Starting phenix.real_space_refine on Sat Mar 7 09:42:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p5v_13202/03_2026/7p5v_13202.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p5v_13202/03_2026/7p5v_13202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p5v_13202/03_2026/7p5v_13202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p5v_13202/03_2026/7p5v_13202.map" model { file = "/net/cci-nas-00/data/ceres_data/7p5v_13202/03_2026/7p5v_13202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p5v_13202/03_2026/7p5v_13202.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 174 5.16 5 C 26757 2.51 5 N 6957 2.21 5 O 7386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41274 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "B" Number of atoms: 6030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6030 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "D" Number of atoms: 6030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6030 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "F" Number of atoms: 6030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6030 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "I" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "J" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "K" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "L" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Time building chain proxies: 9.11, per 1000 atoms: 0.22 Number of scatterers: 41274 At special positions: 0 Unit cell: (179.676, 169.26, 205.716, 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 174 16.00 O 7386 8.00 N 6957 7.00 C 26757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.02 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 1.8 seconds 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9642 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 38 sheets defined 47.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 removed outlier: 3.577A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 146 Proline residue: A 126 - end of helix removed outlier: 5.283A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.878A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.942A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 314 through 347 removed outlier: 3.797A pdb=" N SER A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.550A pdb=" N LEU A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 395 removed outlier: 4.286A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 411 Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.628A pdb=" N GLU A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 510 through 515 removed outlier: 3.863A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 removed outlier: 4.407A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.601A pdb=" N ILE A 610 " --> pdb=" O PRO A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 638 removed outlier: 3.503A pdb=" N ILE A 633 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.690A pdb=" N CYS A 684 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 707 Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.985A pdb=" N GLY A 751 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.961A pdb=" N CYS A 776 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 792 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'B' and resid 15 through 20 removed outlier: 4.189A pdb=" N ARG B 18 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 118 removed outlier: 3.754A pdb=" N LEU B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 5.026A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.928A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 removed outlier: 3.724A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 221 removed outlier: 3.629A pdb=" N GLN B 221 " --> pdb=" O ARG B 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 346 Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.710A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 removed outlier: 3.851A pdb=" N LEU B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 395 removed outlier: 3.935A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 removed outlier: 3.691A pdb=" N GLU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 441 through 445 removed outlier: 3.575A pdb=" N LEU B 445 " --> pdb=" O VAL B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 485 through 495 Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.671A pdb=" N LEU B 515 " --> pdb=" O ILE B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 543 removed outlier: 3.970A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 629 through 637 Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.547A pdb=" N LEU B 661 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.509A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 removed outlier: 3.584A pdb=" N GLY B 705 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 707 " --> pdb=" O ILE B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.570A pdb=" N CYS B 730 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.934A pdb=" N GLY B 751 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 753 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 3.505A pdb=" N GLU B 775 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS B 776 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 5.298A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 3.915A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 removed outlier: 3.962A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 314 through 347 removed outlier: 3.830A pdb=" N SER C 347 " --> pdb=" O MET C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 removed outlier: 3.506A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 removed outlier: 3.537A pdb=" N LEU C 376 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 395 removed outlier: 4.289A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 411 Processing helix chain 'C' and resid 412 through 420 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.872A pdb=" N PHE C 443 " --> pdb=" O ASP C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 495 removed outlier: 3.665A pdb=" N GLU C 493 " --> pdb=" O ALA C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 508 Processing helix chain 'C' and resid 510 through 515 removed outlier: 3.870A pdb=" N TYR C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 543 removed outlier: 3.588A pdb=" N ASP C 538 " --> pdb=" O ILE C 535 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY C 539 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 Processing helix chain 'C' and resid 567 through 569 No H-bonds generated for 'chain 'C' and resid 567 through 569' Processing helix chain 'C' and resid 607 through 613 Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.649A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 678 through 684 removed outlier: 3.719A pdb=" N CYS C 684 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 707 Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.839A pdb=" N GLY C 751 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 776 removed outlier: 3.915A pdb=" N CYS C 776 " --> pdb=" O LEU C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 792 Processing helix chain 'C' and resid 795 through 808 Processing helix chain 'D' and resid 15 through 20 removed outlier: 4.098A pdb=" N ARG D 18 " --> pdb=" O PRO D 15 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 118 removed outlier: 3.718A pdb=" N LEU D 118 " --> pdb=" O TYR D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 146 Proline residue: D 126 - end of helix removed outlier: 4.894A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 165 removed outlier: 3.953A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 176 removed outlier: 3.638A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 221 removed outlier: 3.528A pdb=" N GLN D 221 " --> pdb=" O ARG D 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 218 through 221' Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 347 removed outlier: 4.136A pdb=" N SER D 347 " --> pdb=" O MET D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.674A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 removed outlier: 3.647A pdb=" N LEU D 376 " --> pdb=" O PHE D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 395 removed outlier: 3.905A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 411 removed outlier: 3.758A pdb=" N GLU D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 420 Processing helix chain 'D' and resid 439 through 445 removed outlier: 3.939A pdb=" N PHE D 443 " --> pdb=" O ASP D 440 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU D 445 " --> pdb=" O VAL D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 485 through 495 Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'D' and resid 511 through 515 removed outlier: 3.728A pdb=" N LEU D 515 " --> pdb=" O ILE D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 543 removed outlier: 4.015A pdb=" N GLY D 539 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG D 541 " --> pdb=" O ASP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 566 Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'D' and resid 629 through 637 Processing helix chain 'D' and resid 655 through 661 Processing helix chain 'D' and resid 678 through 684 removed outlier: 3.564A pdb=" N CYS D 684 " --> pdb=" O LEU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 707 removed outlier: 3.576A pdb=" N GLY D 705 " --> pdb=" O ALA D 702 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 707 " --> pdb=" O ILE D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 730 removed outlier: 3.585A pdb=" N CYS D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 753 removed outlier: 3.935A pdb=" N GLY D 751 " --> pdb=" O SER D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 775 removed outlier: 3.519A pdb=" N GLU D 775 " --> pdb=" O GLU D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 795 through 808 Processing helix chain 'E' and resid 16 through 20 Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 146 Proline residue: E 126 - end of helix removed outlier: 5.079A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 3.901A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 176 removed outlier: 3.890A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 314 through 347 removed outlier: 3.793A pdb=" N SER E 347 " --> pdb=" O MET E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 360 removed outlier: 3.564A pdb=" N ARG E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 383 removed outlier: 3.514A pdb=" N LEU E 376 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 395 removed outlier: 4.341A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 411 Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.854A pdb=" N PHE E 443 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP E 444 " --> pdb=" O THR E 441 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 445 " --> pdb=" O VAL E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 484 through 495 removed outlier: 3.616A pdb=" N GLU E 493 " --> pdb=" O ALA E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 508 Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 535 through 543 removed outlier: 3.553A pdb=" N ASP E 538 " --> pdb=" O ILE E 535 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY E 539 " --> pdb=" O VAL E 536 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 Processing helix chain 