Starting phenix.real_space_refine on Thu Sep 26 12:23:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/09_2024/3los_5137.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/09_2024/3los_5137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/09_2024/3los_5137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/09_2024/3los_5137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/09_2024/3los_5137.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/09_2024/3los_5137.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 ------------------------------------------------------------------------------- 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= 0.014 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 448 5.16 5 C 39488 2.51 5 N 11024 2.21 5 O 12752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 735 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 63712 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "B" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "C" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "D" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "E" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "F" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "G" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "H" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "I" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "J" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "K" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "L" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "M" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "N" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "O" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "P" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Residues with excluded nonbonded symmetry interactions: 15 residue: pdb=" N MET B 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET B 1 " occ=0.00 residue: pdb=" N MET C 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET C 1 " occ=0.00 residue: pdb=" N MET D 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET D 1 " occ=0.00 residue: pdb=" N MET E 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET E 1 " occ=0.00 residue: pdb=" N MET F 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET F 1 " occ=0.00 residue: pdb=" N MET G 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET G 1 " occ=0.00 residue: pdb=" N MET H 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET H 1 " occ=0.00 residue: pdb=" N MET I 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET I 1 " occ=0.00 residue: pdb=" N MET J 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET J 1 " occ=0.00 residue: pdb=" N MET K 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET K 1 " occ=0.00 residue: pdb=" N MET L 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET L 1 " occ=0.00 residue: pdb=" N MET M 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET M 1 " occ=0.00 ... (remaining 3 not shown) Time building chain proxies: 27.76, per 1000 atoms: 0.44 Number of scatterers: 63712 At special positions: 0 Unit cell: (176.89, 176.89, 174.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 448 16.00 O 12752 8.00 N 11024 7.00 C 39488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 484 " distance=2.02 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 286 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 484 " distance=2.02 Simple disulfide: pdb=" SG CYS C 237 " - pdb=" SG CYS C 286 " distance=2.03 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 484 " distance=2.02 Simple disulfide: pdb=" SG CYS D 237 " - pdb=" SG CYS D 286 " distance=2.03 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 484 " distance=2.02 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS E 286 " distance=2.03 Simple disulfide: pdb=" SG CYS E 470 " - pdb=" SG CYS E 484 " distance=2.02 Simple disulfide: pdb=" SG CYS F 237 " - pdb=" SG CYS F 286 " distance=2.03 Simple disulfide: pdb=" SG CYS F 470 " - pdb=" SG CYS F 484 " distance=2.02 Simple disulfide: pdb=" SG CYS G 237 " - pdb=" SG CYS G 286 " distance=2.03 Simple disulfide: pdb=" SG CYS G 470 " - pdb=" SG CYS G 484 " distance=2.02 Simple disulfide: pdb=" SG CYS H 237 " - pdb=" SG CYS H 286 " distance=2.03 Simple disulfide: pdb=" SG CYS H 470 " - pdb=" SG CYS H 484 " distance=2.02 Simple disulfide: pdb=" SG CYS I 237 " - pdb=" SG CYS I 286 " distance=2.03 Simple disulfide: pdb=" SG CYS I 470 " - pdb=" SG CYS I 484 " distance=2.02 Simple disulfide: pdb=" SG CYS J 237 " - pdb=" SG CYS J 286 " distance=2.03 Simple disulfide: pdb=" SG CYS J 470 " - pdb=" SG CYS J 484 " distance=2.02 Simple disulfide: pdb=" SG CYS K 237 " - pdb=" SG CYS K 286 " distance=2.03 Simple disulfide: pdb=" SG CYS K 470 " - pdb=" SG CYS K 484 " distance=2.02 Simple disulfide: pdb=" SG CYS L 237 " - pdb=" SG CYS L 286 " distance=2.03 Simple disulfide: pdb=" SG CYS L 470 " - pdb=" SG CYS L 484 " distance=2.02 Simple disulfide: pdb=" SG CYS M 237 " - pdb=" SG CYS M 286 " distance=2.03 Simple disulfide: pdb=" SG CYS M 470 " - pdb=" SG CYS M 484 " distance=2.02 Simple disulfide: pdb=" SG CYS N 237 " - pdb=" SG CYS N 286 " distance=2.03 Simple disulfide: pdb=" SG CYS N 470 " - pdb=" SG CYS N 484 " distance=2.02 Simple disulfide: pdb=" SG CYS O 237 " - pdb=" SG CYS O 286 " distance=2.03 Simple disulfide: pdb=" SG CYS O 470 " - pdb=" SG CYS O 484 " distance=2.02 Simple disulfide: pdb=" SG CYS P 237 " - pdb=" SG CYS P 286 " distance=2.03 Simple disulfide: pdb=" SG CYS P 470 " - pdb=" SG CYS P 484 " distance=2.02 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: 13.12 Conformation dependent library (CDL) restraints added in 6.5 seconds 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15680 Finding SS restraints... Secondary structure from input PDB file: 272 helices and 16 sheets defined 46.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.40 Creating SS restraints... Processing helix chain 'A' and resid 17 through 37 removed outlier: 3.571A pdb=" N GLN A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ARG A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 60 through 67 removed outlier: 3.974A pdb=" N ILE A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.965A pdb=" N GLU A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL A 81 " --> pdb=" O MET A 77 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 110 removed outlier: 3.967A pdb=" N THR A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ARG A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 136 removed outlier: 4.877A pdb=" N VAL A 120 " --> pdb=" O HIS A 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 5.187A pdb=" N GLU A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 removed outlier: 3.785A pdb=" N ILE A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 280 removed outlier: 4.089A pdb=" N GLU A 263 " --> pdb=" O MET A 259 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET A 272 " --> pdb=" O MET A 268 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 276 " --> pdb=" O MET A 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 310 through 319 removed outlier: 3.862A pdb=" N MET A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 396 removed outlier: 4.154A pdb=" N GLU A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLU A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 445 removed outlier: 3.698A pdb=" N ALA A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 3.587A pdb=" N ALA A 445 " --> pdb=" O PRO A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 510 removed outlier: 4.284A pdb=" N ALA A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 503 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 37 removed outlier: 3.575A pdb=" N GLN B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ARG B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.963A pdb=" N GLU B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL B 81 " --> pdb=" O MET B 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ARG B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.557A pdb=" N THR B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 280 removed outlier: 4.089A pdb=" N GLU B 263 " --> pdb=" O MET B 259 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET B 272 " --> pdb=" O MET B 268 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 276 " --> pdb=" O MET B 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLY B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 301 Processing helix chain 'B' and resid 310 through 319 removed outlier: 3.854A pdb=" N MET B 314 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 396 removed outlier: 4.147A pdb=" N GLU B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY B 392 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 419 removed outlier: 3.608A pdb=" N GLU B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 445 removed outlier: 3.695A pdb=" N ALA B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Proline residue: B 441 - end of helix removed outlier: 3.588A pdb=" N ALA B 445 " --> pdb=" O PRO B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 510 removed outlier: 4.287A pdb=" N ALA B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 503 " --> pdb=" O ILE B 499 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 37 removed outlier: 3.574A pdb=" N GLN C 21 " --> pdb=" O GLY C 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG C 22 " --> pdb=" O ARG C 18 