start: 0.7037 (tp) cc_final: 0.6590 (pp) REVERT: F 220 MET cc_start: 0.5867 (mmp) cc_final: 0.5551 (mmp) REVERT: F 298 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6332 (mm) REVERT: G 333 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7554 (tm-30) REVERT: G 456 VAL cc_start: 0.3172 (OUTLIER) cc_final: 0.2828 (m) REVERT: G 514 GLN cc_start: 0.7790 (mt0) cc_final: 0.7176 (mt0) REVERT: G 536 CYS cc_start: 0.7813 (p) cc_final: 0.7372 (p) REVERT: G 537 PHE cc_start: 0.6900 (m-10) cc_final: 0.6618 (m-10) REVERT: G 567 ASN cc_start: 0.8112 (p0) cc_final: 0.7677 (p0) REVERT: H 337 ARG cc_start: 0.7576 (mmm160) cc_final: 0.7165 (mmm160) REVERT: H 415 ARG cc_start: 0.7843 (ptm160) cc_final: 0.7607 (ptm-80) REVERT: H 461 TRP cc_start: 0.7871 (OUTLIER) cc_final: 0.6693 (m-10) REVERT: H 474 ILE cc_start: 0.8496 (tt) cc_final: 0.8167 (tt) REVERT: H 481 GLU cc_start: 0.6421 (mp0) cc_final: 0.6217 (mp0) REVERT: H 483 LEU cc_start: 0.7361 (tp) cc_final: 0.7097 (tp) REVERT: H 638 MET cc_start: 0.7738 (tmm) cc_final: 0.7378 (tmm) REVERT: I 407 GLU cc_start: 0.7960 (pp20) cc_final: 0.7674 (pp20) REVERT: I 446 GLU cc_start: 0.3422 (OUTLIER) cc_final: 0.0002 (pt0) REVERT: I 456 VAL cc_start: 0.0944 (OUTLIER) cc_final: -0.0457 (m) REVERT: I 461 TRP cc_start: 0.5352 (p-90) cc_final: 0.3362 (p-90) REVERT: I 472 ARG cc_start: 0.8374 (mtt-85) cc_final: 0.8107 (mtt90) REVERT: I 480 LYS cc_start: 0.8150 (tmmt) cc_final: 0.7672 (tppt) REVERT: I 541 ARG cc_start: 0.8641 (mtm-85) cc_final: 0.8435 (ttm110) REVERT: I 561 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: I 563 ILE cc_start: 0.8769 (mp) cc_final: 0.8511 (mt) REVERT: I 633 GLU cc_start: 0.7150 (pp20) cc_final: 0.6612 (pp20) REVERT: I 639 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7600 (pp30) REVERT: J 337 ARG cc_start: 0.7680 (mtp180) cc_final: 0.7392 (mtp180) REVERT: J 477 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.6428 (t80) REVERT: J 492 ASN cc_start: 0.8235 (m-40) cc_final: 0.7906 (m-40) REVERT: J 644 GLU cc_start: 0.6537 (pp20) cc_final: 0.6148 (pp20) REVERT: K 477 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: K 548 TYR cc_start: 0.8414 (t80) cc_final: 0.7985 (t80) REVERT: K 549 ARG cc_start: 0.8035 (ptp-170) cc_final: 0.7659 (mtt180) REVERT: L 423 TYR cc_start: 0.8415 (m-10) cc_final: 0.7472 (m-80) REVERT: L 477 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.6825 (m-80) outliers start: 147 outliers final: 104 residues processed: 740 average time/residue: 0.2038 time to fit residues: 232.1335 Evaluate side-chains 750 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 629 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 82 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 67 TRP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 341 TYR Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 477 TYR Chi-restraints excluded: chain G residue 486 THR Chi-restraints excluded: chain G residue 491 PHE Chi-restraints excluded: chain G residue 494 MET Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 551 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 639 GLN Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 355 ARG Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 461 TRP Chi-restraints excluded: chain H residue 499 ASP Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 446 GLU Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 477 TYR Chi-restraints excluded: chain I residue 494 MET Chi-restraints excluded: chain I residue 561 GLU Chi-restraints excluded: chain I residue 585 PHE Chi-restraints excluded: chain I residue 602 VAL Chi-restraints excluded: chain I residue 639 GLN Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 444 PHE Chi-restraints excluded: chain J residue 458 LYS Chi-restraints excluded: chain J residue 470 LEU Chi-restraints excluded: chain J residue 474 ILE Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain J residue 484 GLN Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 638 MET Chi-restraints excluded: chain J residue 641 THR Chi-restraints excluded: chain K residue 346 LEU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 477 TYR Chi-restraints excluded: chain K residue 486 THR Chi-restraints excluded: chain K residue 603 VAL Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 439 CYS Chi-restraints excluded: chain L residue 477 TYR Chi-restraints excluded: chain L residue 486 THR Chi-restraints excluded: chain L residue 499 ASP Chi-restraints excluded: chain L residue 516 ILE Chi-restraints excluded: chain L residue 523 SER Chi-restraints excluded: chain L residue 557 ARG Chi-restraints excluded: chain L residue 597 PHE Chi-restraints excluded: chain L residue 627 HIS Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 653 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 261 optimal weight: 0.8980 chunk 272 optimal weight: 0.7980 chunk 264 optimal weight: 1.9990 chunk 119 optimal weight: 0.0470 chunk 10 optimal weight: 3.9990 chunk 111 optimal weight: 0.0470 chunk 255 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 294 optimal weight: 0.7980 chunk 249 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 492 ASN ** G 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 HIS ** K 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.237186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.193293 restraints weight = 51367.551| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 3.71 r_work: 0.4205 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29303 Z= 0.130 Angle : 0.719 19.724 39800 Z= 0.352 Chirality : 0.045 0.236 4401 Planarity : 0.005 0.065 5147 Dihedral : 6.054 58.433 3973 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 4.68 % Allowed : 30.94 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.88 (0.14), residues: 3538 helix: 0.07 (0.14), residues: 1429 sheet: -0.83 (0.26), residues: 444 loop : -1.01 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 70 TYR 0.025 0.001 TYR G 548 PHE 0.030 0.001 PHE J 364 TRP 0.060 0.002 TRP K 375 HIS 0.016 0.001 HIS I 340 Details of bonding type rmsd covalent geometry : bond 0.00297 (29303) covalent geometry : angle 0.71868 (39800) hydrogen bonds : bond 0.03492 ( 1146) hydrogen bonds : angle 5.03925 ( 3333) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 651 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7338 (mm) cc_final: 0.6926 (mm) REVERT: A 152 ILE cc_start: 0.2075 (OUTLIER) cc_final: 0.1815 (tt) REVERT: A 220 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.4902 (mmm) REVERT: B 220 MET cc_start: 0.5169 (tpt) cc_final: 0.4745 (mmp) REVERT: B 285 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6580 (mp) REVERT: B 287 MET cc_start: 0.3665 (tmm) cc_final: 0.3191 (ttp) REVERT: C 11 MET cc_start: 0.7233 (mmt) cc_final: 0.6883 (ptp) REVERT: C 161 LEU cc_start: 0.2285 (OUTLIER) cc_final: 0.1969 (tp) REVERT: C 233 SER cc_start: 0.6320 (p) cc_final: 0.5996 (p) REVERT: D 11 MET cc_start: 0.6466 (mpp) cc_final: 0.5274 (mpp) REVERT: D 57 TYR cc_start: 0.6694 (m-80) cc_final: 0.6425 (m-80) REVERT: D 82 PHE cc_start: 0.5716 (t80) cc_final: 0.5029 (t80) REVERT: D 220 MET cc_start: 0.5842 (mmm) cc_final: 0.5126 (mmm) REVERT: D 222 ARG cc_start: 0.4445 (OUTLIER) cc_final: 0.3526 (mtt-85) REVERT: E 11 MET cc_start: 0.6255 (pmm) cc_final: 0.5953 (pmm) REVERT: E 287 MET cc_start: 0.2123 (tpt) cc_final: 0.1532 (tpp) REVERT: F 11 MET cc_start: 0.6463 (mmm) cc_final: 0.5864 (mmm) REVERT: F 66 LEU cc_start: 0.7023 (tp) cc_final: 0.6578 (pp) REVERT: F 220 MET cc_start: 0.5861 (mmp) cc_final: 0.5535 (mmp) REVERT: G 447 ASP cc_start: 0.0551 (OUTLIER) cc_final: 0.0348 (m-30) REVERT: G 456 VAL cc_start: 0.3224 (OUTLIER) cc_final: 0.2430 (p) REVERT: G 477 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.6459 (t80) REVERT: G 514 GLN cc_start: 0.7809 (mt0) cc_final: 