'E' and resid 567 through 569 No H-bonds generated for 'chain 'E' and resid 567 through 569' Processing helix chain 'E' and resid 607 through 613 removed outlier: 3.592A pdb=" N ILE E 610 " --> pdb=" O PRO E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 629 through 637 removed outlier: 3.538A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 Processing helix chain 'E' and resid 678 through 684 removed outlier: 3.599A pdb=" N CYS E 684 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 707 Processing helix chain 'E' and resid 724 through 730 Processing helix chain 'E' and resid 747 through 753 removed outlier: 4.085A pdb=" N GLY E 751 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 776 removed outlier: 3.876A pdb=" N CYS E 776 " --> pdb=" O LEU E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 792 Processing helix chain 'E' and resid 795 through 808 Processing helix chain 'F' and resid 15 through 20 removed outlier: 4.231A pdb=" N ARG F 18 " --> pdb=" O PRO F 15 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 102 through 118 removed outlier: 3.707A pdb=" N LEU F 118 " --> pdb=" O TYR F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 146 Proline residue: F 126 - end of helix removed outlier: 4.853A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 3.873A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 176 removed outlier: 3.690A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 221 removed outlier: 3.606A pdb=" N GLN F 221 " --> pdb=" O ARG F 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 218 through 221' Processing helix chain 'F' and resid 233 through 255 Processing helix chain 'F' and resid 259 through 286 Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 314 through 346 Processing helix chain 'F' and resid 353 through 361 removed outlier: 3.731A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 removed outlier: 3.581A pdb=" N LEU F 376 " --> pdb=" O PHE F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 395 removed outlier: 3.957A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE F 393 " --> pdb=" O ARG F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 411 Processing helix chain 'F' and resid 412 through 420 Processing helix chain 'F' and resid 441 through 445 removed outlier: 3.898A pdb=" N LEU F 445 " --> pdb=" O VAL F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 485 through 495 Processing helix chain 'F' and resid 504 through 508 Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 535 through 543 removed outlier: 4.060A pdb=" N GLY F 539 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG F 541 " --> pdb=" O ASP F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 566 Processing helix chain 'F' and resid 609 through 613 Processing helix chain 'F' and resid 629 through 637 Processing helix chain 'F' and resid 655 through 661 removed outlier: 3.505A pdb=" N LEU F 661 " --> pdb=" O ILE F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 684 removed outlier: 3.609A pdb=" N CYS F 684 " --> pdb=" O LEU F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 707 removed outlier: 3.542A pdb=" N GLY F 705 " --> pdb=" O ALA F 702 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU F 707 " --> pdb=" O ILE F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 730 removed outlier: 3.607A pdb=" N CYS F 730 " --> pdb=" O LEU F 727 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 753 removed outlier: 3.966A pdb=" N GLY F 751 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 776 removed outlier: 3.851A pdb=" N CYS F 776 " --> pdb=" O LEU F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 792 Processing helix chain 'F' and resid 795 through 808 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.581A pdb=" N ARG G 31 " --> pdb=" O PRO G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.834A pdb=" N THR G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.621A pdb=" N HIS H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.636A pdb=" N ARG I 31 " --> pdb=" O PRO I 28 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS I 32 " --> pdb=" O VAL I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.808A pdb=" N THR I 91 " --> pdb=" O PRO I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.701A pdb=" N HIS J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.676A pdb=" N ARG K 31 " --> pdb=" O PRO K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.530A pdb=" N HIS L 32 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.528A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 644 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU A 690 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 459 through 460 removed outlier: 6.645A pdb=" N VAL A 459 " --> pdb=" O LYS A 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 735 through 737 removed outlier: 6.581A pdb=" N LEU A 736 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.697A pdb=" N GLU B 484 " --> pdb=" O ILE B 461 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.623A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 498 " --> pdb=" O HIS B 522 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR B 524 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE B 500 " --> pdb=" O THR B 524 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 572 " --> pdb=" O GLU B 597 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE B 599 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE B 574 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 596 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 619 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 714 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU B 713 " --> pdb=" O HIS B 737 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA9, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.645A pdb=" N LEU C 428 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LYS C 452 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU C 430 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLU C 454 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU C 432 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU C 451 " --> pdb=" O TRP C 475 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR C 477 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C 453 " --> pdb=" O TYR C 477 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU C 572 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE C 599 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE C 574 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE C 619 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU C 713 " --> pdb=" O HIS C 737 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU C 736 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 459 through 460 removed outlier: 6.579A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB3, first strand: chain 'D' and resid 223 through 224 removed outlier: 3.692A pdb=" N GLU D 484 " --> pdb=" O ILE D 461 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 421 through 422 removed outlier: 6.589A pdb=" N LEU D 428 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LYS D 452 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU D 430 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU D 454 " --> pdb=" O LEU D 430 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU D 432 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU D 451 " --> pdb=" O TRP D 475 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TYR D 477 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU D 453 " --> pdb=" O TYR D 477 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU D 498 " --> pdb=" O HIS D 522 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR D 524 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE D 500 " --> pdb=" O THR D 524 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU D 572 " --> pdb=" O GLU D 597 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE D 599 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE D 574 " --> pdb=" O ILE D 599 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU D 596 " --> pdb=" O ASP D 620 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE D 619 " --> pdb=" O LYS D 645 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU D 644 " --> pdb=" O TYR D 668 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 714 " --> pdb=" O LEU D 690 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU D 713 " --> pdb=" O HIS D 737 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE D 759 " --> pdb=" O VAL D 785 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AB6, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.554A pdb=" N LEU E 428 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LYS E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU E 451 " --> pdb=" O TRP E 475 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TYR E 477 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU E 453 " --> pdb=" O TYR E 477 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE E 619 " --> pdb=" O LYS E 645 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU E 644 " --> pdb=" O TYR E 668 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 459 through 460 removed outlier: 6.717A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 735 through 737 removed outlier: 6.549A pdb=" N LEU E 736 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AC1, first strand: chain 'F' and resid 223 through 224 removed outlier: 3.643A pdb=" N GLU F 484 " --> pdb=" O ILE F 461 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 421 through 422 removed outlier: 6.693A pdb=" N LEU F 451 " --> pdb=" O TRP F 475 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR F 477 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU F 453 " --> pdb=" O TYR F 477 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU F 498 " --> pdb=" O HIS F 522 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR F 524 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE F 500 " --> pdb=" O THR F 524 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU F 572 " --> pdb=" O GLU F 597 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE F 599 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE F 574 " --> pdb=" O ILE F 599 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU F 596 " --> pdb=" O ASP F 620 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE F 619 " --> pdb=" O LYS F 645 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU F 644 " --> pdb=" O TYR F 668 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA F 714 " --> pdb=" O LEU F 690 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU F 713 " --> pdb=" O HIS F 737 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE F 759 " --> pdb=" O VAL F 785 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.544A pdb=" N VAL G 5 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU G 18 " --> pdb=" O MET G 83 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.952A pdb=" N SER G 114 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 93 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.952A pdb=" N SER G 114 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.568A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AC9, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.528A pdb=" N VAL I 5 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU I 18 " --> pdb=" O MET I 83 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.714A pdb=" N SER I 114 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.714A pdb=" N SER I 114 " --> pdb=" O VAL I 12 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.551A pdb=" N VAL J 5 " --> pdb=" O ALA J 23 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.554A pdb=" N MET J 34 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AD6, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.589A pdb=" N VAL K 5 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU K 18 " --> pdb=" O MET K 83 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.916A pdb=" N SER K 114 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N MET K 34 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.916A pdb=" N SER K 114 " --> pdb=" O VAL K 12 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.503A pdb=" N VAL L 5 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.586A pdb=" N MET L 34 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 11 through 12 1941 hydrogen bonds defined for protein. 