Starting phenix.real_space_refine on Sat Mar 7 04:03:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xzh_33527/03_2026/7xzh_33527_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xzh_33527/03_2026/7xzh_33527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xzh_33527/03_2026/7xzh_33527_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xzh_33527/03_2026/7xzh_33527_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xzh_33527/03_2026/7xzh_33527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xzh_33527/03_2026/7xzh_33527.map" } resolution = 2.78 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= 0.003 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 156 5.16 5 C 24296 2.51 5 N 6095 2.21 5 O 6514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 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: 37073 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 6025 Classifications: {'peptide': 729} Link IDs: {'PTRANS': 29, 'TRANS': 699} Chain breaks: 2 Chain: "B" Number of atoms: 6032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 6032 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 29, 'TRANS': 700} Chain breaks: 2 Chain: "C" Number of atoms: 6032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 6032 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 29, 'TRANS': 700} Chain breaks: 2 Chain: "D" Number of atoms: 6032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 6032 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 29, 'TRANS': 700} Chain breaks: 2 Chain: "E" Number of atoms: 6032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 6032 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 29, 'TRANS': 700} Chain breaks: 2 Chain: "F" Number of atoms: 6032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 6032 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 29, 'TRANS': 700} Chain breaks: 2 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "C" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "E" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "F" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Time building chain proxies: 9.23, per 1000 atoms: 0.25 Number of scatterers: 37073 At special positions: 0 Unit cell: (147.68, 143.52, 192.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 P 12 15.00 O 6514 8.00 N 6095 7.00 C 24296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, 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=2.02 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=2.03 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 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: 3.13 Conformation dependent library (CDL) restraints added in 1.5 seconds 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8518 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 23 sheets defined 53.7% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 14 through 21 removed outlier: 4.414A 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: 5.306A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 166 removed outlier: 4.287A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 172 removed outlier: 4.233A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 258 through 286 removed outlier: 3.721A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) 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 345 Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.796A pdb=" N GLU A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 383 through 391 removed outlier: 4.158A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 412 through 420 removed outlier: 3.763A pdb=" N GLN A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.568A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 543 removed outlier: 4.101A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 removed outlier: 3.553A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 590 Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 629 through 638 removed outlier: 3.749A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 678 through 684 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 Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.513A pdb=" N LEU A 773 " --> pdb=" O PRO A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 793 removed outlier: 3.620A pdb=" N THR A 793 " --> pdb=" O ASP A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 807 removed outlier: 3.995A pdb=" N LYS A 807 " --> pdb=" O TRP A 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.642A 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 116 Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 4.991A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.960A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 removed outlier: 3.645A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) 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 299 through 304 removed outlier: 3.867A pdb=" N THR B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 345 Processing helix chain 'B' and resid 355 through 360 removed outlier: 3.754A pdb=" N GLU B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 removed outlier: 3.659A pdb=" N TYR B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.029A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 removed outlier: 4.168A pdb=" N ASN B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 509 through 515 removed outlier: 3.673A pdb=" N ILE B 512 " --> pdb=" O PRO B 509 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 543 removed outlier: 5.088A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 removed outlier: 3.634A pdb=" N THR B 563 " --> pdb=" O PRO B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 590 Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.790A pdb=" N HIS B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.513A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 724 through 730 Processing helix chain 'B' and resid 747 through 753 Processing helix chain 'B' and resid 770 through 776 Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 807 removed outlier: 3.841A pdb=" N LYS B 807 " --> pdb=" O TRP B 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 14 through 21 removed outlier: 4.490A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 50 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: 5.404A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 removed outlier: 4.469A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 172 removed outlier: 4.355A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 4.112A pdb=" N GLU C 238 " --> pdb=" O LYS C 234 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLN C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 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 345 Processing helix chain 'C' and resid 355 through 360 removed outlier: 3.811A pdb=" N GLU C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 381 removed outlier: 3.998A pdb=" N ILE C 379 " --> pdb=" O MET C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 391 removed outlier: 4.130A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'C' and resid 412 through 420 removed outlier: 3.541A pdb=" N GLN C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 504 through 508 Processing helix chain 'C' and resid 509 through 515 removed outlier: 3.567A pdb=" N ILE C 512 " --> pdb=" O PRO C 509 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 543 removed outlier: 4.101A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 removed outlier: 3.553A pdb=" N THR C 563 " --> pdb=" O PRO C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 590 Processing helix chain 'C' and resid 607 through 613 Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.749A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 678 through 684 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 Processing helix chain 'C' and resid 770 through 776 removed outlier: 3.513A pdb=" N LEU C 773 " --> pdb=" O PRO C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 793 removed outlier: 3.619A pdb=" N THR C 793 " --> pdb=" O ASP C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 807 removed outlier: 3.995A pdb=" N LYS C 807 " --> pdb=" O TRP C 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 8 Processing helix chain 'D' and resid 15 through 19 removed outlier: 3.852A 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 116 Processing helix chain 'D' and resid 119 through 146 Proline residue: D 126 - end of helix removed outlier: 5.081A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 3.824A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 172 removed outlier: 3.652A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.562A pdb=" N LYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 286 removed outlier: 3.540A pdb=" N LEU