0.7172 (mt0) REVERT: G 536 CYS cc_start: 0.7683 (p) cc_final: 0.7264 (p) REVERT: G 537 PHE cc_start: 0.6874 (m-10) cc_final: 0.6639 (m-10) REVERT: G 567 ASN cc_start: 0.8087 (p0) cc_final: 0.7635 (p0) REVERT: G 639 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7757 (pm20) REVERT: H 337 ARG cc_start: 0.7555 (mmm160) cc_final: 0.7120 (mmm160) REVERT: H 368 ASP cc_start: 0.7683 (t0) cc_final: 0.7438 (t0) REVERT: H 411 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6305 (mt-10) REVERT: H 415 ARG cc_start: 0.7813 (ptm160) cc_final: 0.7588 (ptm-80) REVERT: H 461 TRP cc_start: 0.7832 (OUTLIER) cc_final: 0.6672 (m-10) REVERT: H 474 ILE cc_start: 0.8508 (tt) cc_final: 0.8178 (tt) REVERT: H 481 GLU cc_start: 0.6445 (mp0) cc_final: 0.6200 (mp0) REVERT: H 483 LEU cc_start: 0.7487 (tp) cc_final: 0.7262 (tp) REVERT: H 584 SER cc_start: 0.8055 (t) cc_final: 0.7485 (p) REVERT: H 638 MET cc_start: 0.7670 (tmm) cc_final: 0.7363 (tmm) REVERT: I 355 ARG cc_start: 0.7757 (tmm160) cc_final: 0.7503 (tmm160) REVERT: I 407 GLU cc_start: 0.7957 (pp20) cc_final: 0.7671 (pp20) REVERT: I 446 GLU cc_start: 0.3608 (OUTLIER) cc_final: 0.0727 (mp0) REVERT: I 453 VAL cc_start: 0.3418 (OUTLIER) cc_final: 0.3125 (m) REVERT: I 456 VAL cc_start: 0.0930 (OUTLIER) cc_final: -0.0311 (m) REVERT: I 461 TRP cc_start: 0.5204 (p-90) cc_final: 0.3302 (p-90) REVERT: I 470 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7992 (mt) REVERT: I 473 VAL cc_start: 0.8798 (p) cc_final: 0.8526 (t) REVERT: I 480 LYS cc_start: 0.8147 (tmmt) cc_final: 0.7700 (tppt) REVERT: I 561 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: I 563 ILE cc_start: 0.8749 (mp) cc_final: 0.8506 (mt) REVERT: I 633 GLU cc_start: 0.7116 (pp20) cc_final: 0.6874 (pp20) REVERT: I 639 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7215 (pm20) REVERT: J 477 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.6383 (t80) REVERT: J 479 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7331 (tm-30) REVERT: J 480 LYS cc_start: 0.8292 (mmmt) cc_final: 0.7918 (tppt) REVERT: J 492 ASN cc_start: 0.8237 (m-40) cc_final: 0.7893 (m-40) REVERT: J 644 GLU cc_start: 0.6589 (pp20) cc_final: 0.6192 (pp20) REVERT: K 461 TRP cc_start: 0.5206 (m100) cc_final: 0.4445 (t-100) REVERT: K 477 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7537 (m-80) REVERT: K 537 PHE cc_start: 0.6794 (m-10) cc_final: 0.6458 (m-10) REVERT: K 548 TYR cc_start: 0.8391 (t80) cc_final: 0.7974 (t80) REVERT: K 549 ARG cc_start: 0.7997 (ptp-170) cc_final: 0.7626 (mtt180) REVERT: K 635 LYS cc_start: 0.7421 (mmtm) cc_final: 0.7014 (mmtm) REVERT: L 389 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7744 (mt) REVERT: L 422 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7353 (ptmm) REVERT: L 477 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.6767 (m-80) REVERT: L 480 LYS cc_start: 0.7499 (ttpp) cc_final: 0.7116 (tppt) REVERT: L 639 GLN cc_start: 0.8033 (pm20) cc_final: 0.7680 (pm20) outliers start: 142 outliers final: 109 residues processed: 734 average time/residue: 0.2098 time to fit residues: 236.8872 Evaluate side-chains 761 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 631 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 HIS Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 341 TYR Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 477 TYR Chi-restraints excluded: chain G residue 486 THR Chi-restraints excluded: chain G residue 492 ASN Chi-restraints excluded: chain G residue 494 MET Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 551 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 639 GLN Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 461 TRP Chi-restraints excluded: chain H residue 477 TYR Chi-restraints excluded: chain H residue 499 ASP Chi-restraints excluded: chain I residue 340 HIS Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 446 GLU Chi-restraints excluded: chain I residue 