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 31 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'C' and resid 60 through 67 removed outlier: 3.977A pdb=" N ILE C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.960A pdb=" N GLU C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 81 " --> pdb=" O MET C 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 103 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 136 removed outlier: 4.878A pdb=" N VAL C 120 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS C 122 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS C 136 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR C 151 " --> pdb=" O LYS C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 184 removed outlier: 5.190A pdb=" N GLU C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL C 182 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 194 removed outlier: 3.788A pdb=" N ILE C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 280 removed outlier: 4.096A pdb=" N GLU C 263 " --> pdb=" O MET C 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET C 272 " --> pdb=" O MET C 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 276 " --> pdb=" O MET C 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY C 280 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 301 Processing helix chain 'C' and resid 310 through 319 removed outlier: 3.853A pdb=" N MET C 314 " --> pdb=" O LYS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 396 removed outlier: 4.150A pdb=" N GLU C 379 " --> pdb=" O HIS C 375 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL C 380 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 392 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 419 removed outlier: 3.610A pdb=" N GLU C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Proline residue: C 441 - end of helix removed outlier: 3.587A pdb=" N ALA C 445 " --> pdb=" O PRO C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 461 removed outlier: 3.803A pdb=" N VAL C 457 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS C 458 " --> pdb=" O GLU C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 503 " --> pdb=" O ILE C 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 37 removed outlier: 3.572A pdb=" N GLN D 21 " --> pdb=" O GLY D 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG D 22 " --> pdb=" O ARG D 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 43 Processing helix chain 'D' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE D 64 " --> pdb=" O ASP D 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU D 67 " --> pdb=" O THR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 removed outlier: 3.958A pdb=" N GLU D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL D 81 " --> pdb=" O MET D 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR D 95 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 103 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL D 120 " --> pdb=" O HIS D 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS D 136 " --> pdb=" O GLN D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 159 removed outlier: 3.556A pdb=" N THR D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL D 182 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE D 193 " --> pdb=" O ASP D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 280 removed outlier: 4.090A pdb=" N GLU D 263 " --> pdb=" O MET D 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET D 272 " --> pdb=" O MET D 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 276 " --> pdb=" O MET D 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY D 280 " --> pdb=" O ILE D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 301 Processing helix chain 'D' and resid 310 through 319 removed outlier: 3.850A pdb=" N MET D 314 " --> pdb=" O LYS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 396 removed outlier: 4.148A pdb=" N GLU D 379 " --> pdb=" O HIS D 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL D 380 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY D 392 " --> pdb=" O VAL D 388 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU D 396 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET D 413 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 419 " --> pdb=" O LEU D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Proline residue: D 441 - end of helix removed outlier: 3.587A pdb=" N ALA D 445 " --> pdb=" O PRO D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL D 457 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 503 " --> pdb=" O ILE D 499 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU D 507 " --> pdb=" O ALA D 503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET D 508 " --> pdb=" O GLU D 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 37 removed outlier: 3.574A pdb=" N GLN E 21 " --> pdb=" O GLY E 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 43 Processing helix chain 'E' and resid 60 through 67 removed outlier: 3.977A pdb=" N ILE E 64 " --> pdb=" O ASP E 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU E 67 " --> pdb=" O THR E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 87 removed outlier: 3.960A pdb=" N GLU E 80 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL E 81 " --> pdb=" O MET E 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR E 95 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU E 103 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 136 removed outlier: 4.878A pdb=" N VAL E 120 " --> pdb=" O HIS E 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS E 122 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR E 151 " --> pdb=" O LYS E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 184 removed outlier: 5.190A pdb=" N GLU E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL E 182 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 194 removed outlier: 3.788A pdb=" N ILE E 193 " --> pdb=" O ASP E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 280 removed outlier: 4.096A pdb=" N GLU E 263 " --> pdb=" O MET E 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU E 266 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET E 272 " --> pdb=" O MET E 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE E 276 " --> pdb=" O MET E 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY E 280 " --> pdb=" O ILE E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 301 Processing helix chain 'E' and resid 310 through 319 removed outlier: 3.853A pdb=" N MET E 314 " --> pdb=" O LYS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 396 removed outlier: 4.150A pdb=" N GLU E 379 " --> pdb=" O HIS E 375 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL E 380 " --> pdb=" O VAL E 376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP E 385 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY E 392 " --> pdb=" O VAL E 388 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU E 396 " --> pdb=" O GLY E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 419 removed outlier: 3.610A pdb=" N GLU E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET E 413 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA E 419 " --> pdb=" O LEU E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA E 436 " --> pdb=" O ALA E 432 " (cutoff:3.500A) Proline residue: E 441 - end of helix removed outlier: 3.587A pdb=" N ALA E 445 " --> pdb=" O PRO E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 461 removed outlier: 3.803A pdb=" N VAL E 457 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA E 502 " --> pdb=" O ALA E 498 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA E 503 " --> pdb=" O ILE E 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU E 507 " --> pdb=" O ALA E 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET E 508 " --> pdb=" O GLU E 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 37 removed outlier: 3.572A pdb=" N GLN F 21 " --> pdb=" O GLY F 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG F 22 " --> pdb=" O ARG F 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 43 Processing helix chain 'F' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU F 67 " --> pdb=" O THR F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 removed outlier: 3.958A pdb=" N GLU F 80 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL F 81 " --> pdb=" O MET F 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR F 95 " --> pdb=" O ASP F 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU F 103 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU F 104 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL F 120 " --> pdb=" O HIS F 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS F 122 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 159 removed outlier: 3.556A pdb=" N THR F 151 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL F 182 " --> pdb=" O VAL F 178 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE F 193 " --> pdb=" O ASP F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 280 removed outlier: 4.090A pdb=" N GLU F 263 " --> pdb=" O MET F 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU F 266 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET F 272 " --> pdb=" O MET F 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE F 276 " --> pdb=" O MET F 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY F 280 " --> pdb=" O ILE F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 301 Processing helix chain 'F' and resid 310 through 