D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS D 280 " --> pdb=" O ILE D 276 " (cutoff:3.500A) 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 299 through 304 removed outlier: 3.931A pdb=" N THR D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 345 Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.519A pdb=" N SER D 361 " --> pdb=" O ARG D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 removed outlier: 3.754A pdb=" N ILE D 379 " --> pdb=" O MET D 375 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 392 removed outlier: 4.082A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 411 removed outlier: 4.138A pdb=" N ASN D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU D 410 " --> pdb=" O ASN D 406 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP D 411 " --> pdb=" O LEU D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 420 removed outlier: 3.551A pdb=" N ARG D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'D' and resid 509 through 515 removed outlier: 3.672A pdb=" N ILE D 512 " --> pdb=" O PRO D 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR D 513 " --> pdb=" O LEU D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 543 removed outlier: 5.088A pdb=" N GLY D 539 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG D 541 " --> pdb=" O ASP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 566 removed outlier: 3.634A pdb=" N THR D 563 " --> pdb=" O PRO D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 590 Processing helix chain 'D' and resid 608 through 613 Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.790A pdb=" N HIS D 637 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 661 removed outlier: 3.513A pdb=" N ILE D 658 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 Processing helix chain 'D' and resid 701 through 707 Processing helix chain 'D' and resid 724 through 730 Processing helix chain 'D' and resid 747 through 753 Processing helix chain 'D' and resid 770 through 776 Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 795 through 807 removed outlier: 3.841A pdb=" N LYS D 807 " --> pdb=" O TRP D 803 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 10 Processing helix chain 'E' and resid 14 through 19 removed outlier: 4.361A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) 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: 5.322A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 166 removed outlier: 4.295A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 172 removed outlier: 4.045A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 256 removed outlier: 3.694A pdb=" N LYS E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 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 345 Processing helix chain 'E' and resid 353 through 359 removed outlier: 3.689A pdb=" N GLU E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 381 Processing helix chain 'E' and resid 383 through 391 removed outlier: 4.157A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'E' and resid 395 through 411 Processing helix chain 'E' and resid 414 through 420 removed outlier: 3.698A pdb=" N GLN E 418 " --> pdb=" O ASP E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 445 Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 504 through 508 Processing helix chain 'E' and resid 509 through 515 removed outlier: 3.567A pdb=" N ILE E 512 " --> pdb=" O PRO E 509 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 543 removed outlier: 4.102A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 removed outlier: 3.552A pdb=" N THR E 563 " --> pdb=" O PRO E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 590 Processing helix chain 'E' and resid 607 through 613 Processing helix chain 'E' and resid 629 through 638 removed outlier: 3.751A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 Processing helix chain 'E' and resid 678 through 684 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 Processing helix chain 'E' and resid 770 through 776 removed outlier: 3.513A pdb=" N LEU E 773 " --> pdb=" O PRO E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 793 removed outlier: 3.619A pdb=" N THR E 793 " --> pdb=" O ASP E 789 " (cutoff:3.500A) Processing helix chain 'E' and resid 795 through 807 removed outlier: 3.995A pdb=" N LYS E 807 " --> pdb=" O TRP E 803 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 8 Processing helix chain 'F' and resid 9 through 11 No H-bonds generated for 'chain 'F' and resid 9 through 11' Processing helix chain 'F' and resid 15 through 21 removed outlier: 3.660A 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 116 Processing helix chain 'F' and resid 119 through 146 Proline residue: F 126 - end of helix removed outlier: 4.994A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 166 removed outlier: 3.891A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 233 through 255 removed outlier: 3.739A pdb=" N LYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 286 removed outlier: 3.622A pdb=" N LEU F 277 " --> pdb=" O ILE F 273 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N CYS F 280 " --> pdb=" O ILE F 276 " (cutoff:3.500A) 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 345 Processing helix chain 'F' and resid 353 through 360 Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 383 through 392 removed outlier: 4.034A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 411 Processing helix chain 'F' and resid 413 through 420 removed outlier: 3.549A pdb=" N ARG F 419 " --> pdb=" O LYS F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 445 Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 484 through 494 Processing helix chain 'F' and resid 504 through 508 Processing helix chain 'F' and resid 509 through 515 removed outlier: 3.673A pdb=" N ILE F 512 " --> pdb=" O PRO F 509 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR F 513 " --> pdb=" O LEU F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 543 removed outlier: 5.088A pdb=" N GLY F 539 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG F 541 " --> pdb=" O ASP F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 566 removed outlier: 3.634A pdb=" N THR F 563 " --> pdb=" O PRO F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 590 Processing helix chain 'F' and resid 608 through 613 Processing helix chain 'F' and resid 629 through 638 removed outlier: 3.790A pdb=" N HIS F 637 " --> pdb=" O SER F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 661 removed outlier: 3.512A pdb=" N ILE F 658 " --> pdb=" O PRO F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 684 Processing helix chain 'F' and resid 701 through 707 Processing helix chain 'F' and resid 724 through 730 Processing helix chain 'F' and resid 747 through 753 Processing helix chain 'F' and resid 770 through 776 Processing helix chain 'F' and resid 787 through 792 Processing helix chain 'F' and resid 795 through 807 removed outlier: 3.840A pdb=" N LYS F 807 " --> pdb=" O TRP F 803 " (cutoff:3.500A) 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 60 through 61 Processing sheet with id=AA3, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.455A pdb=" N LEU A 451 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N TYR A 477 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 453 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 474 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 550 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 523 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 552 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU A 549 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASN A 575 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 551 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 644 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU A 667 " --> pdb=" O ASP A 691 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU A 690 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 713 " --> pdb=" O HIS A 737 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 736 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 459 through 460 removed outlier: 6.912A pdb=" N VAL A 459 " --> pdb=" O LYS A 482 " (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 60 through 61 Processing sheet with id=AA7, first strand: chain 'B' and resid 421 through 422 removed outlier: 3.612A pdb=" N LEU B 432 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 521 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LYS B 552 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 523 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 572 " --> pdb=" O GLU B 597 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE B 599 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE B 574 " --> pdb=" O ILE B 599 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 