4845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.88 Time building geometry restraints manager: 4.58 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: 13071 1.34 - 1.46: 7844 1.46 - 1.58: 21061 1.58 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 42216 Sorted by residual: bond pdb=" CB CYS F 295 " pdb=" SG CYS F 295 " ideal model delta sigma weight residual 1.808 1.763 0.045 3.30e-02 9.18e+02 1.87e+00 bond pdb=" CB CYS D 295 " pdb=" SG CYS D 295 " ideal model delta sigma weight residual 1.808 1.763 0.045 3.30e-02 9.18e+02 1.82e+00 bond pdb=" CB CYS A 310 " pdb=" SG CYS A 310 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.80e+00 bond pdb=" CB CYS D 310 " pdb=" SG CYS D 310 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.78e+00 bond pdb=" CB CYS A 295 " pdb=" SG CYS A 295 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.77e+00 ... (remaining 42211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 56371 1.67 - 3.35: 763 3.35 - 5.02: 77 5.02 - 6.69: 11 6.69 - 8.37: 3 Bond angle restraints: 57225 Sorted by residual: angle pdb=" N ILE E 535 " pdb=" CA ILE E 535 " pdb=" C ILE E 535 " ideal model delta sigma weight residual 112.96 108.32 4.64 1.00e+00 1.00e+00 2.16e+01 angle pdb=" N ILE C 535 " pdb=" CA ILE C 535 " pdb=" C ILE C 535 " ideal model delta sigma weight residual 112.96 108.34 4.62 1.00e+00 1.00e+00 2.13e+01 angle pdb=" N ILE A 535 " pdb=" CA ILE A 535 " pdb=" C ILE A 535 " ideal model delta sigma weight residual 111.90 108.92 2.98 8.10e-01 1.52e+00 1.35e+01 angle pdb=" N GLN A 711 " pdb=" CA GLN A 711 " pdb=" C GLN A 711 " ideal model delta sigma weight residual 114.56 111.02 3.54 1.27e+00 6.20e-01 7.79e+00 angle pdb=" C GLN L 39 " pdb=" N ALA L 40 " pdb=" CA ALA L 40 " ideal model delta sigma weight residual 120.68 116.71 3.97 1.52e+00 4.33e-01 6.81e+00 ... (remaining 57220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 23764 17.92 - 35.83: 1307 35.83 - 53.75: 287 53.75 - 71.67: 33 71.67 - 89.58: 10 Dihedral angle restraints: 25401 sinusoidal: 10497 harmonic: 14904 Sorted by residual: dihedral pdb=" CA LYS F 51 " pdb=" C LYS F 51 " pdb=" N MET F 52 " pdb=" CA MET F 52 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA LYS D 51 " pdb=" C LYS D 51 " pdb=" N MET D 52 " pdb=" CA MET D 52 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA LYS A 51 " pdb=" C LYS A 51 " pdb=" N MET A 52 " pdb=" CA MET A 52 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 25398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3755 0.030 - 0.061: 1936 0.061 - 0.091: 489 0.091 - 0.121: 272 0.121 - 0.152: 43 Chirality restraints: 6495 Sorted by residual: chirality pdb=" CA ILE F 299 " pdb=" N ILE F 299 " pdb=" C ILE F 299 " pdb=" CB ILE F 299 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA ILE B 654 " pdb=" N ILE B 654 " pdb=" C ILE B 654 " pdb=" CB ILE B 654 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE F 654 " pdb=" N ILE F 654 " pdb=" C ILE F 654 " pdb=" CB ILE F 654 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 6492 not shown) Planarity restraints: 7128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 21 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO D 22 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 22 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 22 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 21 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO B 22 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 22 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 22 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 21 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO F 22 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO F 22 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 22 " -0.018 5.00e-02 4.00e+02 ... (remaining 7125 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 615 2.66 - 3.22: 39335 3.22 - 3.78: 64025 3.78 - 4.34: 90708 4.34 - 4.90: 148415 Nonbonded interactions: 343098 Sorted by model distance: nonbonded pdb=" OG SER C 634 " pdb=" OH TYR I 52 " model vdw 2.106 3.040 nonbonded pdb=" OG SER E 634 " pdb=" OH TYR K 52 " model vdw 2.128 3.040 nonbonded pdb=" OG SER A 634 " pdb=" OH TYR G 52 " model vdw 2.134 3.040 nonbonded pdb=" OE2 GLU B 630 " pdb=" OH TYR B 653 " model vdw 2.177 3.040 nonbonded pdb=" OE2 GLU D 630 " pdb=" OH TYR D 653 " model vdw 2.187 3.040 ... (remaining 343093 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 15 through 176 or resid 230 through 808)) selection = chain 'C' selection = (chain 'D' and (resid 15 through 176 or resid 230 through 808)) selection = chain 'E' selection = (chain 'F' and (resid 15 through 176 or resid 230 through 808)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 37.880 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.110 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 42240 Z= 0.162 Angle : 0.515 8.367 57273 Z= 0.282 Chirality : 0.041 0.152 6495 Planarity : 0.003 0.035 7128 Dihedral : 11.638 89.585 15687 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.53 % Allowed : 6.83 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.12), residues: 4986 helix: -0.31 (0.11), residues: 2178 sheet: -0.41 (0.18), residues: 921 loop : -0.06 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 117 TYR 0.015 0.002 TYR D 106 PHE 0.014 0.001 PHE A 146 TRP 0.019 0.001 TRP E 342 HIS 0.004 0.001 HIS E 694 Details of bonding type rmsd covalent geometry : bond 0.00366 (42216) covalent geometry : angle 0.51417 (57225) SS BOND : bond 0.00334 ( 24) SS BOND : angle 1.04110 ( 48) hydrogen bonds : bond 0.18943 ( 1901) hydrogen bonds : angle 6.24162 ( 4845) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 670 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 505 ILE cc_start: 0.6833 (mm) cc_final: 0.6609 (mm) REVERT: A 515 LEU cc_start: 0.5261 (mt) cc_final: 0.4987 (mt) REVERT: B 35 MET cc_start: 0.7599 (mtm) cc_final: 0.7390 (mtt) REVERT: B 153 LEU cc_start: 0.7213 (mt) cc_final: 0.6985 (mt) REVERT: B 220 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6975 (pt0) REVERT: B 279 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7637 (tp) REVERT: B 375 MET cc_start: 0.5686 (mtt) cc_final: 0.5357 (mtt) REVERT: B 385 LEU cc_start: 0.6607 (tp) cc_final: 0.6297 (mp) REVERT: B 647 TRP cc_start: 0.8418 (OUTLIER) cc_final: 0.7810 (p90) REVERT: C 171 ARG cc_start: 0.4990 (ttt-90) cc_final: 0.4618 (mtp-110) REVERT: C 275 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.8000 (t80) REVERT: C 504 ASP cc_start: 0.4574 (t0) cc_final: 0.4192 (t0) REVERT: C 755 ASN cc_start: 0.7244 (m110) cc_final: 0.6948 (m-40) REVERT: D 102 ASP cc_start: 0.7947 (m-30) cc_final: 0.7742 (m-30) REVERT: D 148 ARG cc_start: 0.7024 (ttt180) cc_final: 0.6658 (mpt-90) REVERT: D 228 GLU cc_start: 0.6425 (mm-30) cc_final: 0.6016 (tt0) REVERT: D 279 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7512 (tp) REVERT: D 370 ASN cc_start: 0.5408 (OUTLIER) cc_final: 0.5028 (p0) REVERT: D 375 MET cc_start: 0.5841 (mtt) cc_final: 0.5614 (mtt) REVERT: D 385 LEU cc_start: 0.6546 (tp) cc_final: 0.6340 (mp) REVERT: D 647 TRP cc_start: 0.8486 (OUTLIER) cc_final: 0.7620 (p90) REVERT: D 770 PRO cc_start: 0.6971 (Cg_endo) cc_final: 0.6474 (Cg_exo) REVERT: E 102 ASP cc_start: 0.7357 (m-30) cc_final: 0.7096 (m-30) REVERT: E 232 LEU cc_start: 0.2296 (OUTLIER) cc_final: 0.1979 (mm) REVERT: E 279 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8285 (tp) REVERT: E 448 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6983 (mp) REVERT: E 505 ILE cc_start: 0.7329 (mm) cc_final: 0.6892 (tp) REVERT: E 623 ASP cc_start: 0.7637 (t0) cc_final: 0.7377 (t70) REVERT: F 15 PRO cc_start: 0.4276 (Cg_endo) cc_final: 0.3975 (Cg_exo) REVERT: F 353 PHE cc_start: 0.6484 (OUTLIER) cc_final: 0.4440 (m-80) REVERT: F 385 LEU cc_start: 0.6981 (tp) cc_final: 0.6199 (mp) REVERT: F 493 GLU cc_start: 0.6773 (mm-30) cc_final: 0.6573 (mm-30) REVERT: F 647 TRP cc_start: 0.8436 (OUTLIER) cc_final: 0.7935 (p90) REVERT: G 68 PHE cc_start: 0.3010 (m-10) cc_final: 0.2681 (m-10) REVERT: H 97 TYR cc_start: 0.6980 (t80) cc_final: 0.6191 (t80) REVERT: I 34 MET cc_start: 0.6070 (mmm) cc_final: 0.5740 (mmm) REVERT: I 58 THR cc_start: 0.7046 (p) cc_final: 0.6720 (t) REVERT: J 67 ARG cc_start: 0.5226 (mtm110) cc_final: 0.4475 (mtp85) REVERT: J 68 PHE cc_start: 0.7000 (m-10) cc_final: 0.6317 (m-10) REVERT: J 103 GLU cc_start: 0.6178 (mt-10) cc_final: 0.5785 (mt-10) REVERT: K 34 MET cc_start: 0.5809 (mmm) cc_final: 0.5539 (mmm) REVERT: K 58 THR cc_start: 0.7167 (p) cc_final: 0.6764 (p) REVERT: K 72 ARG cc_start: 0.5351 (ptt180) cc_final: 0.4696 (ptt90) REVERT: L 84 ASN cc_start: 0.5091 (m110) cc_final: 0.4342 (t0) REVERT: L 86 LEU cc_start: 0.3072 (mp) cc_final: 0.2650 (mt) REVERT: L 103 GLU cc_start: 0.6435 (mt-10) cc_final: 0.6232 (mt-10) outliers start: 162 outliers final: 67 residues processed: 818 average time/residue: 0.2523 time to fit residues: 333.8888 Evaluate side-chains 433 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 354 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 647 TRP Chi-restraints excluded: chain E residue 670 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 670 ASN Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 107 GLN Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 494 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS B 418 GLN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 ASN B 570 GLN C 239 GLN C 560 GLN C 709 ASN D 253 HIS D 404 GLN D 418 GLN D 526 ASN D 568 HIS ** D 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 ASN F 253 HIS F 526 ASN F 554 ASN J 77 ASN J 102 ASN ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN L 110 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.164438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.134787 restraints weight = 74921.814| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.68 r_work: 0.3436 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 42240 Z= 0.278 Angle : 0.670 11.352 57273 Z= 0.352 Chirality : 0.047 0.178 6495 Planarity : 0.005 0.043 7128 Dihedral : 6.507 57.540 5675 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.93 % Allowed : 10.21 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.12), residues: 4986 helix: -0.50 (0.11), residues: 2160 sheet: -0.52 (0.17), residues: 915 loop : -0.31 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 801 TYR 0.022 0.002 TYR B 106 PHE 0.019 0.002 PHE A 146 TRP 0.028 0.002 TRP C 342 HIS 0.010 0.002 HIS K 32 Details of bonding type rmsd covalent geometry : bond 0.00649 (42216) covalent