319 removed outlier: 3.850A pdb=" N MET F 314 " --> pdb=" O LYS F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 396 removed outlier: 4.148A pdb=" N GLU F 379 " --> pdb=" O HIS F 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL F 380 " --> pdb=" O VAL F 376 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP F 385 " --> pdb=" O ALA F 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY F 392 " --> pdb=" O VAL F 388 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU F 396 " --> pdb=" O GLY F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU F 410 " --> pdb=" O SER F 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET F 413 " --> pdb=" O VAL F 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA F 419 " --> pdb=" O LEU F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA F 436 " --> pdb=" O ALA F 432 " (cutoff:3.500A) Proline residue: F 441 - end of helix removed outlier: 3.587A pdb=" N ALA F 445 " --> pdb=" O PRO F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL F 457 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA F 502 " --> pdb=" O ALA F 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA F 503 " --> pdb=" O ILE F 499 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU F 507 " --> pdb=" O ALA F 503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET F 508 " --> pdb=" O GLU F 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 37 removed outlier: 3.574A pdb=" N GLN G 21 " --> pdb=" O GLY G 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG G 22 " --> pdb=" O ARG G 18 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 43 Processing helix chain 'G' and resid 60 through 67 removed outlier: 3.977A pdb=" N ILE G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU G 67 " --> pdb=" O THR G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 removed outlier: 3.960A pdb=" N GLU G 80 " --> pdb=" O LYS G 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL G 81 " --> pdb=" O MET G 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 103 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 136 removed outlier: 4.878A pdb=" N VAL G 120 " --> pdb=" O HIS G 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS G 136 " --> pdb=" O GLN G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR G 151 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 removed outlier: 5.190A pdb=" N GLU G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU G 176 " --> pdb=" O GLU G 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL G 182 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP G 183 " --> pdb=" O SER G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 194 removed outlier: 3.788A pdb=" N ILE G 193 " --> pdb=" O ASP G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 280 removed outlier: 4.096A pdb=" N GLU G 263 " --> pdb=" O MET G 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU G 266 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET G 272 " --> pdb=" O MET G 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE G 276 " --> pdb=" O MET G 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER G 279 " --> pdb=" O GLU G 275 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY G 280 " --> pdb=" O ILE G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 301 Processing helix chain 'G' and resid 310 through 319 removed outlier: 3.853A pdb=" N MET G 314 " --> pdb=" O LYS G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 396 removed outlier: 4.150A pdb=" N GLU G 379 " --> pdb=" O HIS G 375 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL G 380 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP G 385 " --> pdb=" O ALA G 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL G 391 " --> pdb=" O ALA G 387 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY G 392 " --> pdb=" O VAL G 388 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU G 396 " --> pdb=" O GLY G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 419 removed outlier: 3.610A pdb=" N GLU G 410 " --> pdb=" O SER G 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET G 413 " --> pdb=" O VAL G 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 419 " --> pdb=" O LEU G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA G 436 " --> pdb=" O ALA G 432 " (cutoff:3.500A) Proline residue: G 441 - end of helix removed outlier: 3.587A pdb=" N ALA G 445 " --> pdb=" O PRO G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 453 through 461 removed outlier: 3.803A pdb=" N VAL G 457 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS G 458 " --> pdb=" O GLU G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA G 502 " --> pdb=" O ALA G 498 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA G 503 " --> pdb=" O ILE G 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU G 507 " --> pdb=" O ALA G 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET G 508 " --> pdb=" O GLU G 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 37 removed outlier: 3.572A pdb=" N GLN H 21 " --> pdb=" O GLY H 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG H 22 " --> pdb=" O ARG H 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE H 31 " --> pdb=" O ALA H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 43 Processing helix chain 'H' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE H 64 " --> pdb=" O ASP H 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU H 67 " --> pdb=" O THR H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 87 removed outlier: 3.958A pdb=" N GLU H 80 " --> pdb=" O LYS H 76 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL H 81 " --> pdb=" O MET H 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU H 103 " --> pdb=" O VAL H 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL H 120 " --> pdb=" O HIS H 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS H 122 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS H 136 " --> pdb=" O GLN H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 159 removed outlier: 3.556A pdb=" N THR H 151 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU H 172 " --> pdb=" O GLU H 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU H 176 " --> pdb=" O GLU H 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL H 182 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP H 183 " --> pdb=" O SER H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE H 193 " --> pdb=" O ASP H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 280 removed outlier: 4.092A pdb=" N GLU H 263 " --> pdb=" O MET H 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU H 266 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET H 272 " --> pdb=" O MET H 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE H 276 " --> pdb=" O MET H 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER H 279 " --> pdb=" O GLU H 275 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY H 280 " --> pdb=" O ILE H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 301 Processing helix chain 'H' and resid 310 through 319 removed outlier: 3.850A pdb=" N MET H 314 " --> pdb=" O LYS H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 396 removed outlier: 4.148A pdb=" N GLU H 379 " --> pdb=" O HIS H 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL H 380 " --> pdb=" O VAL H 376 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL H 391 " --> pdb=" O ALA H 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY H 392 " --> pdb=" O VAL H 388 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU H 396 " --> pdb=" O GLY H 392 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU H 410 " --> pdb=" O SER H 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET H 413 " --> pdb=" O VAL H 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA H 419 " --> pdb=" O LEU H 415 " (cutoff:3.500A) Processing helix chain 'H' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA H 436 " --> pdb=" O ALA H 432 " (cutoff:3.500A) Proline residue: H 441 - end of helix removed outlier: 3.587A pdb=" N ALA H 445 " --> pdb=" O PRO H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL H 457 " --> pdb=" O ILE H 453 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS H 458 " --> pdb=" O GLU H 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 510 removed outlier: 4.284A pdb=" N ALA H 502 " --> pdb=" O ALA H 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA H 503 " --> pdb=" O ILE H 499 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU H 507 " --> pdb=" O ALA H 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET H 508 " --> pdb=" O GLU H 504 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 37 removed outlier: 3.572A pdb=" N GLN I 21 " --> pdb=" O GLY I 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG I 22 " --> pdb=" O ARG I 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 43 Processing helix chain 'I' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE I 64 " --> pdb=" O ASP I 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU I 67 " --> pdb=" O THR I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 87 removed outlier: 3.958A pdb=" N GLU I 80 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL I 81 " --> pdb=" O MET I 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR I 95 " --> pdb=" O ASP I 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU I 103 " --> pdb=" O VAL I 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU I 104 " --> pdb=" O ALA I 100 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG I 105 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL I 120 " --> pdb=" O HIS I 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS I 122 " --> pdb=" O THR I 118 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS I 136 " --> pdb=" O GLN I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 159 removed outlier: 3.556A pdb=" N THR I 151 " --> pdb=" O LYS I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU I 172 " --> pdb=" O GLU I 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU I 176 " --> pdb=" O GLU I 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL I 182 " --> pdb=" O VAL I 178 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP I 183 " --> pdb=" O SER I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 280 removed outlier: 4.089A pdb=" N GLU I 263 " --> pdb=" O MET I 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU I 266 " --> pdb=" O ILE I 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET I 272 " --> pdb=" O MET I 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE I 276 " --> pdb=" O MET I 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER I 279 " --> pdb=" O GLU I 275 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY I 280 " --> pdb=" O ILE I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 301 Processing helix chain 'I' and resid 310 through 319 removed outlier: 3.850A pdb=" N MET I 314 " --> pdb=" O LYS I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 396 removed outlier: 4.148A pdb=" N GLU I 379 " --> pdb=" O HIS I 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL I 380 " --> pdb=" O VAL I 376 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP I 385 " --> pdb=" O ALA I 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL I 391 " --> pdb=" O ALA I 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY I 392 " --> pdb=" O VAL I 388 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU I 396 " --> pdb=" O GLY I 392 " (cutoff:3.500A) Processing helix chain 'I' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU I 410 " --> pdb=" O SER I 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET I 413 " --> pdb=" O VAL I 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA I 419 " --> pdb=" O LEU I 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA I 436 " --> pdb=" O ALA I 432 " (cutoff:3.500A) Proline residue: I 441 - end of helix removed outlier: 3.587A pdb=" N ALA I 445 " --> pdb=" O PRO I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL I 457 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS I 458 " --> pdb=" O GLU I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA I 502 " --> pdb=" O ALA I 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA I 503 " --> pdb=" O ILE I 499 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU I 507 " --> pdb=" O ALA I 503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET I 508 " --> pdb=" O GLU I 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 37 removed outlier: 3.574A pdb=" N GLN J 21 " --> pdb=" O GLY J 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG J 22 " --> pdb=" O ARG J 18 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE J 31 " --> pdb=" O ALA J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 43 Processing helix chain 'J' and resid 60 through 67 removed outlier: 3.977A pdb=" N ILE J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU J 67 " --> pdb=" O THR J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 87 removed outlier: 3.960A pdb=" N GLU J 80 " --> pdb=" O LYS J 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL J 81 " --> pdb=" O MET J 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR J 95 " --> pdb=" O ASP J 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU J 103 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU J 104 " --> pdb=" O ALA J 100 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 136 removed outlier: 4.878A pdb=" N VAL J 120 " --> pdb=" O HIS J 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS J 122 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS J 136 " --> pdb=" O GLN J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR J 151 " --> pdb=" O LYS J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 184 removed outlier: 5.190A pdb=" N GLU J 172 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU J 176 " --> pdb=" O GLU J 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL J 182 " --> pdb=" O VAL J 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP J 183 " --> pdb=" O SER J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 194 removed outlier: 3.788A pdb=" N ILE J 193 " --> pdb=" O ASP J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 280 removed outlier: 4.095A pdb=" N GLU J 263 " --> pdb=" O MET J 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU J 266 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET J 272 " --> pdb=" O MET J 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE J 276 " --> pdb=" O MET J 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER J 279 " --> pdb=" O GLU J 275 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY J 280 " --> pdb=" O ILE J 276 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 301 Processing helix chain 'J' and resid 310 through 319 removed outlier: 3.853A pdb=" N MET J 314 " --> pdb=" O LYS J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 396 removed outlier: 4.150A pdb=" N GLU J 379 " --> pdb=" O HIS J 375 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL J 380 " --> pdb=" O VAL J 376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP J 385 " --> pdb=" O ALA J 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL J 391 " --> pdb=" O ALA J 387 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY J 392 " --> pdb=" O VAL J 388 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU J 396 " --> pdb=" O GLY J 392 " (cutoff:3.500A) Processing helix chain 'J' and resid 406 through 419 removed outlier: 3.610A pdb=" N GLU J 410 " --> pdb=" O SER J 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET J 413 " --> pdb=" O VAL J 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA J 419 " --> pdb=" O LEU J 415 " (cutoff:3.500A) Processing helix chain 'J' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA J 436 " --> pdb=" O ALA J 432 " (cutoff:3.500A) Proline residue: J 441 - end of helix removed outlier: 3.587A pdb=" N ALA J 445 " --> pdb=" O PRO J 441 " (cutoff:3.500A) Processing helix chain 'J' and resid 453 through 461 removed outlier: 3.803A pdb=" N VAL J 457 " --> pdb=" O ILE J 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS J 458 " --> pdb=" O GLU J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA J 502 " --> pdb=" O ALA J 498 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA J 503 " --> pdb=" O ILE J 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU J 507 " --> pdb=" O ALA J 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET J 508 " --> pdb=" O GLU J 504 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 37 removed outlier: 3.572A pdb=" N GLN K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG K 22 " --> pdb=" O ARG K 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 43 Processing helix chain 'K' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE K 64 " --> pdb=" O ASP K 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU K 67 " --> pdb=" O THR K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 87 removed outlier: 3.958A pdb=" N GLU K 80 " --> pdb=" O LYS K 76 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL K 81 " --> pdb=" O MET K 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA K 82 " --> pdb=" O LEU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR K 95 " --> pdb=" O ASP K 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU K 103 " --> pdb=" O VAL K 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU K 104 " --> pdb=" O ALA K 100 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG K 105 " --> pdb=" O GLY K 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL K 120 " --> pdb=" O HIS K 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS K 122 " --> pdb=" O THR K 118 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS K 136 " --> pdb=" O GLN K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 159 removed outlier: 3.556A pdb=" N THR K 151 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU K 172 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU K 176 " --> pdb=" O GLU K 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL K 182 " --> pdb=" O VAL K 178 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE K 193 " --> pdb=" O ASP K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 280 removed outlier: 4.089A pdb=" N GLU K 263 " --> pdb=" O MET K 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU K 266 " --> pdb=" O ILE K 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET K 272 " --> pdb=" O MET K 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE K 276 " --> pdb=" O MET K 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER K 279 " --> pdb=" O GLU K 275 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY K 280 " --> pdb=" O ILE K 276 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 301 Processing helix chain 'K' and resid 310 through 319 removed outlier: 3.850A pdb=" N MET K 314 " --> pdb=" O LYS K 310 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 396 removed outlier: 4.148A pdb=" N GLU K 379 " --> pdb=" O HIS K 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL K 380 " --> pdb=" O VAL K 376 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP K 385 " --> pdb=" O ALA K 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL K 391 " --> pdb=" O ALA K 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY K 392 " --> pdb=" O VAL K 388 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU K 396 " --> pdb=" O GLY K 392 " (cutoff:3.500A) Processing helix chain 'K' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU K 410 " --> pdb=" O SER K 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET K 413 " --> pdb=" O VAL K 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA K 419 " --> pdb=" O LEU K 415 " (cutoff:3.500A) Processing helix chain 'K' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA K 436 " --> pdb=" O ALA K 432 " (cutoff:3.500A) Proline residue: K 441 - end of helix removed outlier: 3.587A pdb=" N ALA K 445 " --> pdb=" O PRO K 441 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL K 457 " --> pdb=" O ILE K 453 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS K 458 " --> pdb=" O GLU K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA K 502 " --> pdb=" O ALA K 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA K 503 " --> pdb=" O ILE K 499 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU K 507 " --> pdb=" O ALA K 503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET K 508 " --> pdb=" O GLU K 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 37 removed outlier: 3.574A pdb=" N GLN L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG L 22 " --> pdb=" O ARG L 18 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE L 31 " --> pdb=" O ALA L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 43 Processing helix chain 'L' and resid 60 through 67 removed outlier: 3.977A pdb=" N ILE L 64 " --> pdb=" O ASP L 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU L 67 " --> pdb=" O THR L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 87 removed outlier: 3.960A pdb=" N GLU L 80 " --> pdb=" O LYS L 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL L 81 " --> pdb=" O MET L 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA L 82 " --> pdb=" O LEU L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU L 103 " --> pdb=" O VAL L 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU L 104 " --> pdb=" O ALA L 100 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG L 105 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 136 removed outlier: 4.878A pdb=" N VAL L 120 " --> pdb=" O HIS L 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS L 122 " --> pdb=" O THR L 118 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS L 136 " --> pdb=" O GLN L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR L 151 " --> pdb=" O LYS L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 184 removed outlier: 5.190A pdb=" N GLU L 172 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU L 176 " --> pdb=" O GLU L 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL L 182 " --> pdb=" O VAL L 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP L 183 " --> pdb=" O SER L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 194 removed outlier: 3.788A pdb=" N ILE L 193 " --> pdb=" O ASP L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 280 removed outlier: 4.095A pdb=" N GLU L 263 " --> pdb=" O MET L 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU L 266 " --> pdb=" O ILE L 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET L 272 " --> pdb=" O MET L 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE L 276 " --> pdb=" O MET L 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER L 279 " --> pdb=" O GLU L 275 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY L 280 " --> pdb=" O ILE L 276 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 301 Processing helix chain 'L' and resid 310 through 319 removed outlier: 3.853A pdb=" N MET L 314 " --> pdb=" O LYS L 310 " (cutoff:3.500A) Processing helix chain 'L' and resid 374 through 396 removed outlier: 4.150A pdb=" N GLU L 379 " --> pdb=" O HIS L 375 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL L 380 " --> pdb=" O VAL L 376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP L 385 " --> pdb=" O ALA L 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL L 391 " --> pdb=" O ALA L 387 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY L 392 " --> pdb=" O VAL L 388 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU L 396 " --> pdb=" O GLY L 392 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 419 removed outlier: 3.610A pdb=" N GLU L 410 " --> pdb=" O SER L 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET L 413 " --> pdb=" O VAL L 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA L 419 " --> pdb=" O LEU L 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA L 436 " --> pdb=" O ALA L 432 " (cutoff:3.500A) Proline residue: L 441 - end of helix removed outlier: 3.587A pdb=" N ALA L 445 " --> pdb=" O PRO L 441 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 461 removed outlier: 3.803A pdb=" N VAL L 457 " --> pdb=" O ILE L 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS L 458 " --> pdb=" O GLU L 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA L 502 " --> pdb=" O ALA L 498 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA L 503 " --> pdb=" O ILE L 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU L 507 " --> pdb=" O ALA L 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET L 508 " --> pdb=" O GLU L 504 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 37 removed outlier: 3.572A pdb=" N GLN M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG M 22 " --> pdb=" O ARG M 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE M 31 " --> pdb=" O ALA M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 43 Processing helix chain 'M' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE M 64 " --> pdb=" O ASP M 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 87 removed outlier: 3.958A pdb=" N GLU M 80 " --> pdb=" O LYS M 76 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL M 81 " --> pdb=" O MET M 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA M 82 " --> pdb=" O LEU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR M 95 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU M 103 " --> pdb=" O VAL M 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU M 104 " --> pdb=" O ALA M 100 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG M 105 " --> pdb=" O GLY M 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS M 106 " --> pdb=" O GLU M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL M 120 " --> pdb=" O HIS M 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS M 122 " --> pdb=" O THR M 118 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS M 136 " --> pdb=" O GLN M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 159 removed outlier: 3.556A pdb=" N THR M 151 " --> pdb=" O LYS M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU M 172 " --> pdb=" O GLU M 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU M 176 " --> pdb=" O GLU M 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL M 182 " --> pdb=" O VAL M 178 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP M 183 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE M 193 " --> pdb=" O ASP M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 280 removed outlier: 4.089A pdb=" N GLU M 263 " --> pdb=" O MET M 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU M 266 " --> pdb=" O ILE M 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET M 272 " --> pdb=" O MET M 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER M 279 " --> pdb=" O GLU M 275 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY M 280 " --> pdb=" O ILE M 276 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 301 Processing helix chain 'M' and resid 310 through 319 removed outlier: 3.850A pdb=" N MET M 314 " --> pdb=" O LYS M 310 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 396 removed outlier: 4.148A pdb=" N GLU M 379 " --> pdb=" O HIS M 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL M 380 " --> pdb=" O VAL M 376 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP M 385 " --> pdb=" O ALA M 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL M 391 " --> pdb=" O ALA M 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY M 392 " --> pdb=" O VAL M 388 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU M 396 " --> pdb=" O GLY M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU M 410 " --> pdb=" O SER M 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET M 413 " --> pdb=" O VAL M 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA M 419 " --> pdb=" O LEU M 415 " (cutoff:3.500A) Processing helix chain 'M' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA M 436 " --> pdb=" O ALA M 432 " (cutoff:3.500A) Proline residue: M 441 - end of helix removed outlier: 3.587A pdb=" N ALA M 445 " --> pdb=" O PRO M 441 " (cutoff:3.500A) Processing helix chain 'M' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL M 457 " --> pdb=" O ILE M 453 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS M 458 " --> pdb=" O GLU M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA M 502 " --> pdb=" O ALA M 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA M 503 " --> pdb=" O ILE M 499 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU M 507 " --> pdb=" O ALA M 503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET M 508 " --> pdb=" O GLU M 504 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 37 removed outlier: 3.574A pdb=" N GLN N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG N 22 " --> pdb=" O ARG N 18 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE N 31 " --> pdb=" O ALA N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 43 Processing helix chain 'N' and resid 60 through 67 removed outlier: 3.977A pdb=" N ILE N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU N 67 " --> pdb=" O THR N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 87 removed outlier: 3.960A pdb=" N GLU N 80 " --> pdb=" O LYS N 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL N 81 " --> pdb=" O MET N 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR N 95 " --> pdb=" O ASP N 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU N 103 " --> pdb=" O VAL N 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU N 104 " --> pdb=" O ALA N 100 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS N 106 " --> pdb=" O GLU N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 116 through 136 removed outlier: 4.878A pdb=" N VAL N 120 " --> pdb=" O HIS N 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS N 122 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS N 136 " --> pdb=" O GLN N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR N 151 " --> pdb=" O LYS N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 184 removed outlier: 5.190A pdb=" N GLU N 172 " --> pdb=" O GLU N 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU N 176 " --> pdb=" O GLU N 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL N 182 " --> pdb=" O VAL N 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP N 183 " --> pdb=" O SER N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 194 removed outlier: 3.788A pdb=" N ILE N 193 " --> pdb=" O ASP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 280 removed outlier: 4.095A pdb=" N GLU N 263 " --> pdb=" O MET N 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU N 266 " --> pdb=" O ILE N 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET N 272 " --> pdb=" O MET N 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE N 276 " --> pdb=" O MET N 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER N 279 " --> pdb=" O GLU N 275 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY N 280 " --> pdb=" O ILE N 276 " (cutoff:3.500A) Processing helix chain 'N' and resid 295 through 301 Processing helix chain 'N' and resid 310 through 319 removed outlier: 3.853A pdb=" N MET N 314 " --> pdb=" O LYS N 310 " (cutoff:3.500A) Processing helix chain 'N' and resid 374 through 396 removed outlier: 4.150A pdb=" N GLU N 379 " --> pdb=" O HIS N 375 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL N 380 " --> pdb=" O VAL N 376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP N 385 " --> pdb=" O ALA N 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL N 391 " --> pdb=" O ALA N 387 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY N 392 " --> pdb=" O VAL N 388 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU N 396 " --> pdb=" O GLY N 392 " (cutoff:3.500A) Processing helix chain 'N' and resid 406 through 419 removed outlier: 3.610A pdb=" N GLU N 410 " --> pdb=" O SER N 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET N 413 " --> pdb=" O VAL N 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA N 419 " --> pdb=" O LEU N 415 " (cutoff:3.500A) Processing helix chain 'N' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA N 436 " --> pdb=" O ALA N 432 " (cutoff:3.500A) Proline residue: N 441 - end of helix removed outlier: 3.587A pdb=" N ALA N 445 " --> pdb=" O PRO N 441 " (cutoff:3.500A) Processing helix chain 'N' and resid 453 through 461 removed outlier: 3.803A pdb=" N VAL N 457 " --> pdb=" O ILE N 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS N 458 " --> pdb=" O GLU N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA N 502 " --> pdb=" O ALA N 498 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA N 503 " --> pdb=" O ILE N 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU N 507 " --> pdb=" O ALA N 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET N 508 " --> pdb=" O GLU N 504 " (cutoff:3.500A) Processing helix chain 'O' and resid 17 through 37 removed outlier: 3.572A pdb=" N GLN O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE O 31 " --> pdb=" O ALA O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 39 through 43 Processing helix chain 'O' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU O 67 " --> pdb=" O THR O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 87 removed outlier: 3.958A pdb=" N GLU O 80 " --> pdb=" O LYS O 76 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL O 81 " --> pdb=" O MET O 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA O 82 " --> pdb=" O LEU O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR O 95 " --> pdb=" O ASP O 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU O 103 " --> pdb=" O VAL O 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU O 104 " --> pdb=" O ALA O 100 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG O 105 " --> pdb=" O GLY O 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS O 106 " --> pdb=" O GLU O 102 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL O 120 " --> pdb=" O HIS O 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS O 122 " --> pdb=" O THR O 118 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS O 136 " --> pdb=" O GLN O 132 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 159 removed outlier: 3.556A pdb=" N THR O 151 " --> pdb=" O LYS O 147 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU O 172 " --> pdb=" O GLU O 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU O 176 " --> pdb=" O GLU O 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL O 182 " --> pdb=" O VAL O 178 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP O 183 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE O 193 " --> pdb=" O ASP O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 258 through 280 removed outlier: 4.089A pdb=" N GLU O 263 " --> pdb=" O MET O 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU O 266 " --> pdb=" O ILE O 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET O 272 " --> pdb=" O MET O 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE O 276 " --> pdb=" O MET O 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER O 279 " --> pdb=" O GLU O 275 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY O 280 " --> pdb=" O ILE O 276 " (cutoff:3.500A) Processing helix chain 'O' and resid 295 through 301 Processing helix chain 'O' and resid 310 through 319 removed outlier: 3.850A pdb=" N MET O 314 " --> pdb=" O LYS O 310 " (cutoff:3.500A) Processing helix chain 'O' and resid 374 through 396 removed outlier: 4.148A pdb=" N GLU O 379 " --> pdb=" O HIS O 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL O 380 " --> pdb=" O VAL O 376 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP O 385 " --> pdb=" O ALA O 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL O 391 " --> pdb=" O ALA O 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY O 392 " --> pdb=" O VAL O 388 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU O 396 " --> pdb=" O GLY O 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU O 410 " --> pdb=" O SER O 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET O 413 " --> pdb=" O VAL O 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA O 419 " --> pdb=" O LEU O 415 " (cutoff:3.500A) Processing helix chain 'O' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA O 436 " --> pdb=" O ALA O 432 " (cutoff:3.500A) Proline residue: O 441 - end of helix removed outlier: 3.587A pdb=" N ALA O 445 " --> pdb=" O PRO O 441 " (cutoff:3.500A) Processing helix chain 'O' and resid 453 through 461 removed outlier: 3.801A pdb=" N VAL O 457 " --> pdb=" O ILE O 453 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS O 458 " --> pdb=" O GLU O 454 " (cutoff:3.500A) Processing helix chain 'O' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA O 502 " --> pdb=" O ALA O 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA O 503 " --> pdb=" O ILE O 499 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU O 507 " --> pdb=" O ALA O 503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET O 508 " --> pdb=" O GLU O 504 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 37 removed outlier: 3.574A pdb=" N GLN P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ARG P 22 " --> pdb=" O ARG P 18 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE P 31 " --> pdb=" O ALA P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 43 Processing helix chain 'P' and resid 60 through 67 removed outlier: 3.977A pdb=" N ILE P 64 " --> pdb=" O ASP P 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU P 67 " --> pdb=" O THR P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 87 removed outlier: 3.960A pdb=" N GLU P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL P 81 " --> pdb=" O MET P 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA P 82 " --> pdb=" O LEU P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR P 95 " --> pdb=" O ASP P 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU P 103 " --> pdb=" O VAL P 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU P 104 " --> pdb=" O ALA P 100 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG P 105 " --> pdb=" O GLY P 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS P 106 " --> pdb=" O GLU P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 136 removed outlier: 4.878A pdb=" N VAL P 120 " --> pdb=" O HIS P 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS P 122 " --> pdb=" O THR P 118 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS P 136 " --> pdb=" O GLN P 132 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR P 151 " --> pdb=" O LYS P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 184 removed outlier: 5.190A pdb=" N GLU P 172 " --> pdb=" O GLU P 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU P 176 " --> pdb=" O GLU P 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL P 182 " --> pdb=" O VAL P 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP P 183 " --> pdb=" O SER P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 194 removed outlier: 3.788A pdb=" N ILE P 193 " --> pdb=" O ASP P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 258 through 280 removed outlier: 4.095A pdb=" N GLU P 263 " --> pdb=" O MET P 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU P 266 " --> pdb=" O ILE P 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET P 272 " --> pdb=" O MET P 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE P 276 " --> pdb=" O MET P 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER P 279 " --> pdb=" O GLU P 275 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY P 280 " --> pdb=" O ILE P 276 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 301 Processing helix chain 'P' and resid 310 through 319 removed outlier: 3.853A pdb=" N MET P 314 " --> pdb=" O LYS P 310 " (cutoff:3.500A) Processing helix chain 'P' and resid 374 through 396 removed outlier: 4.150A pdb=" N GLU P 379 " --> pdb=" O HIS P 375 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL P 380 " --> pdb=" O VAL P 376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP P 385 " --> pdb=" O ALA P 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL P 391 " --> pdb=" O ALA P 387 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY P 392 " --> pdb=" O VAL P 388 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU P 396 " --> pdb=" O GLY P 392 " (cutoff:3.500A) Processing helix chain 'P' and resid 406 through 419 removed outlier: 3.610A pdb=" N GLU P 410 " --> pdb=" O SER P 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET P 413 " --> pdb=" O VAL P 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA P 419 " --> pdb=" O LEU P 415 " (cutoff:3.500A) Processing helix chain 'P' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA P 436 " --> pdb=" O ALA P 432 " (cutoff:3.500A) Proline residue: P 441 - end of helix removed outlier: 3.587A pdb=" N ALA P 445 " --> pdb=" O PRO P 441 " (cutoff:3.500A) Processing helix chain 'P' and resid 453 through 461 removed outlier: 3.803A pdb=" N VAL P 457 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS P 458 " --> pdb=" O GLU P 454 " (cutoff:3.500A) Processing helix chain 'P' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA P 502 " --> pdb=" O ALA P 498 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA P 503 " --> pdb=" O ILE P 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU P 507 " --> pdb=" O ALA P 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET P 508 " --> pdb=" O GLU P 504 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 46 through 47 removed outlier: 4.104A pdb=" N LYS A 46 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL A 57 " --> pdb=" O LYS A 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=A Processing sheet with id=B, first strand: chain 'B' and resid 46 through 47 removed outlier: 4.104A pdb=" N LYS B 46 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL B 57 " --> pdb=" O LYS B 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=B Processing sheet with id=C, first strand: chain 'C' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS C 46 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL C 57 " --> pdb=" O LYS C 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=C Processing sheet with id=D, first strand: chain 'D' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS D 46 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL D 57 " --> pdb=" O LYS D 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=D Processing sheet with id=E, first strand: chain 'E' and resid 46 through 47 removed outlier: 4.109A pdb=" N LYS E 46 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL E 57 " --> pdb=" O LYS E 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=E Processing sheet with id=F, first strand: chain 'F' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS F 46 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 57 " --> pdb=" O LYS F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=F Processing sheet with id=G, first strand: chain 'G' and resid 46 through 47 removed outlier: 4.109A pdb=" N LYS G 46 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL G 57 " --> pdb=" O LYS G 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=G Processing sheet with id=H, first strand: chain 'H' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS H 46 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL H 57 " --> pdb=" O LYS H 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=H Processing sheet with id=I, first strand: chain 'I' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS I 46 " --> pdb=" O VAL I 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL I 57 " --> pdb=" O LYS I 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=I Processing sheet with id=J, first strand: chain 'J' and resid 46 through 47 removed outlier: 4.109A pdb=" N LYS J 46 " --> pdb=" O VAL J 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL J 57 " --> pdb=" O LYS J 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=J Processing sheet with id=K, first strand: chain 'K' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS K 46 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL K 57 " --> pdb=" O LYS K 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=K Processing sheet with id=L, first strand: chain 'L' and resid 46 through 47 removed outlier: 4.109A pdb=" N LYS L 46 " --> pdb=" O VAL L 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL L 57 " --> pdb=" O LYS L 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=L Processing sheet with id=M, first strand: chain 'M' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS M 46 " --> pdb=" O VAL M 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL M 57 " --> pdb=" O LYS M 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=M Processing sheet with id=N, first strand: chain 'N' and resid 46 through 47 removed outlier: 4.109A pdb=" N LYS N 46 " --> pdb=" O VAL N 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL N 57 " --> pdb=" O LYS N 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=N Processing sheet with id=O, first strand: chain 'O' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS O 46 " --> pdb=" O VAL O 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL O 57 " --> pdb=" O LYS O 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=O Processing sheet with id=P, first strand: chain 'P' and resid 46 through 47 removed outlier: 4.109A pdb=" N LYS P 46 " --> pdb=" O VAL P 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL P 57 " --> pdb=" O LYS P 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=P 2111 hydrogen bonds defined for protein. 6237 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: 16.90 Time building geometry restraints manager: 15.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22009 1.34 - 1.46: 9232 1.46 - 1.58: 32071 1.58 - 1.71: 16 1.71 - 1.83: 784 Bond restraints: 64112 Sorted by residual: bond pdb=" CA VAL C 7 " pdb=" CB VAL C 7 " ideal model delta sigma weight residual 1.540 1.592 -0.052 1.36e-02 5.41e+03 1.46e+01 bond pdb=" CA VAL O 7 " pdb=" CB VAL O 7 " ideal model delta sigma weight residual 1.540 1.592 -0.052 1.36e-02 5.41e+03 1.44e+01 bond pdb=" CA VAL A 7 " pdb=" CB VAL A 7 " ideal model delta sigma weight residual 1.540 1.591 -0.051 1.36e-02 5.41e+03 1.43e+01 bond pdb=" CA VAL L 7 " pdb=" CB VAL L 7 " ideal model delta sigma weight residual 1.540 1.591 -0.051 1.36e-02 5.41e+03 1.42e+01 bond pdb=" CA VAL E 7 " pdb=" CB VAL E 7 " ideal model delta sigma weight residual 1.540 1.591 -0.051 1.36e-02 5.41e+03 1.42e+01 ... (remaining 64107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.87: 82074 4.87 - 9.75: 3028 9.75 - 14.62: 898 14.62 - 19.50: 176 19.50 - 24.37: 64 Bond angle restraints: 86240 Sorted by residual: angle pdb=" N ARG L 308 " pdb=" CA ARG L 308 " pdb=" C ARG L 308 " ideal model delta sigma weight residual 108.99 129.83 -20.84 1.57e+00 4.06e-01 1.76e+02 angle pdb=" N ARG P 308 " pdb=" CA ARG P 308 " pdb=" C ARG P 308 " ideal model delta sigma weight residual 108.99 129.83 -20.84 1.57e+00 4.06e-01 1.76e+02 angle pdb=" N ARG E 308 " pdb=" CA ARG E 308 " pdb=" C ARG E 308 " ideal model delta sigma weight residual 108.99 129.83 -20.84 1.57e+00 4.06e-01 1.76e+02 angle pdb=" N ARG C 308 " pdb=" CA ARG C 308 " pdb=" C ARG C 308 " ideal model delta sigma weight residual 108.99 129.83 -20.84 1.57e+00 4.06e-01 1.76e+02 angle pdb=" N ARG G 308 " pdb=" CA ARG G 308 " pdb=" C ARG G 308 " ideal model delta sigma weight residual 108.99 129.83 -20.84 1.57e+00 4.06e-01 1.76e+02 ... (remaining 86235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 