596 " --> pdb=" O GLU B 618 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP B 620 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 598 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE B 619 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU B 667 " --> pdb=" O ASP B 691 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 690 " --> pdb=" O ALA B 714 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU B 713 " --> pdb=" O HIS B 737 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 459 through 461 Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB1, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AB2, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.456A pdb=" N LEU C 451 " --> pdb=" O TRP C 475 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N TYR C 477 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C 453 " --> pdb=" O TYR C 477 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 474 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG C 550 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C 523 " --> pdb=" O ARG C 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS C 552 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU C 549 " --> pdb=" O SER C 573 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN C 575 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU C 551 " --> pdb=" O ASN C 575 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU C 572 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE C 599 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE C 574 " --> pdb=" O ILE C 599 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 619 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 644 " --> pdb=" O TYR C 668 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU C 667 " --> pdb=" O ASP C 691 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 690 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 713 " --> pdb=" O HIS C 737 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU C 736 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 459 through 460 removed outlier: 6.911A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB5, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AB6, first strand: chain 'D' and resid 421 through 422 removed outlier: 3.612A pdb=" N LEU D 432 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU D 451 " --> pdb=" O TRP D 475 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N TYR D 477 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU D 453 " --> pdb=" O TYR D 477 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU D 521 " --> pdb=" O ARG D 550 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LYS D 552 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU D 523 " --> pdb=" O LYS D 552 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D 572 " --> pdb=" O GLU D 597 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE D 599 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE D 574 " --> pdb=" O ILE D 599 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 596 " --> pdb=" O GLU D 618 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP D 620 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 598 " --> pdb=" O ASP D 620 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE D 619 " --> pdb=" O LYS D 645 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU D 644 " --> pdb=" O TYR D 668 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU D 667 " --> pdb=" O ASP D 691 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU D 690 " --> pdb=" O ALA D 714 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU D 713 " --> pdb=" O HIS D 737 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU D 736 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE D 759 " --> pdb=" O VAL D 785 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 459 through 461 Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 56 removed outlier: 8.772A pdb=" N ARG E 306 " --> pdb=" O VAL E 297 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL E 297 " --> pdb=" O ARG E 306 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.456A pdb=" N LEU E 451 " --> pdb=" O TRP E 475 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N TYR E 477 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 453 " --> pdb=" O TYR E 477 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 474 " --> pdb=" O ALA E 497 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG E 550 " --> pdb=" O LEU E 521 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU E 523 " --> pdb=" O ARG E 550 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS E 552 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU E 549 " --> pdb=" O SER E 573 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN E 575 " --> pdb=" O LEU E 549 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU E 551 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE E 619 " --> pdb=" O LYS E 645 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU E 644 " --> pdb=" O TYR E 668 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU E 667 " --> pdb=" O ASP E 691 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU E 690 " --> pdb=" O ALA E 714 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU E 713 " --> pdb=" O HIS E 737 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU E 736 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 459 through 460 removed outlier: 6.911A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AC3, first strand: chain 'F' and resid 60 through 61 Processing sheet with id=AC4, first strand: chain 'F' and resid 421 through 422 removed outlier: 3.612A pdb=" N LEU F 432 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU F 451 " --> pdb=" O TRP F 475 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N TYR F 477 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU F 453 " --> pdb=" O TYR F 477 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU F 521 " --> pdb=" O ARG F 550 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LYS F 552 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU F 523 " --> pdb=" O LYS F 552 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU F 572 " --> pdb=" O GLU F 597 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE F 599 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE F 574 " --> pdb=" O ILE F 599 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU F 596 " --> pdb=" O GLU F 618 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP F 620 " --> pdb=" O LEU F 596 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU F 598 " --> pdb=" O ASP F 620 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE F 619 " --> pdb=" O LYS F 645 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU F 644 " --> pdb=" O TYR F 668 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU F 667 " --> pdb=" O ASP F 691 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU F 690 " --> pdb=" O ALA F 714 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU F 713 " --> pdb=" O HIS F 737 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU F 736 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE F 759 " --> pdb=" O VAL F 785 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 459 through 461 1634 hydrogen bonds defined for protein. 3858 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: 8.01 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8019 1.33 - 1.45: 7876 1.45 - 1.57: 21772 1.57 - 1.69: 30 1.69 - 1.81: 216 Bond restraints: 37913 Sorted by residual: bond pdb=" C31 POV E 902 " pdb=" O31 POV E 902 " ideal model delta sigma weight residual 1.327 1.457 -0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" C31 POV F 902 " pdb=" O31 POV F 902 " ideal model delta sigma weight residual 1.327 1.457 -0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C31 POV B 904 " pdb=" O31 POV B 904 " ideal model delta sigma weight residual 1.327 1.456 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" C31 POV D 902 " pdb=" O31 POV D 902 " ideal model delta sigma weight residual 1.327 1.456 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C31 POV C 904 " pdb=" O31 POV C 904 " ideal model delta sigma weight residual 1.327 1.456 -0.129 2.00e-02 2.50e+03 4.17e+01 ... (remaining 37908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 50036 2.55 - 5.10: 1067 5.10 - 7.65: 207 7.65 - 10.20: 42 10.20 - 12.75: 22 Bond angle restraints: 51374 Sorted by residual: angle pdb=" N LEU D 584 " pdb=" CA LEU D 584 " pdb=" C LEU D 584 " ideal model delta sigma weight residual 111.52 124.27 -12.75 1.40e+00 5.10e-01 8.29e+01 angle pdb=" N TYR B 683 " pdb=" CA TYR B 683 " pdb=" C TYR B 683 " ideal model delta sigma weight residual 113.28 102.85 10.43 1.22e+00 6.72e-01 7.31e+01 angle pdb=" N GLU C 767 " pdb=" CA GLU