geometry : angle 0.66873 (57225) SS BOND : bond 0.00516 ( 24) SS BOND : angle 1.48345 ( 48) hydrogen bonds : bond 0.05013 ( 1901) hydrogen bonds : angle 5.11504 ( 4845) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 375 time to evaluate : 1.566 Fit side-chains REVERT: A 440 ASP cc_start: 0.5743 (m-30) cc_final: 0.5180 (m-30) REVERT: A 515 LEU cc_start: 0.5309 (mt) cc_final: 0.5081 (mt) REVERT: A 689 TYR cc_start: 0.8059 (m-80) cc_final: 0.7686 (m-80) REVERT: A 740 ASN cc_start: 0.7578 (m110) cc_final: 0.7347 (t0) REVERT: B 35 MET cc_start: 0.8166 (mtm) cc_final: 0.7949 (mtt) REVERT: B 153 LEU cc_start: 0.7277 (mt) cc_final: 0.6941 (mt) REVERT: B 220 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7574 (pt0) REVERT: B 375 MET cc_start: 0.6291 (mtt) cc_final: 0.5982 (mtt) REVERT: B 385 LEU cc_start: 0.6734 (tp) cc_final: 0.6218 (mp) REVERT: B 496 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7841 (mmp80) REVERT: B 647 TRP cc_start: 0.8602 (OUTLIER) cc_final: 0.7710 (p90) REVERT: C 25 ASP cc_start: 0.8329 (m-30) cc_final: 0.8070 (m-30) REVERT: C 104 HIS cc_start: 0.9223 (OUTLIER) cc_final: 0.7999 (t70) REVERT: C 171 ARG cc_start: 0.5932 (ttt-90) cc_final: 0.5144 (mtp-110) REVERT: C 250 PHE cc_start: 0.7197 (t80) cc_final: 0.6996 (t80) REVERT: C 275 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8198 (t80) REVERT: C 755 ASN cc_start: 0.7769 (m110) cc_final: 0.7470 (m-40) REVERT: D 279 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8004 (tp) REVERT: D 375 MET cc_start: 0.6343 (mtt) cc_final: 0.5980 (mtt) REVERT: D 385 LEU cc_start: 0.6871 (tp) cc_final: 0.6417 (mp) REVERT: D 647 TRP cc_start: 0.8689 (OUTLIER) cc_final: 0.7568 (p90) REVERT: D 648 TYR cc_start: 0.8226 (m-80) cc_final: 0.7749 (m-80) REVERT: D 794 LEU cc_start: 0.7147 (mt) cc_final: 0.6915 (mp) REVERT: E 102 ASP cc_start: 0.7924 (m-30) cc_final: 0.7577 (m-30) REVERT: E 448 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7266 (mp) REVERT: E 504 ASP cc_start: 0.5996 (t0) cc_final: 0.5748 (t70) REVERT: E 505 ILE cc_start: 0.7382 (mm) cc_final: 0.7173 (mm) REVERT: E 570 GLN cc_start: 0.7677 (mt0) cc_final: 0.7262 (mm-40) REVERT: F 337 MET cc_start: 0.6479 (ppp) cc_final: 0.6237 (ppp) REVERT: F 353 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.4183 (m-80) REVERT: F 370 ASN cc_start: 0.5325 (OUTLIER) cc_final: 0.5081 (p0) REVERT: F 385 LEU cc_start: 0.7264 (tp) cc_final: 0.6308 (mp) REVERT: F 493 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7466 (mm-30) REVERT: F 570 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6888 (pp30) REVERT: F 625 ASN cc_start: 0.6965 (m-40) cc_final: 0.6232 (t0) REVERT: F 647 TRP cc_start: 0.8631 (OUTLIER) cc_final: 0.8003 (p90) REVERT: F 689 TYR cc_start: 0.7298 (m-80) cc_final: 0.7059 (m-10) REVERT: G 68 PHE cc_start: 0.3907 (m-10) cc_final: 0.3090 (m-10) REVERT: G 83 MET cc_start: 0.3331 (mpp) cc_final: 0.2993 (mpp) REVERT: H 3 GLN cc_start: 0.6384 (tp40) cc_final: 0.5813 (tp40) REVERT: H 38 ARG cc_start: 0.5415 (ptp-170) cc_final: 0.5053 (ptp90) REVERT: I 3 GLN cc_start: 0.4535 (pm20) cc_final: 0.4204 (pm20) REVERT: I 58 THR cc_start: 0.7051 (p) cc_final: 0.6611 (t) REVERT: I 102 ASN cc_start: 0.6363 (t0) cc_final: 0.5855 (t0) REVERT: J 67 ARG cc_start: 0.5886 (mtm110) cc_final: 0.4797 (mtp85) REVERT: J 68 PHE cc_start: 0.7509 (m-10) cc_final: 0.7206 (m-10) REVERT: J 83 MET cc_start: 0.4746 (mtm) cc_final: 0.3536 (ptp) REVERT: K 34 MET cc_start: 0.6619 (mmm) cc_final: 0.5986 (mmm) REVERT: K 58 THR cc_start: 0.6985 (p) cc_final: 0.6629 (t) REVERT: K 68 PHE cc_start: 0.3366 (m-10) cc_final: 0.2612 (m-10) REVERT: K 72 ARG cc_start: 0.5021 (ptt180) cc_final: 0.4615 (ptt180) REVERT: K 102 ASN cc_start: 0.6384 (t0) cc_final: 0.5906 (t0) REVERT: L 83 MET cc_start: 0.5652 (mtm) cc_final: 0.5052 (mtm) REVERT: L 84 ASN cc_start: 0.5513 (m110) cc_final: 0.4188 (t0) REVERT: L 86 LEU cc_start: 0.3691 (mp) cc_final: 0.3333 (mt) outliers start: 180 outliers final: 119 residues processed: 533 average time/residue: 0.2333 time to fit residues: 207.0297 Evaluate side-chains 460 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 329 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 670 ASN Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 647 TRP Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 740 ASN Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 538 ASP Chi-restraints excluded: chain F residue 570 GLN Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 670 ASN Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 102 ASN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 342 optimal weight: 0.9980 chunk 448 optimal weight: 0.9990 chunk 399 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 354 optimal weight: 0.5980 chunk 282 optimal weight: 5.9990 chunk 216 optimal weight: 0.8980 chunk 202 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 306 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN D 253 HIS D 744 GLN E 381 GLN E 709 ASN F 253 HIS ** F 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN H 107 GLN H 110 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 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 = 0.4332 r_free = 0.4332 target = 0.166585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.137274 restraints weight = 75149.089| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.64 r_work: 0.3484 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 42240 Z= 0.132 Angle : 0.533 9.672 57273 Z= 0.284 Chirality : 0.042 0.198 6495 Planarity : 0.004 0.038 7128 Dihedral : 5.957 58.905 5652 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.38 % Allowed : 11.71 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.12), residues: 4986 helix: -0.23 (0.11), residues: 2160 sheet: -0.52 (0.17), residues: 945 loop : -0.20 (0.15), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 801 TYR 0.014 0.001 TYR J 104 PHE 0.014 0.001 PHE K 33 TRP 0.023 0.001 TRP C 342 HIS 0.004 0.001 HIS C 694 Details of bonding type rmsd covalent geometry : bond 0.00291 (42216) covalent geometry : angle 0.53157 (57225) SS BOND : bond 0.00289 ( 24) SS BOND : angle 1.43021 ( 48) hydrogen bonds : bond 0.04024 ( 1901) hydrogen bonds : angle 4.66965 ( 4845) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 368 time to evaluate : 1.287 Fit side-chains REVERT: A 515 LEU cc_start: 0.5486 (mt) cc_final: 0.5273 (mt) REVERT: A 527 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5840 (pp) REVERT: A 689 TYR cc_start: 0.7905 (m-80) cc_final: 0.7580 (m-80) REVERT: B 35 MET cc_start: 0.8101 (mtm) cc_final: 0.7868 (mtt) REVERT: B 153 LEU cc_start: 0.7289 (mt) cc_final: 0.6959 (mt) REVERT: B 238 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7318 (pt0) REVERT: B 375 MET cc_start: 0.5898 (mtt) cc_final: 0.5546 (mtt) REVERT: B 385 LEU cc_start: 0.6658 (tp) cc_final: 0.6155 (mp) REVERT: B 647 TRP cc_start: 0.8445 (OUTLIER) cc_final: 0.7585 (p90) REVERT: C 48 THR cc_start: 0.8217 (m) cc_final: 0.7823 (m) REVERT: C 171 ARG cc_start: 0.5840 (ttt-90) cc_final: 0.5089 (mtp-110) REVERT: C 250 PHE cc_start: 0.7228 (t80) cc_final: 0.6964 (t80) REVERT: C 755 ASN cc_start: 0.7862 (m110) cc_final: 0.7534 (m-40) REVERT: D 102 ASP cc_start: 0.8053 (m-30) cc_final: 0.7771 (m-30) REVERT: D 279 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.8022 (tp) REVERT: D 375 MET cc_start: 0.5982 (mtt) cc_final: 0.5646 (mtt) REVERT: D 385 LEU cc_start: 0.6699 (tp) cc_final: 0.6284 (mp) REVERT: D 483 ILE cc_start: 0.6777 (tt) cc_final: 0.6420 (tt) REVERT: D 570 GLN cc_start: 0.6823 (OUTLIER) cc_final: 0.6301 (pp30) REVERT: D 647 TRP cc_start: 0.8578 (OUTLIER) cc_final: 0.7515 (p90) REVERT: D 648 TYR cc_start: 0.8092 (m-80) cc_final: 0.7499 (m-80) REVERT: E 275 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.7995 (t80) REVERT: E 448 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7336 (mp) REVERT: E 504 ASP cc_start: 0.5763 (t0) cc_final: 0.5557 (t70) REVERT: E 505 ILE cc_start: 0.7460 (mm) cc_final: 0.7181 (mm) REVERT: E 570 GLN cc_start: 0.7565 (mt0) cc_final: 0.7229 (mm-40) REVERT: E 623 ASP cc_start: 0.8141 (t0) cc_final: 0.7843 (t70) REVERT: E 712 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8632 (m-40) REVERT: F 15 PRO cc_start: 0.4715 (Cg_endo) cc_final: 0.4456 (Cg_exo) REVERT: F 153 LEU cc_start: 0.7625 (mt) cc_final: 0.7325 (mt) REVERT: F 279 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7866 (tp) REVERT: F 353 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.4188 (m-80) REVERT: F 385 LEU cc_start: 0.7137 (tp) cc_final: 0.6185 (mp) REVERT: F 415 LYS cc_start: 0.7385 (ttpt) cc_final: 0.7061 (tptm) REVERT: F 427 LYS cc_start: 0.7854 (mttm) cc_final: 0.7463 (mtmm) REVERT: F 625 ASN cc_start: 0.6994 (m-40) cc_final: 0.6326 (t0) REVERT: F 647 TRP cc_start: 0.8532 (OUTLIER) cc_final: 0.8039 (p90) REVERT: F 689 TYR cc_start: 0.7329 (m-80) cc_final: 0.6988 (m-80) REVERT: G 58 THR cc_start: 0.7135 (p) cc_final: 0.6699 (t) REVERT: G 68 PHE cc_start: 0.4025 (m-10) cc_final: 0.3004 (m-10) REVERT: G 83 MET cc_start: 0.3131 (mpp) cc_final: 0.2502 (mpp) REVERT: H 67 ARG cc_start: 0.6526 (ptt180) cc_final: 0.5817 (mtm110) REVERT: I 58 THR cc_start: 0.7030 (p) cc_final: 0.6575 (t) REVERT: I 83 MET cc_start: 0.3427 (mpp) cc_final: 0.2940 (mpt) REVERT: I 102 ASN cc_start: 0.6059 (t0) cc_final: 0.5567 (t0) REVERT: J 67 ARG cc_start: 0.5959 (mtm110) cc_final: 0.4755 (mtp85) REVERT: J 68 PHE cc_start: 0.7494 (m-10) cc_final: 0.7156 (m-10) REVERT: J 83 MET cc_start: 0.4838 (mtm) cc_final: 0.4414 (mtp) REVERT: J 102 ASN cc_start: 0.5894 (p0) cc_final: 0.5369 (p0) REVERT: J 104 TYR cc_start: 0.5779 (m-10) cc_final: 0.5067 (m-10) REVERT: K 34 MET cc_start: 0.6673 (mmm) cc_final: 0.6097 (mmm) REVERT: K 58 THR cc_start: 0.6848 (p) cc_final: 0.6593 (t) REVERT: K 59 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7119 (mm-30) REVERT: K 68 PHE cc_start: 0.3587 (m-10) cc_final: 0.2746 (m-10) REVERT: K 72 ARG cc_start: 0.5207 (ptt180) cc_final: 0.4929 (ptt180) REVERT: K 102 ASN cc_start: 0.6461 (t0) cc_final: 0.5939 (t0) REVERT: L 83 MET cc_start: 0.5487 (mtm) cc_final: 0.4891 (mtm) REVERT: L 84 ASN cc_start: 0.5671 (m110) cc_final: 0.4603 (t0) REVERT: L 86 LEU cc_start: 0.3705 (mp) cc_final: 0.3360 (mt) REVERT: L 102 ASN cc_start: 0.6688 (p0) cc_final: 0.6242 (m-40) outliers start: 155 outliers final: 91 residues processed: 502 average time/residue: 0.2283 time to fit residues: 192.8219 Evaluate side-chains 423 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 320 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 647 TRP Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 712 ASN Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 46 optimal weight: 7.9990 chunk 375 optimal weight: 0.9980 chunk 61 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 312 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 325 optimal weight: 0.9990 chunk 411 optimal weight: 5.9990 chunk 235 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS D 660 ASN E 709 ASN F 253 HIS F 409 ASN ** F 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 ASN I 3 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 ASN ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.166804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.138583 restraints weight = 74921.700| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.52 r_work: 0.3502 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 42240 Z= 0.126 Angle : 0.516 12.201 57273 Z= 0.273 Chirality : 0.042 0.192 6495 Planarity : 0.003 0.039 7128 Dihedral : 5.589 