453 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 470 LEU Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 477 TYR Chi-restraints excluded: chain I residue 494 MET Chi-restraints excluded: chain I residue 561 GLU Chi-restraints excluded: chain I residue 565 ILE Chi-restraints excluded: chain I residue 585 PHE Chi-restraints excluded: chain I residue 602 VAL Chi-restraints excluded: chain I residue 639 GLN Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 444 PHE Chi-restraints excluded: chain J residue 458 LYS Chi-restraints excluded: chain J residue 470 LEU Chi-restraints excluded: chain J residue 474 ILE Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 638 MET Chi-restraints excluded: chain J residue 641 THR Chi-restraints excluded: chain K residue 346 LEU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 477 TYR Chi-restraints excluded: chain K residue 486 THR Chi-restraints excluded: chain K residue 603 VAL Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 422 LYS Chi-restraints excluded: chain L residue 477 TYR Chi-restraints excluded: chain L residue 486 THR Chi-restraints excluded: chain L residue 499 ASP Chi-restraints excluded: chain L residue 516 ILE Chi-restraints excluded: chain L residue 523 SER Chi-restraints excluded: chain L residue 557 ARG Chi-restraints excluded: chain L residue 597 PHE Chi-restraints excluded: chain L residue 627 HIS Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 649 PHE Chi-restraints excluded: chain L residue 653 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 216 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 237 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 191 optimal weight: 0.0470 chunk 124 optimal weight: 5.9990 chunk 188 optimal weight: 0.7980 chunk 63 optimal weight: 20.0000 overall best weight: 1.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS B 73 GLN ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS E 248 HIS ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 484 GLN ** K 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.237751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.194492 restraints weight = 50429.667| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 3.65 r_work: 0.4202 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.216 29303 Z= 0.222 Angle : 0.861 59.200 39800 Z= 0.463 Chirality : 0.053 1.553 4401 Planarity : 0.006 0.207 5147 Dihedral : 6.014 58.220 3971 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 4.72 % Allowed : 30.94 % Favored : 64.35 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.88 (0.14), residues: 3538 helix: 0.05 (0.14), residues: 1430 sheet: -0.82 (0.26), residues: 444 loop : -1.00 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.078 0.001 ARG J 334 TYR 0.023 0.001 TYR G 548 PHE 0.095 0.002 PHE K 356 TRP 0.048 0.002 TRP K 375 HIS 0.332 0.002 HIS I 340 Details of bonding type rmsd covalent geometry : bond 0.00485 (29303) covalent geometry : angle 0.86103 (39800) hydrogen bonds : bond 0.03538 ( 1146) hydrogen bonds : angle 5.04235 ( 3333) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 632 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7356 (mm) cc_final: 0.6938 (mm) REVERT: A 152 ILE cc_start: 0.2091 (OUTLIER) cc_final: 0.1832 (tt) REVERT: A 220 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.4908 (mmm) REVERT: B 220 MET cc_start: 0.5180 (tpt) cc_final: 0.4751 (mmp) REVERT: B 287 MET cc_start: 0.3547 (tmm) cc_final: 0.3233 (ttp) REVERT: C 11 MET cc_start: 0.7166 (mmt) cc_final: 0.6832 (ptp) REVERT: C 161 LEU cc_start: 0.2338 (OUTLIER) cc_final: 0.2011 (tp) REVERT: C 233 SER cc_start: 0.6352 (p) cc_final: 0.6027 (p) REVERT: D 11 MET cc_start: 0.6461 (mpp) cc_final: 0.5267 (mpp) REVERT: D 57 TYR cc_start: 0.6627 (m-80) cc_final: 0.6390 (m-80) REVERT: D 82 PHE cc_start: 0.5716 (t80) cc_final: 0.5026 (t80) REVERT: D 220 MET cc_start: 0.5841 (mmm) cc_final: 0.5130 (mmm) REVERT: D 222 ARG cc_start: 0.4465 (OUTLIER) cc_final: 0.3543 (mtt-85) REVERT: E 11 MET cc_start: 0.6252 (pmm) cc_final: 0.5953 (pmm) REVERT: E 287 MET cc_start: 0.2055 (tpt) cc_final: 0.1497 (tpp) REVERT: F 11 MET cc_start: 0.6456 (mmm) cc_final: 0.5853 (mmm) REVERT: F 66 LEU cc_start: 0.7005 (tp) cc_final: 0.6552 (pp) REVERT: F 220 MET cc_start: 0.5845 (mmp) cc_final: 0.5523 (mmp) REVERT: F 298 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6321 (mm) REVERT: G 456 VAL cc_start: 0.3181 (OUTLIER) cc_final: 0.2370 (p) REVERT: G 477 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.6480 (t80) REVERT: G 492 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7601 (p0) REVERT: G 514 GLN cc_start: 0.7830 (mt0) cc_final: 0.7209 (mt0) REVERT: G 567 ASN cc_start: 0.8096 (p0) cc_final: 0.7626 (p0) REVERT: G 639 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: H 337 ARG cc_start: 0.7577 (mmm160) cc_final: 0.7147 (mmm160) REVERT: H 368 ASP cc_start: 0.7669 (t0) cc_final: 0.7445 (t0) REVERT: H 415 ARG cc_start: 0.7821 (ptm160) cc_final: 0.7593 (ptm-80) REVERT: H 461 TRP cc_start: 0.7842 (OUTLIER) cc_final: 0.6682 (m-10) REVERT: H 474 ILE cc_start: 0.8504 (tt) cc_final: 0.8181 (tt) REVERT: H 481 GLU cc_start: 0.6456 (mp0) cc_final: 0.6223 (mp0) REVERT: H 483 LEU cc_start: 0.7463 (tp) cc_final: 0.7236 (tp) REVERT: H 584 SER cc_start: 0.8051 (t) cc_final: 0.7504 (p) REVERT: H 638 MET cc_start: 0.7626 (tmm) cc_final: 0.7335 (tmm) REVERT: I 355 ARG cc_start: 0.7750 (tmm160) cc_final: 0.7497 (tmm160) REVERT: I 407 GLU cc_start: 0.8001 (pp20) cc_final: 0.7722 (pp20) REVERT: I 446 GLU cc_start: 0.3659 (OUTLIER) cc_final: 0.0757 (mp0) REVERT: I 453 VAL cc_start: 0.3520 (OUTLIER) cc_final: 0.3210 (m) REVERT: I 456 VAL cc_start: 0.1020 (OUTLIER) cc_final: -0.0448 (m) REVERT: I 461 TRP cc_start: 0.5229 (p-90) cc_final: 0.3312 (p-90) REVERT: I 462 ILE cc_start: 0.7893 (pt) cc_final: 0.7568 (pt) REVERT: I 470 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8067 (mt) REVERT: I 473 VAL cc_start: 0.8816 (p) cc_final: 0.8545 (t) REVERT: I 480 LYS cc_start: 0.8141 (tmmt) cc_final: 0.7717 (tppt) REVERT: I 563 ILE cc_start: 0.8754 (mp) cc_final: 0.8520 (mt) REVERT: I 633 GLU cc_start: 0.7115 (pp20) cc_final: 0.6589 (pp20) REVERT: I 639 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: J 477 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.6416 (t80) REVERT: J 479 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7308 (tm-30) REVERT: J 480 LYS cc_start: 0.8312 (mmmt) cc_final: 0.7953 (tppt) REVERT: J 492 ASN cc_start: 0.8225 (m-40) cc_final: 0.7887 (m-40) REVERT: J 644 GLU cc_start: 0.6612 (pp20) cc_final: 0.6212 (pp20) REVERT: K 477 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: K 537 PHE cc_start: 0.6813 (m-10) cc_final: 0.6486 (m-10) REVERT: K 548 TYR cc_start: 0.8406 (t80) cc_final: 0.8020 (t80) REVERT: K 549 ARG cc_start: 0.7982 (ptp-170) cc_final: 0.7610 (mtt180) REVERT: L 389 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7782 (mt) REVERT: L 422 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7400 (ptmm) REVERT: L 477 TYR cc_start: 0.7722 (OUTLIER) cc_final: 0.6828 (m-80) REVERT: L 480 LYS cc_start: 0.7459 (ttpp) cc_final: 0.7074 (tppt) REVERT: L 639 GLN cc_start: 0.8033 (pm20) cc_final: 0.7681 (pm20) outliers start: 143 outliers final: 117 residues processed: 711 average time/residue: 0.2012 time to fit residues: 221.6053 Evaluate side-chains 769 residues out of total 3071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 632 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 175 GLN Chi-restraints excluded: chain E residue 276 ILE Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 133 HIS Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain G residue 341 TYR Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 477 TYR Chi-restraints excluded: chain G residue 486 THR Chi-restraints excluded: chain