C 767 " pdb=" C GLU C 767 " ideal model delta sigma weight residual 113.55 103.34 10.21 1.26e+00 6.30e-01 6.57e+01 angle pdb=" N TYR A 683 " pdb=" CA TYR A 683 " pdb=" C TYR A 683 " ideal model delta sigma weight residual 113.28 103.93 9.35 1.22e+00 6.72e-01 5.87e+01 angle pdb=" N TYR E 683 " pdb=" CA TYR E 683 " pdb=" C TYR E 683 " ideal model delta sigma weight residual 113.18 104.26 8.92 1.21e+00 6.83e-01 5.44e+01 ... (remaining 51369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 23155 35.91 - 71.83: 511 71.83 - 107.74: 42 107.74 - 143.66: 30 143.66 - 179.57: 12 Dihedral angle restraints: 23750 sinusoidal: 10685 harmonic: 13065 Sorted by residual: dihedral pdb=" CA GLU D 6 " pdb=" C GLU D 6 " pdb=" N LEU D 7 " pdb=" CA LEU D 7 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA VAL E 4 " pdb=" C VAL E 4 " pdb=" N THR E 5 " pdb=" CA THR E 5 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ARG D 8 " pdb=" C ARG D 8 " pdb=" N TYR D 9 " pdb=" CA TYR D 9 " ideal model delta harmonic sigma weight residual 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 23747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 5686 0.119 - 0.239: 199 0.239 - 0.358: 20 0.358 - 0.477: 1 0.477 - 0.596: 2 Chirality restraints: 5908 Sorted by residual: chirality pdb=" CA LEU D 584 " pdb=" N LEU D 584 " pdb=" C LEU D 584 " pdb=" CB LEU D 584 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.89e+00 chirality pdb=" CA PHE F 682 " pdb=" N PHE F 682 " pdb=" C PHE F 682 " pdb=" CB PHE F 682 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" CA ARG D 346 " pdb=" N ARG D 346 " pdb=" C ARG D 346 " pdb=" CB ARG D 346 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 5905 not shown) Planarity restraints: 6251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 409 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C ASN A 409 " 0.072 2.00e-02 2.50e+03 pdb=" O ASN A 409 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU A 410 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 345 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C ARG D 345 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG D 345 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG D 346 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 582 " 0.016 2.00e-02 2.50e+03 3.08e-02 9.50e+00 pdb=" C ILE D 582 " -0.053 2.00e-02 2.50e+03 pdb=" O ILE D 582 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL D 583 " 0.018 2.00e-02 2.50e+03 ... (remaining 6248 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 467 2.63 - 3.20: 34182 3.20 - 3.77: 55380 3.77 - 4.33: 81253 4.33 - 4.90: 131632 Nonbonded interactions: 302914 Sorted by model distance: nonbonded pdb=" OG1 THR F 48 " pdb=" OE1 GLN F 49 " model vdw 2.064 3.040 nonbonded pdb=" O LEU A 584 " pdb=" CB ASN A 585 " model vdw 2.182 3.440 nonbonded pdb=" OE2 GLU E 577 " pdb=" NZ LYS F 516 " model vdw 2.223 3.120 nonbonded pdb=" OG1 THR D 303 " pdb=" OH TYR D 308 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR F 303 " pdb=" OH TYR F 308 " model vdw 2.232 3.040 ... (remaining 302909 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 807) selection = (chain 'B' and (resid 1 through 175 or resid 231 through 807)) selection = (chain 'C' and (resid 1 through 175 or resid 231 through 807)) selection = (chain 'D' and (resid 1 through 175 or resid 231 through 807)) selection = (chain 'E' and (resid 1 through 175 or resid 231 through 807)) selection = (chain 'F' and (resid 1 through 175 or resid 231 through 807)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 34.750 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 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 : 0.008 0.130 37931 Z= 0.380 Angle : 0.993 12.749 51410 Z= 0.505 Chirality : 0.055 0.596 5908 Planarity : 0.005 0.078 6251 Dihedral : 16.042 179.570 15178 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.47 % Favored : 95.37 % Rotamer: Outliers : 1.23 % Allowed : 7.73 % Favored : 91.04 % Cbeta Deviations : 0.07 % 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: -1.32 (0.13), residues: 4343 helix: -0.56 (0.12), residues: 2042 sheet: -1.68 (0.21), residues: 576 loop : -0.71 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 781 TYR 0.019 0.002 TYR E 281 PHE 0.023 0.002 PHE E 728 TRP 0.028 0.003 TRP E 143 HIS 0.011 0.002 HIS B 694 Details of bonding type rmsd covalent geometry : bond 0.00813 (37913) covalent geometry : angle 0.99341 (51374) SS BOND : bond 0.00342 ( 18) SS BOND : angle 0.99269 ( 36) hydrogen bonds : bond 0.18959 ( 1634) hydrogen bonds : angle 5.83817 ( 3858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 458 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8351 (mm-30) REVERT: A 371 ASP cc_start: 0.8885 (t0) cc_final: 0.8654 (t0) REVERT: A 526 ASN cc_start: 0.6391 (t0) cc_final: 0.6086 (t0) REVERT: B 476 LEU cc_start: 0.8949 (mt) cc_final: 0.8625 (pp) REVERT: B 500 ILE cc_start: 0.8314 (mt) cc_final: 0.7700 (mt) REVERT: B 692 LEU cc_start: 0.8902 (mt) cc_final: 0.8153 (tt) REVERT: C 410 GLU cc_start: 0.8306 (pt0) cc_final: 0.8008 (tm-30) REVERT: C 413 LEU cc_start: 0.6319 (OUTLIER) cc_final: 0.6017 (tp) REVERT: C 414 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7777 (t0) REVERT: C 444 ASP cc_start: 0.7632 (m-30) cc_final: 0.7349 (m-30) REVERT: C 451 LEU cc_start: 0.8528 (tp) cc_final: 0.8316 (tm) REVERT: C 501 LYS cc_start: 0.8580 (tttm) cc_final: 0.8330 (tptp) REVERT: C 691 ASP cc_start: 0.7805 (t0) cc_final: 0.7567 (p0) REVERT: C 692 LEU cc_start: 0.9073 (mt) cc_final: 0.8746 (pp) REVERT: D 500 ILE cc_start: 0.8180 (mt) cc_final: 0.7522 (mt) REVERT: E 154 GLU cc_start: 0.8796 (tt0) cc_final: 0.8496 (mm-30) REVERT: E 409 ASN cc_start: 0.8388 (m110) cc_final: 0.7428 (t0) REVERT: E 451 LEU cc_start: 0.8650 (tp) cc_final: 0.8408 (tm) REVERT: E 499 HIS cc_start: 0.6438 (m90) cc_final: 0.6182 (m90) REVERT: E 510 LEU cc_start: 0.7868 (mt) cc_final: 0.7493 (pp) REVERT: E 692 LEU cc_start: 0.9090 (mt) cc_final: 0.8802 (pp) REVERT: E 713 LEU cc_start: 0.8568 (tp) cc_final: 0.8319 (mt) REVERT: F 63 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7412 (t0) REVERT: F 476 LEU cc_start: 0.8652 (mt) cc_final: 0.8292 (pp) REVERT: F 692 LEU cc_start: 0.8934 (mt) cc_final: 0.8698 (pt) outliers start: 50 outliers final: 5 residues processed: 497 average time/residue: 0.7890 time to fit residues: 469.3652 Evaluate side-chains 251 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 243 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 415 LYS Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain F residue 63 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 HIS C 522 HIS C 554 ASN C 718 ASN ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 ASN D 404 GLN D 409 ASN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 HIS E 522 HIS E 554 ASN F 467 GLN ** F 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 HIS F 737 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.167371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.099299 restraints weight = 73753.276| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.54 r_work: 0.3235 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37931 Z= 0.155 Angle : 0.728 15.351 51410 Z= 0.356 Chirality : 0.044 0.178 5908 Planarity : 0.005 0.056 6251 Dihedral : 15.695 178.405 6112 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.14 % Allowed : 11.56 % Favored : 86.30 % 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: -0.94 (0.13), residues: 4343 helix: -0.26 (0.12), residues: 2069 sheet: -1.38 (0.21), residues: 572 loop : -0.56 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 666 TYR 0.014 0.001 TYR A 477 PHE 0.012 0.002 PHE F 682 TRP 0.018 0.002 TRP D 168 HIS 0.007 0.001 HIS E 478 Details of bonding type rmsd covalent geometry : bond 0.00345 (37913) covalent geometry : angle 0.72829 (51374) SS BOND : bond 0.00214 ( 18) SS BOND : angle 0.93276 ( 36) hydrogen bonds : bond 0.04611 ( 1634) hydrogen bonds : angle 4.58992 ( 3858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 278 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ASP cc_start: 0.8815 (t0) cc_final: 0.8270 (t0) REVERT: A 398 SER cc_start: 0.8508 (m) cc_final: 0.8016 (p) REVERT: A 399 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: A 477 TYR cc_start: 0.8381 (m-10) cc_final: 0.7704 (m-10) REVERT: A 671 ARG cc_start: 0.9314 (mmt180) cc_final: 0.9109 (tpt90) REVERT: B 238 GLU cc_start: 0.9115 (tp30) cc_final: 0.8154 (tm-30) REVERT: B 692 LEU cc_start: 0.8874 (mt) cc_final: 0.8229 (tt) REVERT: C 399 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: C 501 LYS cc_start: 0.8490 (tttm) cc_final: 0.8286 (tptp) REVERT: C 590 MET cc_start: 0.3531 (mpm) cc_final: 0.3256 (mpm) REVERT: C 692 LEU cc_start: 0.9486 (mt) cc_final: 0.9274 (pp) REVERT: C 736 LEU cc_start: 0.9183 (tp) cc_final: 0.8765 (mm) REVERT: D 473 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6881 (tp30) REVERT: E 154 GLU cc_start: 0.9114 (tt0) cc_final: 0.8762 (mm-30) REVERT: E 165 ASP cc_start: 0.9113 (t0) cc_final: 0.8774 (t0) REVERT: E 245 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8644 (mm-30) REVERT: E 399 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: E 499 HIS cc_start: 0.6580 (m90) cc_final: 0.6188 (m90) REVERT: E 692 LEU cc_start: 0.9486 (mt) cc_final: 0.9205 (pp) REVERT: F 63 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7305 (t0) REVERT: F 410 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8198 (pm20) REVERT: F 440 ASP cc_start: 0.8347 (m-30) cc_final: 0.7913 (m-30) REVERT: F 500 ILE cc_start: 0.7290 (mt) cc_final: 0.6828 (tt) REVERT: F 581 LEU cc_start: 0.5753 (tm) cc_final: 0.5363 (mt) REVERT: F 692 LEU cc_start: 0.8948 (mt) cc_final: 0.8690 (pt) outliers start: 87 outliers final: 18 residues processed: 351 average time/residue: 0.7514 time to fit residues: 319.7415 Evaluate side-chains 239 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 622 LYS Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 442 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 22 optimal weight: 3.9990 chunk 184 optimal weight: 30.0000 chunk 82 optimal weight: 2.9990 chunk 422 optimal weight: 20.0000 chunk 12 optimal weight: 0.4980 chunk 370 optimal weight: 9.9990 chunk 329 optimal weight: 8.9990 chunk 218 optimal weight: 8.9990 chunk 383 optimal weight: 0.9980 chunk 160 optimal weight: 0.0470 chunk 409 optimal weight: 9.9990 overall best weight: 1.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN D 408 ASN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 729 GLN E 617 GLN ** F 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.166021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.097190 restraints weight = 73987.214| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.54 r_work: 0.3215 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 37931 Z= 0.163 Angle : 0.676 12.626 51410 Z= 0.330 Chirality : 0.043 0.215 5908 Planarity : 0.004 0.057 6251 Dihedral : 14.160 177.566 6100 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.33 % Allowed : 12.28 % Favored : 85.39 % 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: -0.76 (0.13), residues: 4343 helix: -0.21 (0.12), residues: 2073 sheet: -1.31 (0.22), residues: 572 loop : -0.32 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 417 TYR 0.012 0.001 TYR C 338 PHE 0.012 0.001 PHE B 433 TRP 0.020 0.001 TRP A 411 HIS 0.005 0.001 HIS F 694 Details of bonding type rmsd covalent geometry : bond 0.00374 (37913) covalent geometry : angle 0.67563 (51374) SS BOND : bond 0.00219 ( 18) SS BOND : angle 1.04127 ( 36) hydrogen bonds : bond 0.04024 ( 1634) hydrogen bonds : angle 4.44783 ( 3858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 230 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ASP cc_start: 0.8740 (t0) cc_final: 0.8145 (t0) REVERT: A 398 SER cc_start: 0.8584 (m) cc_final: 0.8062 (p) REVERT: A 399 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8214 (mp0) REVERT: A 590 MET cc_start: 0.4662 (mpm) cc_final: 0.4280 (mpm) REVERT: B 238 GLU cc_start: 0.9079 (tp30) cc_final: 0.8142 (tm-30) REVERT: B 581 LEU cc_start: 0.6316 (tm) cc_final: 0.6012 (mt) REVERT: B 590 MET cc_start: 0.2458 (mpp) cc_final: 0.2237 (mpp) REVERT: B 692 LEU cc_start: 0.8904 (mt) cc_final: 0.8273 (tt) REVERT: C 154 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8588 (mm-30) REVERT: C 399 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: C 411 TRP cc_start: 0.6915 (m100) cc_final: 0.6642 (m100) REVERT: C 692 LEU cc_start: 0.9486 (mt) cc_final: 0.9239 (pp) REVERT: C 736 LEU cc_start: 0.9246 (tp) cc_final: 0.8718 (mm) REVERT: C 792 ASN cc_start: 0.6182 (m-40) cc_final: 0.5949 (m110) REVERT: D 473 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7371 (tp30) REVERT: D 581 LEU cc_start: 0.4897 (tm) cc_final: 0.4556 (mt) REVERT: E 154 GLU cc_start: 0.9139 (tt0) cc_final: 0.8789 (mm-30) REVERT: E 165 ASP cc_start: 0.9113 (t0) cc_final: 0.8749 (t0) REVERT: E 245 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8627 (mm-30) REVERT: E 399 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: E 499 HIS cc_start: 0.6856 (m90) cc_final: 0.6489 (m90) REVERT: E 692 LEU cc_start: 0.9493 (mt) cc_final: 0.9226 (pp) REVERT: E 738 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7714 (tp) REVERT: F 63 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7229 (t0) REVERT: F 410 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8487 (pm20) REVERT: F 440 ASP cc_start: 0.8456 (m-30) cc_final: 0.7997 (m-30) REVERT: F 500 ILE cc_start: 0.7440 (mt) cc_final: 0.7014 (tt) REVERT: F 519 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8357 (pp20) REVERT: F 581 LEU cc_start: 0.5992 (tm) cc_final: 0.5623 (mt) REVERT: F 692 LEU cc_start: 0.8948 (mt) cc_final: 0.8611 (pp) outliers start: 95 outliers final: 28 residues processed: 308 average time/residue: 0.6370 time to fit residues: 244.6894 Evaluate side-chains 232 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 519 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 36 optimal weight: 0.0970 chunk 230 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 379 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 255 optimal weight: 0.9980 chunk 300 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 405 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 373 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 617 GLN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN ** F 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 ASN F 737 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.166489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.098593 restraints weight = 73654.833| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.50 r_work: 0.3234 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37931 Z= 0.135 Angle : 0.640 11.401 51410 Z= 0.311 Chirality : 0.043 0.248 5908 Planarity : 0.004 0.100 6251 Dihedral : 13.036 179.749 6100 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.26 % Allowed : 12.96 % Favored : 84.78 % 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: -0.70 (0.13), residues: 4343 helix: -0.18 (0.12), residues: 2092 sheet: -1.22 (0.22), residues: 572 loop : -0.28 (0.16), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 671 TYR 0.014 0.001 TYR F 513 PHE 0.031 0.001 PHE B 490 TRP 0.018 0.001 TRP A 411 HIS 0.004 0.001 HIS D 694 Details of bonding type rmsd covalent geometry : bond 0.00295 (37913) covalent geometry : angle 0.63945 (51374) SS BOND : bond 0.00196 ( 18) SS BOND : angle 0.96937 ( 36) hydrogen bonds : bond 0.03595 ( 1634) hydrogen bonds : angle 4.29691 ( 3858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 228 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 LYS cc_start: 0.9280 (tppp) cc_final: 0.9052 (tppp) REVERT: A 371 ASP cc_start: 0.8584 (t0) cc_final: 0.8014 (t0) REVERT: A 398 SER cc_start: 0.8582 (m) cc_final: 0.8070 (p) REVERT: A 671 ARG cc_start: 0.8844 (tpt90) cc_final: 0.8573 (tmt-80) REVERT: B 238 GLU cc_start: 0.9075 (tp30) cc_final: 0.8128 (tm-30) REVERT: B 581 LEU cc_start: 0.6255 (tm) cc_final: 0.5942 (mt) REVERT: B 692 LEU cc_start: 0.8948 (mt) cc_final: 0.8345 (tt) REVERT: C 154 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8695 (mm-30) REVERT: C 399 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: C 499 HIS cc_start: 0.6862 (m90) cc_final: 0.6517 (m90) REVERT: C 590 MET cc_start: 0.3697 (mpm) cc_final: 0.3070 (mpm) REVERT: C 692 LEU cc_start: 0.9476 (mt) cc_final: 0.9238 (pp) REVERT: C 792 ASN cc_start: 0.6193 (m-40) cc_final: 0.5954 (m110) REVERT: D 468 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8156 (pp) REVERT: D 581 LEU cc_start: 0.4912 (tm) cc_final: 0.4595 (mt) REVERT: E 154 GLU cc_start: 0.9087 (tt0) cc_final: 0.8752 (mm-30) REVERT: E 165 ASP cc_start: 0.9107 (t0) cc_final: 0.8734 (t0) REVERT: E 245 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8627 (mm-30) REVERT: E 399 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: E 499 HIS cc_start: 0.6798 (m90) cc_final: 0.6440 (m90) REVERT: E 644 LEU cc_start: 0.8707 (tp) cc_final: 0.8494 (mm) REVERT: E 692 LEU cc_start: 0.9481 (mt) cc_final: 0.9203 (pp) REVERT: E 738 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7638 (tp) REVERT: F 239 GLN cc_start: 0.8543 (pp30) cc_final: 0.8267 (pp30) REVERT: F 410 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8501 (pm20) REVERT: F 413 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8027 (tm) REVERT: F 482 LYS cc_start: 0.6728 (tptp) cc_final: 0.6488 (tptp) REVERT: F 491 LEU cc_start: 0.7970 (mm) cc_final: 0.7598 (mm) REVERT: F 500 ILE cc_start: 0.7536 (mt) cc_final: 0.7135 (tt) REVERT: F 519 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8339 (pp20) REVERT: F 581 LEU cc_start: 0.6038 (tm) cc_final: 0.5690 (mt) REVERT: F 692 LEU cc_start: 0.8956 (mt) cc_final: 0.8612 (pp) outliers start: 92 outliers final: 24 residues processed: 304 average time/residue: 0.6220 time to fit residues: 234.1488 Evaluate side-chains 231 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 519 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 415 optimal weight: 40.0000 chunk 200 optimal weight: 10.0000 chunk 330 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 416 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 274 optimal weight: 50.0000 chunk 29 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 HIS B 431 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 HIS ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 608 HIS F 431 HIS ** F 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.163484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.094686 restraints weight = 73217.739| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.47 r_work: 0.3172 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 37931 Z= 0.228 Angle : 0.668 11.929 51410 Z= 0.328 Chirality : 0.044 0.218 5908 Planarity : 0.004 0.063 6251 Dihedral : 12.343 169.332 6097 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.28 % Allowed : 13.82 % Favored : 83.89 % 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: -0.67 (0.13), residues: 4343 helix: -0.21 (0.12), residues: 2060 sheet: -1.14 (0.22), residues: 573 loop : -0.22 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 600 TYR 0.017 0.002 TYR A 281 PHE 0.027 0.002 PHE F 490 TRP 0.017 0.002 TRP A 411 HIS 0.005 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00527 (37913) covalent geometry : angle 0.66745 (51374) SS BOND : bond 0.00268 ( 18) SS BOND : angle 1.14032 ( 36) hydrogen bonds : bond 0.03908 ( 1634) hydrogen bonds : angle 4.38761 ( 3858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 215 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.9186 (t0) cc_final: 0.8924 (t0) REVERT: A 254 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8796 (t) REVERT: A 371 ASP cc_start: 0.8796 (t0) cc_final: 0.8388 (t0) REVERT: A 398 SER cc_start: 0.8714 (m) cc_final: 0.8288 (p) REVERT: A 434 MET cc_start: 0.8223 (mmm) cc_final: 0.7957 (mmm) REVERT: A 455 LEU cc_start: 0.9573 (mt) cc_final: 0.9234 (pp) REVERT: A 476 LEU cc_start: 0.8756 (mt) cc_final: 0.8236 (tt) REVERT: A 590 MET cc_start: 0.4500 (mpm) cc_final: 0.4190 (mpm) REVERT: A 737 HIS cc_start: 0.8742 (OUTLIER) cc_final: 0.8541 (m90) REVERT: A 740 ASN cc_start: 0.8226 (m-40) cc_final: 0.7999 (t0) REVERT: B 238 GLU cc_start: 0.9097 (tp30) cc_final: 0.8186 (tm-30) REVERT: B 692 LEU cc_start: 0.8905 (mt) cc_final: 0.8403 (pt) REVERT: C 154 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8625 (mm-30) REVERT: C 399 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: C 590 MET cc_start: 0.3522 (mpm) cc_final: 0.2814 (mpm) REVERT: C 692 LEU cc_start: 0.9475 (mt) cc_final: 0.9228 (pp) REVERT: C 765 ARG cc_start: 0.4064 (OUTLIER) cc_final: 0.2565 (ptm160) REVERT: D 433 PHE cc_start: 0.7410 (p90) cc_final: 0.7204 (p90) REVERT: D 572 LEU cc_start: 0.8137 (mt) cc_final: 0.7715 (tm) REVERT: D 581 LEU cc_start: 0.4852 (tm) cc_final: 0.4585 (mt) REVERT: E 154 GLU cc_start: 0.9081 (tt0) cc_final: 0.8750 (mm-30) REVERT: E 165 ASP cc_start: 0.9136 (t0) cc_final: 0.8762 (t0) REVERT: E 245 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8759 (mm-30) REVERT: E 399 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: E 409 ASN cc_start: 0.8434 (m110) cc_final: 0.7606 (t0) REVERT: E 499 HIS cc_start: 0.6842 (m90) cc_final: 0.6578 (m90) REVERT: E 692 LEU cc_start: 0.9460 (mt) cc_final: 0.9190 (pp) REVERT: E 738 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7552 (tp) REVERT: F 410 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8576 (pm20) REVERT: F 411 TRP cc_start: 0.6235 (m-10) cc_final: 0.6000 (m-10) REVERT: F 413 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7993 (tm) REVERT: F 500 ILE cc_start: 0.7582 (mt) cc_final: 0.7206 (tt) REVERT: F 519 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8363 (pp20) REVERT: F 581 LEU cc_start: 0.6035 (tm) cc_final: 0.5676 (mt) REVERT: F 692 LEU cc_start: 0.8954 (mt) cc_final: 0.8613 (pp) outliers start: 93 outliers final: 26 residues processed: 294 average time/residue: 0.5794 time to fit residues: 213.8838 Evaluate side-chains 226 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 519 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 70 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 392 optimal weight: 0.9990 chunk 285 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 400 optimal weight: 6.9990 chunk 398 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 436 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 GLN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.162628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.093143 restraints weight = 73993.226| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.54 r_work: 0.3140 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 37931 Z= 0.269 Angle : 0.686 20.665 51410 Z= 0.335 Chirality : 0.045 0.171 5908 Planarity : 0.004 0.058 6251 Dihedral : 12.040 171.312 6097 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.46 % Allowed : 14.44 % Favored : 83.11 % 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: -0.64 (0.13), residues: 4343 helix: -0.21 (0.12), residues: 2029 sheet: -1.10 (0.23), residues: 576 loop : -0.17 (0.16), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 492 TYR 0.022 0.002 TYR D 362 PHE 0.018 0.002 PHE B 490 TRP 0.018 0.002 TRP A 411 HIS 0.006 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00626 (37913) covalent geometry : angle 0.68577 (51374) SS BOND : bond 0.00301 ( 18) SS BOND : angle 1.28086 ( 36) hydrogen bonds : bond 0.03939 ( 1634) hydrogen bonds : angle 4.44730 ( 3858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 202 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 VAL cc_start: 0.9076 (OUTLIER) cc_final: 0.8797 (t) REVERT: A 371 ASP cc_start: 0.8798 (t0) cc_final: 0.8235 (t0) REVERT: A 433 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7899 (t80) REVERT: A 550 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8466 (ttm110) REVERT: A 669 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9086 (pt) REVERT: A 671 ARG cc_start: 0.8772 (tpt90) cc_final: 0.8484 (tmt-80) REVERT: A 737 HIS cc_start: 0.8761 (OUTLIER) cc_final: 0.8508 (m90) REVERT: A 740 ASN cc_start: 0.8281 (m-40) cc_final: 0.8049 (t0) REVERT: B 238 GLU cc_start: 0.9096 (tp30) cc_final: 0.8246 (tm-30) REVERT: B 692 LEU cc_start: 0.8814 (mt) cc_final: 0.8346 (pt) REVERT: B 713 LEU cc_start: 0.9107 (pp) cc_final: 0.8898 (tm) REVERT: C 165 ASP cc_start: 0.9181 (t0) cc_final: 0.8754 (t0) REVERT: C 245 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8641 (mm-30) REVERT: C 399 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: C 471 LEU cc_start: 0.8618 (tm) cc_final: 0.8389 (pt) REVERT: C 585 ASN cc_start: 0.7408 (m-40) cc_final: 0.7063 (p0) REVERT: C 590 MET cc_start: 0.3556 (mpm) cc_final: 0.2810 (mpm) REVERT: C 692 LEU cc_start: 0.9492 (mt) cc_final: 0.9223 (pp) REVERT: C 765 ARG cc_start: 0.4147 (OUTLIER) cc_final: 0.2785 (ptm160) REVERT: D 482 LYS cc_start: 0.8971 (mttt) cc_final: 0.8698 (tptp) REVERT: D 572 LEU cc_start: 0.8109 (mt) cc_final: 0.7710 (tm) REVERT: D 581 LEU cc_start: 0.4535 (tm) cc_final: 0.4297 (mt) REVERT: D 669 LEU cc_start: 0.9122 (mm) cc_final: 0.8868 (mt) REVERT: E 154 GLU cc_start: 0.9084 (tt0) cc_final: 0.8754 (mm-30) REVERT: E 165 ASP cc_start: 0.9124 (t0) cc_final: 0.8773 (t0) REVERT: E 236 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7543 (pp20) REVERT: E 245 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8648 (mm-30) REVERT: E 371 ASP cc_start: 0.8555 (t0) cc_final: 0.8353 (t0) REVERT: E 399 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: E 433 PHE cc_start: 0.8450 (p90) cc_final: 0.8139 (p90) REVERT: E 499 HIS cc_start: 0.6963 (m90) cc_final: 0.6761 (m90) REVERT: E 692 LEU cc_start: 0.9468 (mt) cc_final: 0.9181 (pp) REVERT: E 738 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7570 (tp) REVERT: F 413 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8151 (tm) REVERT: F 519 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8283 (pp20) REVERT: F 581 LEU cc_start: 0.6175 (tm) cc_final: 0.5793 (mt) REVERT: F 692 LEU cc_start: 0.8949 (mt) cc_final: 0.8632 (pp) outliers start: 100 outliers final: 33 residues processed: 284 average time/residue: 0.5891 time to fit residues: 210.7381 Evaluate side-chains 232 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 442 VAL Chi-restraints excluded: chain F residue 519 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 