56.703 5630 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.58 % Allowed : 12.24 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.12), residues: 4986 helix: -0.13 (0.11), residues: 2160 sheet: -0.53 (0.17), residues: 945 loop : -0.17 (0.15), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 801 TYR 0.021 0.001 TYR D 513 PHE 0.012 0.001 PHE E 250 TRP 0.023 0.001 TRP C 342 HIS 0.005 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00281 (42216) covalent geometry : angle 0.51550 (57225) SS BOND : bond 0.00281 ( 24) SS BOND : angle 1.20264 ( 48) hydrogen bonds : bond 0.03712 ( 1901) hydrogen bonds : angle 4.46929 ( 4845) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 351 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: A 429 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.6259 (pm20) REVERT: A 473 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6637 (mt-10) REVERT: A 689 TYR cc_start: 0.8007 (m-80) cc_final: 0.7686 (m-80) REVERT: B 35 MET cc_start: 0.8104 (mtm) cc_final: 0.7884 (mtt) REVERT: B 153 LEU cc_start: 0.7275 (mt) cc_final: 0.6951 (mt) REVERT: B 220 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7424 (pt0) REVERT: B 375 MET cc_start: 0.6019 (mtt) cc_final: 0.5655 (mtt) REVERT: B 385 LEU cc_start: 0.6575 (tp) cc_final: 0.6108 (mp) REVERT: B 647 TRP cc_start: 0.8582 (OUTLIER) cc_final: 0.7862 (p90) REVERT: B 767 GLU cc_start: 0.4287 (OUTLIER) cc_final: 0.3175 (mp0) REVERT: C 48 THR cc_start: 0.8190 (m) cc_final: 0.7798 (m) REVERT: C 171 ARG cc_start: 0.5838 (ttt-90) cc_final: 0.5072 (mtp-110) REVERT: C 527 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5634 (pp) REVERT: C 734 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7584 (ttm-80) REVERT: C 755 ASN cc_start: 0.7862 (m110) cc_final: 0.7542 (m-40) REVERT: D 102 ASP cc_start: 0.7803 (m-30) cc_final: 0.7491 (m-30) REVERT: D 279 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7998 (tp) REVERT: D 375 MET cc_start: 0.5845 (mtt) cc_final: 0.5518 (mtt) REVERT: D 385 LEU cc_start: 0.6720 (tp) cc_final: 0.6290 (mp) REVERT: D 483 ILE cc_start: 0.6885 (tt) cc_final: 0.6666 (tt) REVERT: D 570 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6337 (pp30) REVERT: D 647 TRP cc_start: 0.8528 (OUTLIER) cc_final: 0.7527 (p90) REVERT: D 648 TYR cc_start: 0.8130 (m-80) cc_final: 0.7545 (m-80) REVERT: D 689 TYR cc_start: 0.7490 (m-80) cc_final: 0.7210 (t80) REVERT: D 749 ARG cc_start: 0.6586 (mtp180) cc_final: 0.6045 (mtp180) REVERT: E 275 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7959 (t80) REVERT: E 448 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7267 (mp) REVERT: E 504 ASP cc_start: 0.6108 (t0) cc_final: 0.5849 (t70) REVERT: E 505 ILE cc_start: 0.7476 (mm) cc_final: 0.7168 (mm) REVERT: E 570 GLN cc_start: 0.7513 (mt0) cc_final: 0.7242 (mm-40) REVERT: E 623 ASP cc_start: 0.8135 (t0) cc_final: 0.7826 (t70) REVERT: E 712 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8563 (m-40) REVERT: F 15 PRO cc_start: 0.4696 (Cg_endo) cc_final: 0.4430 (Cg_exo) REVERT: F 153 LEU cc_start: 0.7587 (mt) cc_final: 0.7280 (mt) REVERT: F 353 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.4178 (m-80) REVERT: F 385 LEU cc_start: 0.6954 (tp) cc_final: 0.6044 (mp) REVERT: F 427 LYS cc_start: 0.7822 (mttm) cc_final: 0.7564 (mtmm) REVERT: F 570 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6987 (pp30) REVERT: F 625 ASN cc_start: 0.6984 (m-40) cc_final: 0.6331 (t0) REVERT: F 647 TRP cc_start: 0.8461 (OUTLIER) cc_final: 0.7949 (p90) REVERT: F 726 GLU cc_start: 0.6435 (mp0) cc_final: 0.6176 (pm20) REVERT: G 34 MET cc_start: 0.6399 (mmm) cc_final: 0.5966 (mmp) REVERT: G 58 THR cc_start: 0.7196 (p) cc_final: 0.6860 (t) REVERT: G 68 PHE cc_start: 0.4049 (m-10) cc_final: 0.3179 (m-10) REVERT: G 83 MET cc_start: 0.3385 (mpp) cc_final: 0.2805 (mpp) REVERT: I 58 THR cc_start: 0.6735 (p) cc_final: 0.6482 (t) REVERT: I 83 MET cc_start: 0.4070 (mpp) cc_final: 0.3819 (mpt) REVERT: I 102 ASN cc_start: 0.6287 (t0) cc_final: 0.5984 (t0) REVERT: J 83 MET cc_start: 0.4846 (mtm) cc_final: 0.4457 (mtp) REVERT: J 102 ASN cc_start: 0.6457 (OUTLIER) cc_final: 0.5816 (p0) REVERT: J 104 TYR cc_start: 0.5937 (m-10) cc_final: 0.5286 (m-10) REVERT: K 3 GLN cc_start: 0.4362 (pm20) cc_final: 0.3952 (tp40) REVERT: K 34 MET cc_start: 0.6510 (mmm) cc_final: 0.5984 (mmm) REVERT: K 58 THR cc_start: 0.6971 (p) cc_final: 0.6739 (t) REVERT: K 59 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6983 (mm-30) REVERT: K 68 PHE cc_start: 0.3727 (m-10) cc_final: 0.2890 (m-10) REVERT: K 72 ARG cc_start: 0.5667 (ptt180) cc_final: 0.5370 (ptt180) REVERT: L 83 MET cc_start: 0.5261 (mtm) cc_final: 0.4639 (mtm) REVERT: L 84 ASN cc_start: 0.5701 (m110) cc_final: 0.4733 (t0) REVERT: L 86 LEU cc_start: 0.3671 (mp) cc_final: 0.3251 (mt) REVERT: L 102 ASN cc_start: 0.7443 (p0) cc_final: 0.6714 (m-40) REVERT: L 104 TYR cc_start: 0.5208 (m-10) cc_final: 0.4631 (m-10) outliers start: 164 outliers final: 99 residues processed: 492 average time/residue: 0.2334 time to fit residues: 193.8203 Evaluate side-chains 437 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 321 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 734 ARG Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 393 PHE Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 647 TRP Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 712 ASN Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 393 PHE Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 570 GLN Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ASN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 74 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 276 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 490 optimal weight: 9.9990 chunk 373 optimal weight: 10.0000 chunk 448 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 311 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS E 709 ASN F 253 HIS F 554 ASN I 3 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 ASN ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.166677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.137345 restraints weight = 74765.149| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.62 r_work: 0.3478 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 42240 Z= 0.133 Angle : 0.515 9.067 57273 Z= 0.272 Chirality : 0.042 0.184 6495 Planarity : 0.003 0.040 7128 Dihedral : 5.298 56.691 5612 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.64 % Allowed : 12.24 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.12), residues: 4986 helix: -0.17 (0.11), residues: 2190 sheet: -0.54 (0.17), residues: 945 loop : -0.18 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 171 TYR 0.018 0.001 TYR H 104 PHE 0.016 0.001 PHE I 68 TRP 0.018 0.001 TRP C 342 HIS 0.005 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00302 (42216) covalent geometry : angle 0.51392 (57225) SS BOND : bond 0.00303 ( 24) SS BOND : angle 1.17482 ( 48) hydrogen bonds : bond 0.03652 ( 1901) hydrogen bonds : angle 4.38550 ( 4845) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 343 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7519 (mp) REVERT: A 429 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.6068 (pm20) REVERT: A 527 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5873 (pp) REVERT: A 689 TYR cc_start: 0.7967 (m-80) cc_final: 0.7665 (m-80) REVERT: B 35 MET cc_start: 0.8128 (mtm) cc_final: 0.7894 (mtt) REVERT: B 153 LEU cc_start: 0.7244 (mt) cc_final: 0.6909 (mt) REVERT: B 162 LYS cc_start: 0.6595 (ptpt) cc_final: 0.6156 (mtpp) REVERT: B 220 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: B 375 MET cc_start: 0.6048 (mtt) cc_final: 0.5660 (mtt) REVERT: B 385 LEU cc_start: 0.6464 (tp) cc_final: 0.6013 (mp) REVERT: B 647 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.7846 (p90) REVERT: B 767 GLU cc_start: 0.4271 (OUTLIER) cc_final: 0.3194 (mp0) REVERT: C 48 THR cc_start: 0.8229 (m) cc_final: 0.7842 (m) REVERT: C 171 ARG cc_start: 0.5876 (ttt-90) cc_final: 0.5123 (mtp-110) REVERT: C 527 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5577 (pp) REVERT: C 570 GLN cc_start: 0.7480 (mt0) cc_final: 0.7208 (mm-40) REVERT: C 755 ASN cc_start: 0.7852 (m110) cc_final: 0.7564 (m-40) REVERT: D 102 ASP cc_start: 0.7919 (m-30) cc_final: 0.7686 (m-30) REVERT: D 279 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8074 (tp) REVERT: D 375 MET cc_start: 0.5686 (mtt) cc_final: 0.5326 (mtt) REVERT: D 385 LEU cc_start: 0.6640 (tp) cc_final: 0.6203 (mp) REVERT: D 483 ILE cc_start: 0.6935 (tt) cc_final: 0.6691 (tt) REVERT: D 570 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.6281 (pp30) REVERT: D 619 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8010 (tp) REVERT: D 647 TRP cc_start: 0.8549 (OUTLIER) cc_final: 0.7499 (p90) REVERT: D 648 TYR cc_start: 0.8110 (m-80) cc_final: 0.7516 (m-80) REVERT: D 689 TYR cc_start: 0.7488 (m-80) cc_final: 0.7135 (t80) REVERT: E 275 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8139 (t80) REVERT: E 448 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7416 (mp) REVERT: E 504 ASP cc_start: 0.6000 (t0) cc_final: 0.5776 (t70) REVERT: E 570 GLN cc_start: 0.7495 (mt0) cc_final: 0.7226 (mm-40) REVERT: E 585 ASN cc_start: 0.4688 (t0) cc_final: 0.4418 (t0) REVERT: E 623 ASP cc_start: 0.8090 (t0) cc_final: 0.7770 (t70) REVERT: E 712 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8563 (m-40) REVERT: F 15 PRO cc_start: 0.4697 (Cg_endo) cc_final: 0.4441 (Cg_exo) REVERT: F 153 LEU cc_start: 0.7536 (mt) cc_final: 0.7199 (mt) REVERT: F 269 ILE cc_start: 0.6974 (OUTLIER) cc_final: 0.6648 (mm) REVERT: F 353 PHE cc_start: 0.6456 (OUTLIER) cc_final: 0.4092 (m-10) REVERT: F 385 LEU cc_start: 0.7091 (tp) cc_final: 0.6123 (mp) REVERT: F 570 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6913 (pp30) REVERT: F 625 ASN cc_start: 0.6985 (m-40) cc_final: 0.6436 (t0) REVERT: F 647 TRP cc_start: 0.8605 (OUTLIER) cc_final: 0.8140 (p90) REVERT: F 726 GLU cc_start: 0.6697 (mp0) cc_final: 0.6489 (pm20) REVERT: G 58 THR cc_start: 0.7036 (p) cc_final: 0.6658 (t) REVERT: G 68 PHE cc_start: 0.4072 (m-10) cc_final: 0.3173 (m-10) REVERT: G 83 MET cc_start: 0.3541 (mpp) cc_final: 0.2778 (mpp) REVERT: H 83 MET cc_start: 0.4021 (mtm) cc_final: 0.3414 (ttp) REVERT: I 58 THR cc_start: 0.6730 (p) cc_final: 0.6411 (t) REVERT: I 83 MET cc_start: 0.3528 (mpp) cc_final: 0.3029 (mpt) REVERT: I 102 ASN cc_start: 0.6298 (t0) cc_final: 0.5983 (t0) REVERT: J 38 ARG cc_start: 0.5434 (ptp-170) cc_final: 0.5181 (ptp-110) REVERT: J 56 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6400 (tm-30) REVERT: J 67 ARG cc_start: 0.6118 (mtm110) cc_final: 0.5016 (mtp85) REVERT: J 83 MET cc_start: 0.4631 (mtm) cc_final: 0.4357 (mtp) REVERT: K 34 MET cc_start: 0.6467 (mmm) cc_final: 0.6071 (mmm) REVERT: K 58 THR cc_start: 0.6811 (p) cc_final: 0.6427 (t) REVERT: K 68 PHE cc_start: 0.3767 (m-10) cc_final: 0.2752 (m-10) REVERT: K 72 ARG cc_start: 0.5510 (ptt180) cc_final: 0.5239 (ptt180) REVERT: K 83 MET cc_start: 0.3328 (mpt) cc_final: 0.2943 (mpp) REVERT: K 102 ASN cc_start: 0.6077 (t0) cc_final: 0.5803 (t0) REVERT: L 36 TRP cc_start: 0.4510 (m100) cc_final: 0.3710 (m100) REVERT: L 83 MET cc_start: 0.5188 (mtm) cc_final: 0.4880 (mtm) REVERT: L 84 ASN cc_start: 0.5640 (m110) cc_final: 0.4617 (t0) REVERT: L 86 LEU cc_start: 0.3632 (mp) cc_final: 0.3237 (mt) REVERT: L 102 ASN cc_start: 0.7177 (p0) cc_final: 0.6564 (m-40) REVERT: L 104 TYR cc_start: 0.5101 (m-10) cc_final: 0.4791 (m-10) outliers start: 167 outliers final: 118 residues