G residue 492 ASN Chi-restraints excluded: chain G residue 494 MET Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 551 ILE Chi-restraints excluded: chain G residue 557 ARG Chi-restraints excluded: chain G residue 577 LEU Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 639 GLN Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 356 PHE Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 461 TRP Chi-restraints excluded: chain H residue 477 TYR Chi-restraints excluded: chain H residue 499 ASP Chi-restraints excluded: chain H residue 577 LEU Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 446 GLU Chi-restraints excluded: chain I residue 453 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 470 LEU Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 477 TYR Chi-restraints excluded: chain I residue 494 MET Chi-restraints excluded: chain I residue 565 ILE Chi-restraints excluded: chain I residue 585 PHE Chi-restraints excluded: chain I residue 602 VAL Chi-restraints excluded: chain I residue 639 GLN Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 444 PHE Chi-restraints excluded: chain J residue 458 LYS Chi-restraints excluded: chain J residue 470 LEU Chi-restraints excluded: chain J residue 474 ILE Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain J residue 484 GLN Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 638 MET Chi-restraints excluded: chain J residue 641 THR Chi-restraints excluded: chain K residue 346 LEU Chi-restraints excluded: chain K residue 355 ARG Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 439 CYS Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 477 TYR Chi-restraints excluded: chain K residue 486 THR Chi-restraints excluded: chain K residue 603 VAL Chi-restraints excluded: chain L residue 320 ILE Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 357 LEU Chi-restraints excluded: chain L residue 386 VAL Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 422 LYS Chi-restraints excluded: chain L residue 477 TYR Chi-restraints excluded: chain L residue 486 THR Chi-restraints excluded: chain L residue 499 ASP Chi-restraints excluded: chain L residue 516 ILE Chi-restraints excluded: chain L residue 523 SER Chi-restraints excluded: chain L residue 557 ARG Chi-restraints excluded: chain L residue 597 PHE Chi-restraints excluded: chain L residue 627 HIS Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 653 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 108 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 264 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 chunk 277 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 67 optimal weight: 50.0000 chunk 275 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS ** B 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.237669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.194266 restraints weight = 50971.352| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 3.70 r_work: 0.4195 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.216 29303 Z= 0.222 Angle : 0.861 59.197 39800 Z= 0.463 Chirality : 0.053 1.551 4401 Planarity : 0.006 0.207 5147 Dihedral : 6.014 58.220 3971 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 4.55 % Allowed : 31.10 % Favored : 64.35 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.88 (0.14), residues: 3538 helix: 0.05 (0.14), residues: 1430 sheet: -0.82 (0.26), residues: 444 loop : -1.00 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.078 0.001 ARG J 334 TYR 0.023 0.001 TYR G 548 PHE 0.095 0.002 PHE K 356 TRP 0.048 0.002 TRP K 375 HIS 0.332 0.002 HIS I 340 Details of bonding type rmsd covalent geometry : bond 0.00485 (29303) covalent geometry : angle 0.86098 (39800) hydrogen bonds : bond 0.03538 ( 1146) hydrogen bonds : angle 5.04235 ( 3333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9319.94 seconds wall clock time: 159 minutes 32.12 seconds (9572.12 seconds total)