122 optimal weight: 20.0000 chunk 411 optimal weight: 10.0000 chunk 414 optimal weight: 30.0000 chunk 431 optimal weight: 8.9990 chunk 311 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 317 optimal weight: 0.9990 chunk 371 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 160 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 708 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.166264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.098146 restraints weight = 74065.231| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.62 r_work: 0.3226 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 37931 Z= 0.172 Angle : 0.636 14.893 51410 Z= 0.310 Chirality : 0.043 0.175 5908 Planarity : 0.004 0.061 6251 Dihedral : 11.700 173.826 6097 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.96 % Allowed : 15.25 % Favored : 82.79 % 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: -0.55 (0.13), residues: 4343 helix: -0.13 (0.12), residues: 2026 sheet: -1.11 (0.23), residues: 573 loop : -0.12 (0.16), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 492 TYR 0.014 0.001 TYR D 362 PHE 0.033 0.001 PHE D 490 TRP 0.030 0.002 TRP F 411 HIS 0.005 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00398 (37913) covalent geometry : angle 0.63554 (51374) SS BOND : bond 0.00227 ( 18) SS BOND : angle 1.10927 ( 36) hydrogen bonds : bond 0.03634 ( 1634) hydrogen bonds : angle 4.36365 ( 3858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 200 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8790 (t) REVERT: A 371 ASP cc_start: 0.8761 (t0) cc_final: 0.8210 (t0) REVERT: A 433 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7910 (t80) REVERT: A 434 MET cc_start: 0.8242 (mmm) cc_final: 0.7921 (mmm) REVERT: A 455 LEU cc_start: 0.9317 (mm) cc_final: 0.8890 (pp) REVERT: A 669 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9118 (pt) REVERT: A 737 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8544 (m90) REVERT: A 740 ASN cc_start: 0.8344 (m-40) cc_final: 0.8113 (t0) REVERT: B 1 MET cc_start: 0.6332 (ptm) cc_final: 0.6010 (ttt) REVERT: B 238 GLU cc_start: 0.9123 (tp30) cc_final: 0.8267 (tm-30) REVERT: B 482 LYS cc_start: 0.6762 (tptp) cc_final: 0.6532 (tptp) REVERT: B 713 LEU cc_start: 0.9130 (pp) cc_final: 0.8892 (tm) REVERT: C 154 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8633 (mm-30) REVERT: C 165 ASP cc_start: 0.9151 (t0) cc_final: 0.8723 (t0) REVERT: C 399 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: C 471 LEU cc_start: 0.8632 (tm) cc_final: 0.8342 (pt) REVERT: C 585 ASN cc_start: 0.7464 (m-40) cc_final: 0.7094 (p0) REVERT: C 590 MET cc_start: 0.3622 (mpm) cc_final: 0.2856 (mpm) REVERT: C 692 LEU cc_start: 0.9465 (mt) cc_final: 0.9216 (pp) REVERT: C 765 ARG cc_start: 0.4222 (OUTLIER) cc_final: 0.2953 (ptm160) REVERT: D 482 LYS cc_start: 0.9003 (mttt) cc_final: 0.8719 (tptp) REVERT: D 581 LEU cc_start: 0.4449 (tm) cc_final: 0.4208 (mt) REVERT: D 669 LEU cc_start: 0.9081 (mm) cc_final: 0.8837 (mt) REVERT: E 154 GLU cc_start: 0.9087 (tt0) cc_final: 0.8765 (mm-30) REVERT: E 165 ASP cc_start: 0.9197 (t0) cc_final: 0.8843 (t0) REVERT: E 236 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7450 (pp20) REVERT: E 245 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8711 (mm-30) REVERT: E 399 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: E 433 PHE cc_start: 0.8427 (p90) cc_final: 0.8084 (p90) REVERT: E 692 LEU cc_start: 0.9479 (mt) cc_final: 0.9198 (pp) REVERT: E 738 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7632 (tp) REVERT: F 413 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8069 (tm) REVERT: F 519 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8303 (pp20) REVERT: F 581 LEU cc_start: 0.6120 (tm) cc_final: 0.5765 (mt) REVERT: F 692 LEU cc_start: 0.9007 (mt) cc_final: 0.8724 (pp) outliers start: 80 outliers final: 29 residues processed: 266 average time/residue: 0.6091 time to fit residues: 203.2378 Evaluate side-chains 224 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 PHE Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 738 LEU Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 519 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 102 optimal weight: 2.9990 chunk 208 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 397 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 197 optimal weight: 0.0070 chunk 386 optimal weight: 0.2980 chunk 153 optimal weight: 0.9980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 408 ASN A 744 GLN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 HIS E 522 HIS ** F 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.167269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.099893 restraints weight = 73874.810| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.71 r_work: 0.3293 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37931 Z= 0.125 Angle : 0.627 14.411 51410 Z= 0.303 Chirality : 0.042 0.170 5908 Planarity : 0.004 0.060 6251 Dihedral : 11.290 168.923 6095 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.74 % Allowed : 15.91 % Favored : 82.35 % 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 (0.13), residues: 4343 helix: -0.04 (0.12), residues: 2039 sheet: -1.03 (0.23), residues: 569 loop : -0.04 (0.16), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 550 TYR 0.012 0.001 TYR E 338 PHE 0.021 0.001 PHE D 490 TRP 0.038 0.002 TRP F 411 HIS 0.005 0.001 HIS D 377 Details of bonding type rmsd covalent geometry : bond 0.00283 (37913) covalent geometry : angle 0.62648 (51374) SS BOND : bond 0.00192 ( 18) SS BOND : angle 1.00726 ( 36) hydrogen bonds : bond 0.03434 ( 1634) hydrogen bonds : angle 4.30810 ( 3858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 205 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8797 (t) REVERT: A 371 ASP cc_start: 0.8505 (t0) cc_final: 0.7886 (t0) REVERT: A 433 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.8075 (t80) REVERT: A 434 MET cc_start: 0.8220 (mmm) cc_final: 0.7808 (mmm) REVERT: A 455 LEU cc_start: 0.9315 (mm) cc_final: 0.8759 (pp) REVERT: A 590 MET cc_start: 0.4820 (mpm) cc_final: 0.4593 (mpt) REVERT: A 669 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9116 (pt) REVERT: A 737 HIS cc_start: 0.8780 (OUTLIER) cc_final: 0.8541 (m90) REVERT: A 740 ASN cc_start: 0.8344 (m-40) cc_final: 0.8116 (t0) REVERT: B 238 GLU cc_start: 0.9087 (tp30) cc_final: 0.8207 (tm-30) REVERT: B 713 LEU cc_start: 0.9131 (pp) cc_final: 0.8917 (tm) REVERT: C 154 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8646 (mm-30) REVERT: C 165 ASP cc_start: 0.9100 (t0) cc_final: 0.8629 (t0) REVERT: C 399 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: C 585 ASN cc_start: 0.7444 (m-40) cc_final: 0.7095 (p0) REVERT: C 590 MET cc_start: 0.3563 (mpm) cc_final: 0.3205 (mpm) REVERT: C 692 LEU cc_start: 0.9454 (mt) cc_final: 0.9201 (pp) REVERT: C 765 ARG cc_start: 0.4356 (OUTLIER) cc_final: 0.2924 (ptm160) REVERT: D 482 LYS cc_start: 0.9028 (mttt) cc_final: 0.8714 (tptp) REVERT: D 572 LEU cc_start: 0.8269 (mt) cc_final: 0.7954 (tm) REVERT: D 581 LEU cc_start: 0.4519 (tm) cc_final: 0.4242 (mt) REVERT: D 669 LEU cc_start: 0.9082 (mm) cc_final: 0.8835 (mt) REVERT: E 154 GLU cc_start: 0.9054 (tt0) cc_final: 0.8761 (mm-30) REVERT: E 165 ASP cc_start: 0.9171 (t0) cc_final: 0.8811 (t0) REVERT: E 235 LYS cc_start: 0.9096 (mmtm) cc_final: 0.8884 (mmpt) REVERT: E 236 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7489 (pp20) REVERT: E 245 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8703 (mm-30) REVERT: E 399 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: E 433 PHE cc_start: 0.8474 (p90) cc_final: 0.8041 (p90) REVERT: E 447 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6835 (pm20) REVERT: E 692 LEU cc_start: 0.9479 (mt) cc_final: 0.9209 (pp) REVERT: F 410 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8539 (pm20) REVERT: F 491 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7687 (mm) REVERT: F 519 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8264 (pp20) REVERT: F 581 LEU cc_start: 0.6168 (tm) cc_final: 0.5810 (mt) REVERT: F 692 LEU cc_start: 0.9007 (mt) cc_final: 0.8710 (pp) outliers start: 71 outliers final: 28 residues processed: 267 average time/residue: 0.6310 time to fit residues: 210.3723 Evaluate side-chains 222 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 519 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 240 optimal weight: 4.9990 chunk 288 optimal weight: 4.9990 chunk 370 optimal weight: 9.9990 chunk 359 optimal weight: 40.0000 chunk 244 optimal weight: 1.9990 chunk 292 optimal weight: 5.9990 chunk 271 optimal weight: 8.9990 chunk 183 optimal weight: 0.6980 chunk 213 optimal weight: 9.9990 chunk 259 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.164688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.096134 