processed: 488 average time/residue: 0.2246 time to fit residues: 185.0099 Evaluate side-chains 460 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 324 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 393 PHE Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 647 TRP Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 712 ASN Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 393 PHE Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 538 ASP Chi-restraints excluded: chain F residue 570 GLN Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 149 optimal weight: 3.9990 chunk 341 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 390 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 375 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 222 optimal weight: 0.5980 chunk 479 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS E 709 ASN F 253 HIS I 3 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 ASN J 102 ASN ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.166296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.139860 restraints weight = 74984.937| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.44 r_work: 0.3512 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.003 0.034 42240 Z= 0.144 Angle : 0.513 8.552 57273 Z= 0.272 Chirality : 0.042 0.194 6495 Planarity : 0.003 0.040 7128 Dihedral : 5.212 56.520 5606 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.84 % Allowed : 12.57 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.12), residues: 4986 helix: -0.16 (0.11), residues: 2181 sheet: -0.53 (0.17), residues: 939 loop : -0.20 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 749 TYR 0.017 0.001 TYR F 513 PHE 0.017 0.001 PHE A 635 TRP 0.016 0.001 TRP C 342 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00329 (42216) covalent geometry : angle 0.51236 (57225) SS BOND : bond 0.00319 ( 24) SS BOND : angle 1.10892 ( 48) hydrogen bonds : bond 0.03662 ( 1901) hydrogen bonds : angle 4.33565 ( 4845) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 337 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7638 (mp) REVERT: A 527 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5741 (pp) REVERT: A 689 TYR cc_start: 0.7978 (m-80) cc_final: 0.7682 (m-80) REVERT: B 35 MET cc_start: 0.8098 (mtm) cc_final: 0.7870 (mtt) REVERT: B 153 LEU cc_start: 0.7234 (mt) cc_final: 0.6890 (mt) REVERT: B 162 LYS cc_start: 0.6652 (ptpt) cc_final: 0.6341 (mtpp) REVERT: B 220 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: B 375 MET cc_start: 0.6113 (mtt) cc_final: 0.5766 (mtt) REVERT: B 385 LEU cc_start: 0.6409 (tp) cc_final: 0.6028 (mp) REVERT: B 599 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8469 (mt) REVERT: B 647 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.7870 (p90) REVERT: B 767 GLU cc_start: 0.4005 (OUTLIER) cc_final: 0.2970 (mp0) REVERT: C 48 THR cc_start: 0.8119 (m) cc_final: 0.7720 (m) REVERT: C 104 HIS cc_start: 0.9153 (OUTLIER) cc_final: 0.7810 (t70) REVERT: C 171 ARG cc_start: 0.5859 (ttt-90) cc_final: 0.5314 (mtp85) REVERT: C 527 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5599 (pp) REVERT: C 723 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7612 (mt) REVERT: C 755 ASN cc_start: 0.7834 (m110) cc_final: 0.7546 (m-40) REVERT: D 279 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.8015 (tp) REVERT: D 375 MET cc_start: 0.5573 (mtt) cc_final: 0.5200 (mtt) REVERT: D 385 LEU cc_start: 0.6693 (tp) cc_final: 0.6260 (mp) REVERT: D 483 ILE cc_start: 0.6883 (tt) cc_final: 0.6502 (tt) REVERT: D 570 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6299 (pp30) REVERT: D 619 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7969 (tp) REVERT: D 647 TRP cc_start: 0.8542 (OUTLIER) cc_final: 0.7500 (p90) REVERT: D 648 TYR cc_start: 0.8148 (m-80) cc_final: 0.7624 (m-80) REVERT: D 689 TYR cc_start: 0.7420 (m-80) cc_final: 0.7188 (t80) REVERT: E 64 SER cc_start: 0.6877 (OUTLIER) cc_final: 0.6546 (t) REVERT: E 275 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8022 (t80) REVERT: E 504 ASP cc_start: 0.5942 (t0) cc_final: 0.5718 (t70) REVERT: E 505 ILE cc_start: 0.7549 (mm) cc_final: 0.6860 (tp) REVERT: E 570 GLN cc_start: 0.7483 (mt0) cc_final: 0.7261 (mm-40) REVERT: E 585 ASN cc_start: 0.4800 (t0) cc_final: 0.4561 (t0) REVERT: E 587 LEU cc_start: 0.7418 (tp) cc_final: 0.7120 (tp) REVERT: E 623 ASP cc_start: 0.8083 (t0) cc_final: 0.7771 (t70) REVERT: E 712 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8615 (m-40) REVERT: F 15 PRO cc_start: 0.4695 (Cg_endo) cc_final: 0.4446 (Cg_exo) REVERT: F 153 LEU cc_start: 0.7531 (mt) cc_final: 0.7198 (mt) REVERT: F 353 PHE cc_start: 0.6368 (OUTLIER) cc_final: 0.3991 (m-10) REVERT: F 385 LEU cc_start: 0.7129 (tp) cc_final: 0.6161 (mp) REVERT: F 570 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6966 (pp30) REVERT: F 625 ASN cc_start: 0.6949 (m-40) cc_final: 0.6440 (t0) REVERT: F 647 TRP cc_start: 0.8491 (OUTLIER) cc_final: 0.7993 (p90) REVERT: G 34 MET cc_start: 0.5910 (mmm) cc_final: 0.5316 (mmp) REVERT: G 58 THR cc_start: 0.6982 (p) cc_final: 0.6720 (t) REVERT: G 68 PHE cc_start: 0.4064 (m-10) cc_final: 0.3197 (m-10) REVERT: G 83 MET cc_start: 0.3577 (mpp) cc_final: 0.2815 (mpp) REVERT: H 83 MET cc_start: 0.3921 (mtm) cc_final: 0.3518 (ttp) REVERT: I 102 ASN cc_start: 0.6529 (t0) cc_final: 0.6318 (t0) REVERT: J 56 GLU cc_start: 0.6825 (tm-30) cc_final: 0.6505 (tm-30) REVERT: J 67 ARG cc_start: 0.6108 (mtm110) cc_final: 0.5119 (mtp85) REVERT: J 83 MET cc_start: 0.4379 (mtm) cc_final: 0.4100 (mtp) REVERT: K 68 PHE cc_start: 0.3771 (m-10) cc_final: 0.2847 (m-10) REVERT: K 72 ARG cc_start: 0.5708 (ptt180) cc_final: 0.5353 (ptt180) REVERT: K 83 MET cc_start: 0.3432 (mpt) cc_final: 0.3006 (mpp) REVERT: K 102 ASN cc_start: 0.6184 (t0) cc_final: 0.5926 (t0) REVERT: L 36 TRP cc_start: 0.4562 (m100) cc_final: 0.3796 (m100) REVERT: L 38 ARG cc_start: 0.5652 (ptp-170) cc_final: 0.5403 (ptp-110) REVERT: L 59 GLU cc_start: 0.6374 (mp0) cc_final: 0.6083 (mp0) REVERT: L 83 MET cc_start: 0.5115 (mtm) cc_final: 0.4810 (mtm) REVERT: L 84 ASN cc_start: 0.5659 (m110) cc_final: 0.4666 (t0) REVERT: L 86 LEU cc_start: 0.3580 (mp) cc_final: 0.3174 (mt) REVERT: L 102 ASN cc_start: 0.7093 (p0) cc_final: 0.6501 (m-40) REVERT: L 104 TYR cc_start: 0.5369 (m-10) cc_final: 0.5056 (m-10) outliers start: 176 outliers final: 124 residues processed: 484 average time/residue: 0.2261 time to fit residues: 185.6876 Evaluate side-chains 464 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 321 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 647 TRP Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 712 ASN Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 538 ASP Chi-restraints excluded: chain F residue 570 GLN Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 102 ASN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 146 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 380 optimal weight: 1.9990 chunk 448 optimal weight: 6.9990 chunk 345 optimal weight: 0.7980 chunk 360 optimal weight: 1.9990 chunk 318 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 330 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS E 709 ASN F 253 HIS I 3 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 ASN ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.166345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.140949 restraints weight = 74938.432| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.34 r_work: 0.3529 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 42240 Z= 0.140 Angle : 0.516 9.484 57273 Z= 0.273 Chirality : 0.042 0.174 6495 Planarity : 0.003 0.040 7128 Dihedral : 5.132 56.378 5599 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.56 % Allowed : 13.31 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.12), residues: 4986 helix: -0.15 (0.11), residues: 2178 sheet: -0.54 (0.17), residues: 939 loop : -0.22 (0.15), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 171 TYR 0.013 0.001 TYR F 513 PHE 0.015 0.001 PHE B 393 TRP 0.018 0.001 TRP E 342 HIS 0.005 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00319 (42216) covalent geometry : angle 0.51553 (57225) SS BOND : bond 0.00313 ( 24) SS BOND : angle 1.06424 ( 48) hydrogen bonds : bond 0.03616 ( 1901) hydrogen bonds : angle 4.29679 ( 4845) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 327 time to evaluate : 1.603 Fit side-chains revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7620 (mp) REVERT: A 527 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5789 (pp) REVERT: A 689 TYR cc_start: 0.7968 (m-80) cc_final: 0.7688 (m-80) REVERT: B 35 MET cc_start: 0.8084 (mtm) cc_final: 0.7859 (mtt) REVERT: B 153 LEU cc_start: 0.7218 (mt) cc_final: 0.6905 (mt) REVERT: B 162 LYS cc_start: 0.6963 (ptpt) cc_final: 0.6563 (mtpp) REVERT: B 220 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7388 (pt0) REVERT: B 375 MET cc_start: 0.6061 (mtt) cc_final: 0.5699 (mtt) REVERT: B 385 LEU cc_start: 0.6419 (tp) cc_final: 0.6050 (mp) REVERT: B 599 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8467 (mt) REVERT: B 647 TRP cc_start: 0.8560 (OUTLIER) cc_final: 0.7862 (p90) REVERT: B 767 GLU cc_start: 0.4001 (OUTLIER) cc_final: 0.2963 (mp0) REVERT: C 48 THR cc_start: 0.8115 (m) cc_final: 0.7717 (m) REVERT: C 104 HIS cc_start: 0.9155 (OUTLIER) cc_final: 0.7813 (t70) REVERT: C 171 ARG cc_start: 0.5873 (ttt-90) cc_final: 0.5395 (mtp180) REVERT: C 250 PHE cc_start: 0.7059 (t80) cc_final: 0.6834 (t80) REVERT: C 527 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5590 (pp) REVERT: C 723 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7612 (mt) REVERT: C 755 ASN cc_start: 0.7826 (m110) cc_final: 0.7541 (m-40) REVERT: D 279 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.8014 (tp) REVERT: D 375 MET cc_start: 0.5480 (mtt) cc_final: 0.5102 (mtt) REVERT: D 385 LEU cc_start: 0.6676 (tp) cc_final: 0.6191 (mp) REVERT: D 570 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6311 (pp30) REVERT: D 619 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7973 (tp) REVERT: D 647 TRP cc_start: 0.8533 (OUTLIER) cc_final: 0.7507 (p90) REVERT: D 648 TYR cc_start: 0.8139 (m-80) cc_final: 0.7678 (m-80) REVERT: D 689 TYR cc_start: 0.7482 (m-80) cc_final: 0.7207 (t80) REVERT: D 767 GLU cc_start: 0.5073 (OUTLIER) cc_final: 0.3963 (mp0) REVERT: E 64 SER cc_start: 0.6927 (OUTLIER) cc_final: 0.6557 (t) REVERT: E 275 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7992 (t80) REVERT: E 505 ILE cc_start: 0.7564 (mm) cc_final: 0.7179 (tp) REVERT: E 585 ASN cc_start: 0.4776 (t0) cc_final: 0.4504 (t0) REVERT: E 587 LEU cc_start: 0.7451 (tp) cc_final: 0.7123 (tp) REVERT: E 623 ASP cc_start: 0.8058 (t0) cc_final: 0.7742 (t70) REVERT: F 15 PRO cc_start: 0.4816 (Cg_endo) cc_final: 0.4571 (Cg_exo) REVERT: F 153 LEU cc_start: 0.7535 (mt) cc_final: 0.7207 (mt) REVERT: F 353 PHE cc_start: 0.6377 (OUTLIER) cc_final: 0.4009 (m-10) REVERT: F 385 LEU cc_start: 0.7154 (tp) cc_final: 0.6184 (mp) REVERT: F 415 LYS cc_start: 0.7295 (ttpt) cc_final: 0.7072 (tptm) REVERT: F 570 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6989 (pp30) REVERT: F 587 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7810 (tp) REVERT: F 625 ASN cc_start: 0.6916 (m-40) cc_final: 0.6439 (t0) REVERT: F 647 TRP cc_start: 0.8582 (OUTLIER) cc_final: 0.8124 (p90) REVERT: G 34 MET cc_start: 0.5888 (mmm) cc_final: 0.5331 (mmp) REVERT: G 58 THR cc_start: 0.6996 (p) cc_final: 0.6652 (t) REVERT: G 68 PHE cc_start: 0.4044 (m-10) cc_final: 0.3195 (m-10) REVERT: G 83 MET cc_start: 0.3611 (mpp) cc_final: 0.2867 (mpp) REVERT: H 59 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6864 (mt-10) REVERT: I 102 ASN cc_start: 0.6518 (t0) cc_final: 0.6312 (t0) REVERT: J 34 MET cc_start: 0.6975 (tmm) cc_final: 0.6749 (mmm) REVERT: J 36 TRP cc_start: 0.5003 (m100) cc_final: 0.4676 (m100) REVERT: J 38 ARG cc_start: 0.5509 (ptp-110) cc_final: 0.5304 (ptp-110) REVERT: J 56 GLU cc_start: 0.6928 (tm-30) cc_final: 0.6650 (tm-30) REVERT: J 67 ARG cc_start: 0.6094 (mtm110) cc_final: 0.5101 (mtp85) REVERT: J 83 MET cc_start: 0.4341 (mtm) cc_final: 0.4047 (mtp) REVERT: K 58 THR cc_start: 0.6849 (p) cc_final: 0.6648 (t) REVERT: K 68 PHE cc_start: 0.3730 (m-10) cc_final: 0.2828 (m-10) REVERT: K 72 ARG cc_start: 0.5844 (ptt180) cc_final: 0.5395 (ptt180) REVERT: K 83 MET cc_start: 0.3470 (mpt) cc_final: 0.3030 (mpp) REVERT: K 102 ASN cc_start: 0.6203 (t0) cc_final: 0.5935 (t0) REVERT: L 36 TRP cc_start: 0.4585 (m100) cc_final: 0.3783 (m100) REVERT: L 59 GLU cc_start: 0.6381 (mp0) cc_final: 0.6101 (mt-10) REVERT: L 84 ASN cc_start: 0.5729 (m110) cc_final: 0.4766 (t0) REVERT: L 86 LEU cc_start: 0.3577 (mp) cc_final: 0.3164 (mt) REVERT: L 102 ASN cc_start: 0.7037 (p0) cc_final: 0.6422 (m-40) REVERT: L 104 TYR cc_start: 0.5434 (m-10) cc_final: 0.5131 (m-10) outliers start: 163 outliers final: 126 residues processed: 467 average time/residue: 0.2260 time to fit residues: 177.9725 Evaluate side-chains 464 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 318 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 647 TRP Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 393 PHE Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 538 ASP Chi-restraints excluded: chain F residue 570 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 759 ILE Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 1 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 308 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 470 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 475 optimal weight: 0.5980 chunk 243 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS E 709 ASN F 253 HIS I 3 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 ASN ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.166384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.140974 restraints weight = 74922.292| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.34 r_work: 0.3516 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 42240 Z= 0.138 Angle : 0.515 8.998 57273 Z= 0.273 Chirality : 0.042 0.151 6495 Planarity : 0.003 0.040 7128 Dihedral : 5.139 57.399 5599 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.64 % Allowed : 13.20 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.12), residues: 4986 helix: -0.14 (0.11), residues: 2178 sheet: -0.53 (0.17), residues: 939 loop : -0.23 (0.15), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 67 TYR 0.013 0.001 TYR C 332 PHE 0.012 0.001 PHE I 68 TRP 0.021 0.001 TRP E 342 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00314 (42216) covalent geometry : angle 0.51400 (57225) SS BOND : bond 0.00313 ( 24) SS BOND : angle 1.03066 ( 48) hydrogen bonds : bond 0.03591 ( 1901) hydrogen bonds : angle 4.25596 ( 4845) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 336 time to evaluate : 1.668 Fit side-chains revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7608 (mp) REVERT: A 527 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5693 (pp) REVERT: A 689 TYR cc_start: 0.7968 (m-80) cc_final: 0.7680 (m-80) REVERT: B 35 MET cc_start: 0.8076 (mtm) cc_final: 0.7851 (mtt) REVERT: B 153 LEU cc_start: 0.7203 (mt) cc_final: 0.6881 (mt) REVERT: B 162 LYS cc_start: 0.7074 (ptpt) cc_final: 0.6588 (mtpp) REVERT: B 220 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7341 (pt0) REVERT: B 375 MET cc_start: 0.6043 (mtt) cc_final: 0.5679 (mtt) REVERT: B 385 LEU cc_start: 0.6394 (tp) cc_final: 0.6020 (mp) REVERT: B 599 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8462 (mt) REVERT: B 647 TRP cc_start: 0.8563 (OUTLIER) cc_final: 0.7851 (p90) REVERT: B 767 GLU cc_start: 0.3986 (OUTLIER) cc_final: 0.2977 (mp0) REVERT: C 48 THR cc_start: 0.8123 (m) cc_final: 0.7727 (m) REVERT: C 104 HIS cc_start: 0.9153 (OUTLIER) cc_final: 0.7813 (t70) REVERT: C 171 ARG cc_start: 0.5917 (ttt-90) cc_final: 0.5398 (mtp180) REVERT: C 250 PHE cc_start: 0.7147 (t80) cc_final: 0.6892 (t80) REVERT: C 527 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5566 (pp) REVERT: C 723 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7643 (mt) REVERT: C 755 ASN cc_start: 0.7854 (m110) cc_final: 0.7591 (m-40) REVERT: D 279 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8126 (tp) REVERT: D 375 MET cc_start: 0.5323 (mtt) cc_final: 0.4906 (mtt) REVERT: D 385 LEU cc_start: 0.6643 (tp) cc_final: 0.6151 (mp) REVERT: D 570 GLN cc_start: 0.6802 (OUTLIER) cc_final: 0.6291 (pp30) REVERT: D 619 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7968 (tp) REVERT: D 647 TRP cc_start: 0.8530 (OUTLIER) cc_final: 0.7493 (p90) REVERT: D 648 TYR cc_start: 0.8145 (m-80) cc_final: 0.7669 (m-80) REVERT: D 689 TYR cc_start: 0.7473 (m-80) cc_final: 0.7195 (t80) REVERT: D 767 GLU cc_start: 0.5058 (OUTLIER) cc_final: 0.3968 (mp0) REVERT: E 64 SER cc_start: 0.6937 (OUTLIER) cc_final: 0.6570 (t) REVERT: E 275 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7994 (t80) REVERT: E 505 ILE cc_start: 0.7537 (mm) cc_final: 0.7158 (tp) REVERT: E 585 ASN cc_start: 0.5141 (t0) cc_final: 0.4785 (t0) REVERT: E 712 ASN cc_start: 0.8922 (OUTLIER) cc_final: 0.8517 (m-40) REVERT: F 15 PRO cc_start: 0.4782 (Cg_endo) cc_final: 0.4547 (Cg_exo) REVERT: F 153 LEU cc_start: 0.7510 (mt) cc_final: 0.7170 (mt) REVERT: F 353 PHE cc_start: 0.6346 (OUTLIER) cc_final: 0.3946 (m-10) REVERT: F 385 LEU cc_start: 0.7109 (tp) cc_final: 0.6133 (mp) REVERT: F 415 LYS cc_start: 0.7359 (ttpt) cc_final: 0.7090 (tptm) REVERT: F 570 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6977 (pp30) REVERT: F 587 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7799 (tp) REVERT: F 625 ASN cc_start: 0.6946 (m-40) cc_final: 0.6426 (t0) REVERT: F 647 TRP cc_start: 0.8578 (OUTLIER) cc_final: 0.8113 (p90) REVERT: G 58 THR cc_start: 0.6958 (p) cc_final: 0.6634 (t) REVERT: G 68 PHE cc_start: 0.3912 (m-10) cc_final: 0.3038 (m-10) REVERT: G 83 MET cc_start: 0.3564 (mpp) cc_final: 0.2793 (mpp) REVERT: H 83 MET cc_start: 0.3970 (mtm) cc_final: 0.3518 (ttp) REVERT: J 36 TRP cc_start: 0.4963 (m100) cc_final: 0.4327 (m100) REVERT: J 56 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6669 (tm-30) REVERT: J 59 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6880 (mp0) REVERT: J 67 ARG cc_start: 0.6090 (mtm110) cc_final: 0.5086 (mtp85) REVERT: J 83 MET cc_start: 0.4328 (mtm) cc_final: 0.4048 (mtp) REVERT: K 34 MET cc_start: 0.6959 (mmm) cc_final: 0.6363 (mmm) REVERT: K 58 THR cc_start: 0.6831 (p) cc_final: 0.6582 (t) REVERT: K 68 PHE cc_start: 0.3741 (m-10) cc_final: 0.2851 (m-10) REVERT: K 72 ARG cc_start: 0.5803 (ptt180) cc_final: 0.5363 (ptt180) REVERT: K 102 ASN cc_start: 0.6233 (t0) cc_final: 0.5950 (t0) REVERT: L 36 TRP cc_start: 0.4380 (m100) cc_final: 0.4068 (m100) REVERT: L 83 MET cc_start: 0.5418 (mtm) cc_final: 0.4585 (mtt) REVERT: L 84 ASN cc_start: 0.5675 (m110) cc_final: 0.4737 (t0) REVERT: L 86 LEU cc_start: 0.3756 (mp) cc_final: 0.3385 (mt) REVERT: L 102 ASN cc_start: 0.7077 (p0) cc_final: 0.6420 (m-40) REVERT: L 104 TYR cc_start: 0.5381 (m-10) cc_final: 0.4829 (m-10) outliers start: 167 outliers final: 128 residues processed: 476 average time/residue: 0.2322 time to fit residues: 186.6811 Evaluate side-chains 468 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 319 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 395 SER Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 647 TRP Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 712 ASN Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 393 PHE Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 538 ASP Chi-restraints excluded: chain F residue 570 GLN Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 102 ASN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 112 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 223 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 325 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 474 optimal weight: 4.9990 chunk 459 optimal weight: 0.0770 chunk 197 optimal weight: 0.5980 chunk 395 optimal weight: 1.9990 chunk 483 optimal weight: 0.8980 chunk 164 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS D 624 ASN E 709 ASN F 253 HIS I 3 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 ASN ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.166777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.139941 restraints weight = 74897.570| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.48 r_work: 0.3511 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 42240 Z= 0.126 Angle : 0.510 8.844 57273 Z= 0.269 Chirality : 0.041 0.176 6495 Planarity : 0.003 0.043 7128 Dihedral : 5.109 58.191 5599 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.27 % Allowed : 13.68 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.12), residues: 4986 helix: -0.09 (0.11), residues: 2178 sheet: -0.53 (0.17), residues: 939 loop : -0.23 (0.15), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 171 TYR 0.013 0.001 TYR C 332 PHE 0.014 0.001 PHE E 250 TRP 0.020 0.001 TRP E 342 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00286 (42216) covalent geometry : angle 0.50905 (57225) SS BOND : bond 0.00313 ( 24) SS BOND : angle 1.13286 ( 48) hydrogen bonds : bond 0.03512 ( 1901) hydrogen bonds : angle 4.21489 ( 4845) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 333 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7618 (mp) REVERT: A 527 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5707 (pp) REVERT: A 689 TYR cc_start: 0.7990 (m-80) cc_final: 0.7709 (m-80) REVERT: B 35 MET cc_start: 0.8082 (mtm) cc_final: 0.7859 (mtt) REVERT: B 162 LYS cc_start: 0.6920 (ptpt) cc_final: 0.6467 (mtpp) REVERT: B 220 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7388 (pt0) REVERT: B 375 MET cc_start: 0.6076 (mtt) cc_final: 0.5791 (mtt) REVERT: B 385 LEU cc_start: 0.6382 (tp) cc_final: 0.6013 (mp) REVERT: B 599 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8469 (mt) REVERT: B 647 TRP cc_start: 0.8549 (OUTLIER) cc_final: 0.7832 (p90) REVERT: B 767 GLU cc_start: 0.3971 (OUTLIER) cc_final: 0.2974 (mp0) REVERT: C 48 THR cc_start: 0.8119 (m) cc_final: 0.7720 (m) REVERT: C 171 ARG cc_start: 0.5935 (ttt-90) cc_final: 0.5400 (mtp180) REVERT: C 250 PHE cc_start: 0.7051 (t80) cc_final: 0.6849 (t80) REVERT: C 527 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5672 (pp) REVERT: C 723 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7636 (mt) REVERT: C 755 ASN cc_start: 0.7860 (m110) cc_final: 0.7614 (m-40) REVERT: D 173 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5812 (mm) REVERT: D 279 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8162 (tp) REVERT: D 375 MET cc_start: 0.5599 (mtt) cc_final: 0.5243 (mtt) REVERT: D 385 LEU cc_start: 0.6579 (tp) cc_final: 0.6066 (mp) REVERT: D 570 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6339 (pp30) REVERT: D 619 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7971 (tp) REVERT: D 647 TRP cc_start: 0.8514 (OUTLIER) cc_final: 0.7472 (p90) REVERT: D 648 TYR cc_start: 0.8149 (m-80) cc_final: 0.7669 (m-80) REVERT: D 664 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7868 (tp) REVERT: D 689 TYR cc_start: 0.7472 (m-80) cc_final: 0.7198 (t80) REVERT: D 767 GLU cc_start: 0.5064 (OUTLIER) cc_final: 0.3976 (mp0) REVERT: E 64 SER cc_start: 0.6937 (OUTLIER) cc_final: 0.6586 (t) REVERT: E 275 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.8109 (t80) REVERT: E 587 LEU cc_start: 0.7430 (tp) cc_final: 0.7132 (tp) REVERT: E 712 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8504 (m-40) REVERT: F 15 PRO cc_start: 0.4789 (Cg_endo) cc_final: 0.4553 (Cg_exo) REVERT: F 153 LEU cc_start: 0.7506 (mt) cc_final: 0.7163 (mt) REVERT: F 353 PHE cc_start: 0.6324 (OUTLIER) cc_final: 0.4000 (m-10) REVERT: F 385 LEU cc_start: 0.7113 (tp) cc_final: 0.6139 (mp) REVERT: F 415 LYS cc_start: 0.7449 (ttpt) cc_final: 0.7179 (tptm) REVERT: F 496 ARG cc_start: 0.8020 (mmp80) cc_final: 0.7626 (mmp-170) REVERT: F 570 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.7002 (pp30) REVERT: F 625 ASN cc_start: 0.6947 (m-40) cc_final: 0.6427 (t0) REVERT: F 647 TRP cc_start: 0.8641 (OUTLIER) cc_final: 0.8219 (p90) REVERT: G 34 MET cc_start: 0.6061 (mmm) cc_final: 0.5625 (mmp) REVERT: G 58 THR cc_start: 0.7026 (p) cc_final: 0.6698 (t) REVERT: G 68 PHE cc_start: 0.3781 (m-10) cc_final: 0.3043 (m-10) REVERT: G 83 MET cc_start: 0.3765 (mpp) cc_final: 0.2944 (mpp) REVERT: H 83 MET cc_start: 0.4064 (mtm) cc_final: 0.3455 (ttm) REVERT: J 36 TRP cc_start: 0.5089 (m100) cc_final: 0.4404 (m100) REVERT: J 59 GLU cc_start: 0.7265 (mt-10) cc_final: 0.7016 (mp0) REVERT: J 67 ARG cc_start: 0.6202 (mtm110) cc_final: 0.5096 (mtp85) REVERT: J 83 MET cc_start: 0.4288 (mtm) cc_final: 0.3984 (mtp) REVERT: K 34 MET cc_start: 0.6954 (mmm) cc_final: 0.6380 (mmm) REVERT: K 58 THR cc_start: 0.6787 (p) cc_final: 0.6536 (t) REVERT: K 68 PHE cc_start: 0.3723 (m-10) cc_final: 0.2818 (m-10) REVERT: K 72 ARG cc_start: 0.5805 (ptt180) cc_final: 0.5348 (ptt180) REVERT: K 83 MET cc_start: 0.3516 (mpt) cc_final: 0.3026 (mpp) REVERT: K 102 ASN cc_start: 0.6272 (t0) cc_final: 0.5980 (t0) REVERT: L 34 MET cc_start: 0.6916 (tmm) cc_final: 0.6567 (mmt) REVERT: L 59 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6214 (mt-10) REVERT: L 83 MET cc_start: 0.5431 (mtm) cc_final: 0.4846 (mtt) REVERT: L 84 ASN cc_start: 0.5618 (m110) cc_final: 0.4776 (t0) REVERT: L 86 LEU cc_start: 0.3706 (mp) cc_final: 0.3356 (mt) REVERT: L 102 ASN cc_start: 0.7011 (p0) cc_final: 0.6558 (m-40) REVERT: L 104 TYR cc_start: 0.5399 (m-10) cc_final: 0.4780 (m-10) outliers start: 150 outliers final: 121 residues processed: 462 average time/residue: 0.2375 time to fit residues: 183.5311 Evaluate side-chains 457 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 315 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 395 SER Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 647 TRP Chi-restraints excluded: chain E residue 712 ASN Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 393 PHE Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 538 ASP Chi-restraints excluded: chain F residue 570 GLN Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 102 ASN Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 384 optimal weight: 0.8980 chunk 240 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 465 optimal weight: 0.9990 chunk 462 optimal weight: 1.9990 chunk 215 optimal weight: 0.0570 chunk 98 optimal weight: 0.3980 chunk 422 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 407 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS E 709 ASN F 253 HIS G 3 GLN I 3 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.167300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.140716 restraints weight = 74749.120| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.45 r_work: 0.3520 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 42240 Z= 0.109 Angle : 0.506 11.390 57273 Z= 0.266 Chirality : 0.041 0.272 6495 Planarity : 0.003 0.041 7128 Dihedral : 5.016 59.189 5599 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.05 % Allowed : 13.87 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.12), residues: 4986 helix: -0.02 (0.11), residues: 2178 sheet: -0.49 (0.17), residues: 939 loop : -0.20 (0.15), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 171 TYR 0.013 0.001 TYR J 104 PHE 0.014 0.001 PHE E 250 TRP 0.032 0.001 TRP L 36 HIS 0.005 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00241 (42216) covalent geometry : angle 0.50484 (57225) SS BOND : bond 0.00291 ( 24) SS BOND : angle 1.12877 ( 48) hydrogen bonds : bond 0.03387 ( 1901) hydrogen bonds : angle 4.14986 ( 4845) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9972 Ramachandran restraints generated. 4986 Oldfield, 0 Emsley, 4986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 325 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 516 LYS cc_start: 0.5751 (mmmt) cc_final: 0.5082 (ttmt) REVERT: A 527 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5812 (pp) REVERT: A 689 TYR cc_start: 0.7979 (m-80) cc_final: 0.7692 (m-80) REVERT: B 35 MET cc_start: 0.8097 (mtm) cc_final: 0.7881 (mtt) REVERT: B 155 HIS cc_start: 0.6910 (t-170) cc_final: 0.6535 (t-170) REVERT: B 162 LYS cc_start: 0.6864 (ptpt) cc_final: 0.6435 (mtpp) REVERT: B 220 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7386 (pt0) REVERT: B 375 MET cc_start: 0.5965 (mtt) cc_final: 0.5603 (mtt) REVERT: B 385 LEU cc_start: 0.6335 (tp) cc_final: 0.5973 (mp) REVERT: B 599 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8450 (mt) REVERT: B 647 TRP cc_start: 0.8512 (OUTLIER) cc_final: 0.7786 (p90) REVERT: B 767 GLU cc_start: 0.4234 (OUTLIER) cc_final: 0.3187 (mp0) REVERT: C 48 THR cc_start: 0.8095 (m) cc_final: 0.7695 (m) REVERT: C 171 ARG cc_start: 0.5959 (ttt-90) cc_final: 0.5444 (mtp180) REVERT: C 542 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6056 (mp0) REVERT: C 723 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7644 (mt) REVERT: C 755 ASN cc_start: 0.7922 (m110) cc_final: 0.7697 (m-40) REVERT: D 173 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5827 (mm) REVERT: D 279 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8110 (tp) REVERT: D 375 MET cc_start: 0.5572 (mtt) cc_final: 0.5263 (mtt) REVERT: D 385 LEU cc_start: 0.6510 (tp) cc_final: 0.6064 (mp) REVERT: D 570 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6303 (pp30) REVERT: D 619 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7962 (tp) REVERT: D 647 TRP cc_start: 0.8472 (OUTLIER) cc_final: 0.7428 (p90) REVERT: D 648 TYR cc_start: 0.8167 (m-80) cc_final: 0.7678 (m-80) REVERT: D 664 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7869 (tp) REVERT: D 689 TYR cc_start: 0.7419 (m-80) cc_final: 0.7215 (t80) REVERT: D 767 GLU cc_start: 0.5042 (OUTLIER) cc_final: 0.3980 (mp0) REVERT: E 64 SER cc_start: 0.6923 (OUTLIER) cc_final: 0.6577 (t) REVERT: E 275 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8040 (t80) REVERT: E 505 ILE cc_start: 0.7298 (mm) cc_final: 0.6867 (tp) REVERT: E 587 LEU cc_start: 0.7356 (tp) cc_final: 0.7066 (tp) REVERT: E 712 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8492 (m-40) REVERT: F 15 PRO cc_start: 0.4765 (Cg_endo) cc_final: 0.4524 (Cg_exo) REVERT: F 153 LEU cc_start: 0.7489 (mt) cc_final: 0.7145 (mt) REVERT: F 279 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7858 (tp) REVERT: F 353 PHE cc_start: 0.6209 (OUTLIER) cc_final: 0.4006 (m-10) REVERT: F 385 LEU cc_start: 0.7067 (tp) cc_final: 0.6091 (mp) REVERT: F 504 ASP cc_start: 0.7006 (t0) cc_final: 0.6790 (t70) REVERT: F 570 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7017 (pp30) REVERT: F 625 ASN cc_start: 0.6953 (m-40) cc_final: 0.6430 (t0) REVERT: F 647 TRP cc_start: 0.8591 (OUTLIER) cc_final: 0.8272 (p90) REVERT: G 34 MET cc_start: 0.6062 (mmm) cc_final: 0.5672 (mmm) REVERT: G 58 THR cc_start: 0.6912 (p) cc_final: 0.6588 (t) REVERT: G 68 PHE cc_start: 0.3787 (m-10) cc_final: 0.3062 (m-10) REVERT: G 83 MET cc_start: 0.3788 (mpp) cc_final: 0.2971 (mpp) REVERT: H 86 LEU cc_start: 0.3241 (mp) cc_final: 0.2909 (mt) REVERT: J 36 TRP cc_start: 0.5076 (m100) cc_final: 0.4281 (m100) REVERT: J 67 ARG cc_start: 0.6184 (mtm110) cc_final: 0.5076 (mtp85) REVERT: J 83 MET cc_start: 0.4263 (mtm) cc_final: 0.3953 (mtp) REVERT: K 34 MET cc_start: 0.6875 (mmm) cc_final: 0.6379 (mmm) REVERT: K 58 THR cc_start: 0.6737 (p) cc_final: 0.6478 (t) REVERT: K 68 PHE cc_start: 0.3718 (m-10) cc_final: 0.2803 (m-10) REVERT: K 72 ARG cc_start: 0.5710 (ptt180) cc_final: 0.5239 (ptt180) REVERT: K 83 MET cc_start: 0.3461 (mpt) cc_final: 0.2948 (mpp) REVERT: K 102 ASN cc_start: 0.6282 (t0) cc_final: 0.5990 (t0) REVERT: L 19 ARG cc_start: 0.5537 (mtt-85) cc_final: 0.4878 (mmt180) REVERT: L 28 PRO cc_start: 0.5267 (Cg_endo) cc_final: 0.5047 (Cg_exo) REVERT: L 31 ARG cc_start: 0.6491 (ttp-110) cc_final: 0.6198 (ttp-170) REVERT: L 36 TRP cc_start: 0.4955 (m100) cc_final: 0.4257 (m100) REVERT: L 59 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6089 (mt-10) REVERT: L 83 MET cc_start: 0.5420 (mtm) cc_final: 0.4879 (mtt) REVERT: L 84 ASN cc_start: 0.5692 (m110) cc_final: 0.4794 (t0) REVERT: L 86 LEU cc_start: 0.3736 (mp) cc_final: 0.3382 (mt) REVERT: L 102 ASN cc_start: 0.6962 (p0) cc_final: 0.6532 (m-40) REVERT: L 104 TYR cc_start: 0.5338 (m-10) cc_final: 0.4741 (m-10) outliers start: 140 outliers final: 103 residues processed: 446 average time/residue: 0.2255 time to fit residues: 169.6403 Evaluate side-chains 439 residues out of total 4587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 315 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 395 SER Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 647 TRP Chi-restraints excluded: chain E residue 712 ASN Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 780 LYS Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 393 PHE Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 538 ASP Chi-restraints excluded: chain F residue 570 GLN Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 647 TRP Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 793 THR Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 311 optimal weight: 1.9990 chunk 341 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 225 optimal weight: 0.9990 chunk 373 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS D 253 HIS D 312 HIS D 744 GLN E 709 ASN F 253 HIS G 3 GLN I 3 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN J 102 ASN ** K 32 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 = 0.4319 r_free = 0.4319 target = 0.165249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.138790 restraints weight = 75300.585| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.41 r_work: 0.3494 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 42240 Z= 0.199 Angle : 0.578 10.855 57273 Z= 0.302 Chirality : 0.044 0.296 6495 Planarity : 0.004 0.038 7128 Dihedral : 5.185 58.660 5591 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.08 % Allowed : 14.16 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.12), residues: 4986 helix: -0.25 (0.11), residues: 2178 sheet: -0.58 (0.17), residues: 939 loop : -0.32 (0.15), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 171 TYR 0.020 0.002 TYR L 97 PHE 0.018 0.002 PHE E 250 TRP 0.017 0.002 TRP L 36 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00465 (42216) covalent geometry : angle 0.57701 (57225) SS BOND : bond 0.00417 ( 24) SS BOND : angle 1.27024 ( 48) hydrogen bonds : bond 0.03930 ( 1901) hydrogen bonds : angle 4.36300 ( 4845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10784.04 seconds wall clock time: 185 minutes 14.07 seconds (11114.07 seconds total)