restraints weight = 74653.163| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.51 r_work: 0.3195 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 37931 Z= 0.270 Angle : 0.700 15.666 51410 Z= 0.342 Chirality : 0.045 0.176 5908 Planarity : 0.004 0.091 6251 Dihedral : 11.425 166.760 6095 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.82 % Allowed : 16.28 % Favored : 81.91 % 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: -0.54 (0.13), residues: 4343 helix: -0.18 (0.12), residues: 2034 sheet: -1.09 (0.23), residues: 575 loop : -0.03 (0.16), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 550 TYR 0.018 0.002 TYR F 648 PHE 0.019 0.002 PHE E 374 TRP 0.031 0.002 TRP C 411 HIS 0.005 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00628 (37913) covalent geometry : angle 0.69925 (51374) SS BOND : bond 0.00324 ( 18) SS BOND : angle 1.17952 ( 36) hydrogen bonds : bond 0.03898 ( 1634) hydrogen bonds : angle 4.45330 ( 3858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 187 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8826 (t) REVERT: A 371 ASP cc_start: 0.8816 (t0) cc_final: 0.8459 (t0) REVERT: A 590 MET cc_start: 0.4769 (mpm) cc_final: 0.4548 (mpt) REVERT: A 737 HIS cc_start: 0.8840 (OUTLIER) cc_final: 0.8616 (m90) REVERT: A 740 ASN cc_start: 0.8398 (m-40) cc_final: 0.8162 (t0) REVERT: B 238 GLU cc_start: 0.9138 (tp30) cc_final: 0.8316 (tm-30) REVERT: B 692 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8070 (pt) REVERT: C 165 ASP cc_start: 0.9138 (t0) cc_final: 0.8673 (t0) REVERT: C 371 ASP cc_start: 0.8598 (t0) cc_final: 0.8092 (t0) REVERT: C 399 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: C 585 ASN cc_start: 0.7380 (m-40) cc_final: 0.6948 (p0) REVERT: C 590 MET cc_start: 0.3575 (mpm) cc_final: 0.3206 (mpm) REVERT: C 692 LEU cc_start: 0.9498 (mt) cc_final: 0.9246 (pp) REVERT: C 765 ARG cc_start: 0.4407 (OUTLIER) cc_final: 0.3064 (ptm160) REVERT: D 482 LYS cc_start: 0.9093 (mttt) cc_final: 0.8826 (tptt) REVERT: D 669 LEU cc_start: 0.9046 (mm) cc_final: 0.8816 (mt) REVERT: D 738 LEU cc_start: 0.8933 (mt) cc_final: 0.8617 (pp) REVERT: E 154 GLU cc_start: 0.9107 (tt0) cc_final: 0.8765 (mm-30) REVERT: E 165 ASP cc_start: 0.9170 (t0) cc_final: 0.8822 (t0) REVERT: E 236 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7537 (pp20) REVERT: E 245 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8702 (mm-30) REVERT: E 371 ASP cc_start: 0.8540 (t0) cc_final: 0.8025 (t0) REVERT: E 399 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: E 433 PHE cc_start: 0.8408 (p90) cc_final: 0.8051 (p90) REVERT: E 692 LEU cc_start: 0.9488 (mt) cc_final: 0.9209 (pp) REVERT: F 238 GLU cc_start: 0.8997 (tp30) cc_final: 0.8764 (tm-30) REVERT: F 410 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8652 (pm20) REVERT: F 491 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7633 (mm) REVERT: F 581 LEU cc_start: 0.6090 (tm) cc_final: 0.5758 (mt) REVERT: F 692 LEU cc_start: 0.9000 (mt) cc_final: 0.8730 (pp) outliers start: 74 outliers final: 32 residues processed: 245 average time/residue: 0.5552 time to fit residues: 172.7870 Evaluate side-chains 218 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 491 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 432 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 271 optimal weight: 4.9990 chunk 422 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 326 optimal weight: 10.0000 chunk 426 optimal weight: 30.0000 chunk 305 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 354 optimal weight: 5.9990 chunk 360 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.165886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.097875 restraints weight = 73940.928| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.68 r_work: 0.3216 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37931 Z= 0.178 Angle : 0.673 15.252 51410 Z= 0.323 Chirality : 0.043 0.183 5908 Planarity : 0.004 0.065 6251 Dihedral : 11.264 165.216 6095 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.15 % Allowed : 17.09 % Favored : 81.76 % 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 (0.13), residues: 4343 helix: -0.13 (0.12), residues: 2041 sheet: -1.12 (0.23), residues: 575 loop : 0.01 (0.16), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 671 TYR 0.013 0.001 TYR B 281 PHE 0.020 0.002 PHE D 490 TRP 0.039 0.002 TRP C 411 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00415 (37913) covalent geometry : angle 0.67242 (51374) SS BOND : bond 0.00233 ( 18) SS BOND : angle 1.12003 ( 36) hydrogen bonds : bond 0.03627 ( 1634) hydrogen bonds : angle 4.38221 ( 3858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8686 Ramachandran restraints generated. 4343 Oldfield, 0 Emsley, 4343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8791 (t) REVERT: A 371 ASP cc_start: 0.8765 (t0) cc_final: 0.8335 (t0) REVERT: A 590 MET cc_start: 0.4764 (mpm) cc_final: 0.4546 (mpt) REVERT: A 737 HIS cc_start: 0.8832 (OUTLIER) cc_final: 0.8617 (m90) REVERT: A 740 ASN cc_start: 0.8444 (m-40) cc_final: 0.8212 (t0) REVERT: B 238 GLU cc_start: 0.9142 (tp30) cc_final: 0.8316 (tm-30) REVERT: B 692 LEU cc_start: 0.8781 (mm) cc_final: 0.8043 (pt) REVERT: C 165 ASP cc_start: 0.9146 (t0) cc_final: 0.8686 (t0) REVERT: C 371 ASP cc_start: 0.8362 (t0) cc_final: 0.7945 (t0) REVERT: C 399 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: C 585 ASN cc_start: 0.7425 (m-40) cc_final: 0.6976 (p0) REVERT: C 590 MET cc_start: 0.3750 (mpm) cc_final: 0.3353 (mpm) REVERT: C 692 LEU cc_start: 0.9497 (mt) cc_final: 0.9244 (pp) REVERT: C 765 ARG cc_start: 0.4431 (OUTLIER) cc_final: 0.3053 (ptm160) REVERT: D 482 LYS cc_start: 0.9151 (mttt) cc_final: 0.8879 (tptt) REVERT: D 572 LEU cc_start: 0.8290 (mt) cc_final: 0.8016 (tm) REVERT: D 669 LEU cc_start: 0.9043 (mm) cc_final: 0.8807 (mt) REVERT: D 738 LEU cc_start: 0.8980 (mt) cc_final: 0.8603 (pp) REVERT: E 154 GLU cc_start: 0.9114 (tt0) cc_final: 0.8778 (mm-30) REVERT: E 165 ASP cc_start: 0.9178 (t0) cc_final: 0.8829 (t0) REVERT: E 236 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7600 (pp20) REVERT: E 245 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8730 (mm-30) REVERT: E 399 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: E 433 PHE cc_start: 0.8322 (p90) cc_final: 0.7958 (p90) REVERT: E 692 LEU cc_start: 0.9489 (mt) cc_final: 0.9211 (pp) REVERT: F 238 GLU cc_start: 0.9022 (tp30) cc_final: 0.8772 (tm-30) REVERT: F 410 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8656 (pm20) REVERT: F 491 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7699 (mm) REVERT: F 581 LEU cc_start: 0.6071 (tm) cc_final: 0.5741 (mt) REVERT: F 692 LEU cc_start: 0.9008 (mt) cc_final: 0.8736 (pp) outliers start: 47 outliers final: 30 residues processed: 227 average time/residue: 0.5724 time to fit residues: 163.9290 Evaluate side-chains 213 residues out of total 4073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 PHE Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 765 ARG Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 743 LEU Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 265 MET Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 491 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 238 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 274 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 chunk 222 optimal weight: 1.9990 chunk 346 optimal weight: 8.9990 chunk 315 optimal weight: 0.6980 chunk 291 optimal weight: 0.3980 chunk 161 optimal weight: 3.9990 chunk 378 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 737 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.166153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.098415 restraints weight = 73806.446| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.57 r_work: 0.3237 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 37931 Z= 0.160 Angle : 0.659 15.584 51410 Z= 0.318 Chirality : 0.043 0.176 5908 Planarity : 0.004 0.063 6251 Dihedral : 10.973 162.598 6095 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.30 % Allowed : 17.09 % Favored : 81.61 % 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: -0.43 (0.13), residues: 4343 helix: -0.09 (0.12), residues: 2039 sheet: -1.09 (0.23), residues: 575 loop : 0.04 (0.16), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 671 TYR 0.013 0.001 TYR B 281 PHE 0.020 0.001 PHE A 433 TRP 0.046 0.002 TRP C 411 HIS 0.006 0.001 HIS D 377 Details of bonding type rmsd covalent geometry : bond 0.00372 (37913) covalent geometry : angle 0.65904 (51374) SS BOND : bond 0.00209 ( 18) SS BOND : angle 1.06490 ( 36) hydrogen bonds : bond 0.03546 ( 1634) hydrogen bonds : angle 4.34752 ( 3858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23807.72 seconds wall clock time: 403 minutes 22.29 seconds (24202.29 seconds total)