34547 18.14 - 36.27: 3807 36.27 - 54.41: 1391 54.41 - 72.55: 463 72.55 - 90.68: 288 Dihedral angle restraints: 40496 sinusoidal: 16256 harmonic: 24240 Sorted by residual: dihedral pdb=" C ILE B 195 " pdb=" N ILE B 195 " pdb=" CA ILE B 195 " pdb=" CB ILE B 195 " ideal model delta harmonic sigma weight residual -122.00 -142.38 20.38 0 2.50e+00 1.60e-01 6.64e+01 dihedral pdb=" C ILE H 195 " pdb=" N ILE H 195 " pdb=" CA ILE H 195 " pdb=" CB ILE H 195 " ideal model delta harmonic sigma weight residual -122.00 -142.36 20.36 0 2.50e+00 1.60e-01 6.63e+01 dihedral pdb=" C ILE K 195 " pdb=" N ILE K 195 " pdb=" CA ILE K 195 " pdb=" CB ILE K 195 " ideal model delta harmonic sigma weight residual -122.00 -142.34 20.34 0 2.50e+00 1.60e-01 6.62e+01 ... (remaining 40493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 7647 0.168 - 0.335: 1947 0.335 - 0.503: 518 0.503 - 0.671: 272 0.671 - 0.839: 64 Chirality restraints: 10448 Sorted by residual: chirality pdb=" CA ILE H 195 " pdb=" N ILE H 195 " pdb=" C ILE H 195 " pdb=" CB ILE H 195 " both_signs ideal model delta sigma weight residual False 2.43 1.59 0.84 2.00e-01 2.50e+01 1.76e+01 chirality pdb=" CA ILE G 195 " pdb=" N ILE G 195 " pdb=" C ILE G 195 " pdb=" CB ILE G 195 " both_signs ideal model delta sigma weight residual False 2.43 1.59 0.84 2.00e-01 2.50e+01 1.76e+01 chirality pdb=" CA ILE C 195 " pdb=" N ILE C 195 " pdb=" C ILE C 195 " pdb=" CB ILE C 195 " both_signs ideal model delta sigma weight residual False 2.43 1.59 0.84 2.00e-01 2.50e+01 1.76e+01 ... (remaining 10445 not shown) Planarity restraints: 11216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN P 4 " 0.087 5.00e-02 4.00e+02 1.31e-01 2.73e+01 pdb=" N PRO P 5 " -0.226 5.00e-02 4.00e+02 pdb=" CA PRO P 5 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO P 5 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 4 " 0.087 5.00e-02 4.00e+02 1.31e-01 2.73e+01 pdb=" N PRO E 5 " -0.226 5.00e-02 4.00e+02 pdb=" CA PRO E 5 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO E 5 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN N 4 " -0.087 5.00e-02 4.00e+02 1.31e-01 2.73e+01 pdb=" N PRO N 5 " 0.226 5.00e-02 4.00e+02 pdb=" CA PRO N 5 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO N 5 " -0.067 5.00e-02 4.00e+02 ... (remaining 11213 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 14267 2.79 - 3.32: 80856 3.32 - 3.84: 109180 3.84 - 4.37: 130979 4.37 - 4.90: 190043 Nonbonded interactions: 525325 Sorted by model distance: nonbonded pdb=" N CYS L 484 " pdb=" N GLU L 485 " model vdw 2.259 2.560 nonbonded pdb=" N CYS E 484 " pdb=" N GLU E 485 " model vdw 2.259 2.560 nonbonded pdb=" N CYS P 484 " pdb=" N GLU P 485 " model vdw 2.259 2.560 nonbonded pdb=" N CYS C 484 " pdb=" N GLU C 485 " model vdw 2.259 2.560 nonbonded pdb=" N CYS J 484 " pdb=" N GLU J 485 " model vdw 2.259 2.560 ... (remaining 525320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.100 Extract box with map and model: 1.840 Check model and map are aligned: 0.390 Set scattering table: 0.460 Process input model: 103.980 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5064 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 0.080 64112 Z= 0.491 Angle : 2.440 24.374 86240 Z= 1.514 Chirality : 0.189 0.839 10448 Planarity : 0.011 0.131 11216 Dihedral : 19.869 90.683 24720 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 87.93 Ramachandran Plot: Outliers : 13.79 % Allowed : 17.36 % Favored : 68.86 % Rotamer: Outliers : 23.89 % Allowed : 16.28 % Favored : 59.84 % Cbeta Deviations : 2.86 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.57 (0.06), residues: 8480 helix: -3.70 (0.05), residues: 3152 sheet: None (None), residues: 0 loop : -5.15 (0.06), residues: 5328 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 361 PHE 0.036 0.009 PHE B 433 TYR 0.037 0.009 TYR E 418 ARG 0.018 0.003 ARG M 416 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3358 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1632 poor density : 1726 time to evaluate : 5.460 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: 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: 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: 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 64 ILE cc_start: 0.5223 (OUTLIER) cc_final: 0.4758 (mt) REVERT: A 72 HIS cc_start: 0.4439 (OUTLIER) cc_final: 0.4199 (t70) REVERT: A 88 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.4928 (tp30) REVERT: A 187 LYS cc_start: 0.5189 (ptmm) cc_final: 0.4680 (mttp) REVERT: A 241 ILE cc_start: 0.5361 (OUTLIER) cc_final: 0.5093 (mm) REVERT: A 243 GLU cc_start: 0.3741 (OUTLIER) cc_final: 0.3333 (pt0) REVERT: A 382 ARG cc_start: 0.4310 (OUTLIER) cc_final: 0.3911 (ptm160) REVERT: A 412 SER cc_start: 0.5402 (OUTLIER) cc_final: 0.4960 (p) REVERT: A 475 VAL cc_start: 0.7288 (t) cc_final: 0.7081 (p) REVERT: A 510 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6784 (tm) REVERT: A 513 ASP cc_start: 0.5302 (m-30) cc_final: 0.4406 (p0) REVERT: A 527 MET cc_start: 0.3650 (OUTLIER) cc_final: 0.3096 (ttt) REVERT: A 530 MET cc_start: 0.4546 (OUTLIER) cc_final: 0.3281 (mmt) REVERT: B 25 ILE cc_start: 0.7691 (mm) cc_final: 0.7422 (mt) REVERT: B 45 ASP cc_start: 0.2207 (m-30) cc_final: 0.0908 (m-30) REVERT: B 64 ILE cc_start: 0.4980 (OUTLIER) cc_final: 0.4499 (mt) REVERT: B 88 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.5963 (tp30) REVERT: B 161 LYS cc_start: 0.2093 (OUTLIER) cc_final: 0.1496 (tptt) REVERT: B 187 LYS cc_start: 0.5239 (ptmm) cc_final: 0.4624 (mttt) REVERT: B 194 LYS cc_start: 0.3305 (OUTLIER) cc_final: 0.3054 (tttp) REVERT: B 210 LYS cc_start: 0.4247 (OUTLIER) cc_final: 0.3350 (tptt) REVERT: B 241 ILE cc_start: 0.4476 (OUTLIER) cc_final: 0.4181 (mm) REVERT: B 243 GLU cc_start: 0.3164 (OUTLIER) cc_final: 0.2253 (pt0) REVERT: B 249 GLU cc_start: 0.6193 (tp30) cc_final: 0.5357 (mm-30) REVERT: B 382 ARG cc_start: 0.4218 (OUTLIER) cc_final: 0.3798 (ptp-110) REVERT: B 413 MET cc_start: 0.5925 (pp-130) cc_final: 0.5704 (pp-130) REVERT: B 497 GLN cc_start: 0.6484 (mm110) cc_final: 0.6231 (tp40) REVERT: B 510 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6799 (tm) REVERT: B 513 ASP cc_start: 0.4600 (m-30) cc_final: 0.4179 (p0) REVERT: B 519 GLU cc_start: 0.3693 (OUTLIER) cc_final: 0.2592 (tt0) REVERT: B 527 MET cc_start: 0.3018 (OUTLIER) cc_final: 0.1442 (mtt) REVERT: B 530 MET cc_start: 0.4102 (OUTLIER) cc_final: 0.2836 (mmt) REVERT: C 64 ILE cc_start: 0.5077 (OUTLIER) cc_final: 0.4667 (mt) REVERT: C 72 HIS cc_start: 0.4431 (OUTLIER) cc_final: 0.4202 (t70) REVERT: C 88 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.4903 (tp30) REVERT: C 187 LYS cc_start: 0.5186 (ptmm) cc_final: 0.4666 (mttp) REVERT: C 241 ILE cc_start: 0.5353 (OUTLIER) cc_final: 0.5103 (mm) REVERT: C 243 GLU cc_start: 0.3743 (OUTLIER) cc_final: 0.3317 (pt0) REVERT: C 382 ARG cc_start: 0.4317 (OUTLIER) cc_final: 0.3933 (ptm160) REVERT: C 412 SER cc_start: 0.5404 (OUTLIER) cc_final: 0.4954 (p) REVERT: C 475 VAL cc_start: 0.7284 (t) cc_final: 0.7084 (p) REVERT: C 510 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6859 (tm) REVERT: C 513 ASP cc_start: 0.5290 (m-30) cc_final: 0.4422 (p0) REVERT: C 527 MET cc_start: 0.3720 (OUTLIER) cc_final: 0.3117 (ttt) REVERT: C 530 MET cc_start: 0.4530 (OUTLIER) cc_final: 0.3312 (mmt) REVERT: D 25 ILE cc_start: 0.7695 (mm) cc_final: 0.7426 (mt) REVERT: D 45 ASP cc_start: 0.2174 (m-30) cc_final: 0.0925 (m-30) REVERT: D 64 ILE cc_start: 0.4970 (OUTLIER) cc_final: 0.4497 (mt) REVERT: D 88 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.5877 (tp30) REVERT: D 93 THR cc_start: 0.4908 (OUTLIER) cc_final: 0.4696 (t) REVERT: D 161 LYS cc_start: 0.2081 (OUTLIER) cc_final: 0.1509 (tptt) REVERT: D 187 LYS cc_start: 0.5241 (ptmm) cc_final: 0.4608 (mttt) REVERT: D 194 LYS cc_start: 0.3331 (OUTLIER) cc_final: 0.3067 (tttp) REVERT: D 210 LYS cc_start: 0.4243 (OUTLIER) cc_final: 0.3331 (tptt) REVERT: D 241 ILE cc_start: 0.4477 (OUTLIER) cc_final: 0.4183 (mm) REVERT: D 243 GLU cc_start: 0.3157 (OUTLIER) cc_final: 0.2235 (pt0) REVERT: D 249 GLU cc_start: 0.6191 (tp30) cc_final: 0.5354 (mm-30) REVERT: D 382 ARG cc_start: 0.4234 (OUTLIER) cc_final: 0.3802 (ptp-110) REVERT: D 413 MET cc_start: 0.5941 (pp-130) cc_final: 0.5721 (pp-130) REVERT: D 510 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6813 (tm) REVERT: D 513 ASP cc_start: 0.4602 (m-30) cc_final: 0.4146 (p0) REVERT: D 519 GLU cc_start: 0.3686 (OUTLIER) cc_final: 0.2578 (tt0) REVERT: D 527 MET cc_start: 0.3002 (OUTLIER) cc_final: 0.1432 (mtt) REVERT: D 530 MET cc_start: 0.4103 (OUTLIER) cc_final: 0.2838 (mmt) REVERT: E 64 ILE cc_start: 0.5091 (OUTLIER) cc_final: 0.4678 (mt) REVERT: E 72 HIS cc_start: 0.4437 (OUTLIER) cc_final: 0.4213 (t70) REVERT: E 88 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.4904 (tp30) REVERT: E 187 LYS cc_start: 0.5183 (ptmm) cc_final: 0.4672 (mttp) REVERT: E 241 ILE cc_start: 0.5374 (OUTLIER) cc_final: 0.5115 (mm) REVERT: E 243 GLU cc_start: 0.3748 (OUTLIER) cc_final: 0.3325 (pt0) REVERT: E 382 ARG cc_start: 0.4311 (OUTLIER) cc_final: 0.3916 (ptm160) REVERT: E 412 SER cc_start: 0.5400 (OUTLIER) cc_final: 0.4934 (p) REVERT: E 475 VAL cc_start: 0.7290 (t) cc_final: 0.7083 (p) REVERT: E 510 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6859 (tm) REVERT: E 513 ASP cc_start: 0.5313 (m-30) cc_final: 0.4446 (p0) REVERT: E 527 MET cc_start: 0.3738 (OUTLIER) cc_final: 0.3121 (ttt) REVERT: E 530 MET cc_start: 0.4549 (OUTLIER) cc_final: 0.3328 (mmt) REVERT: F 25 ILE cc_start: 0.7705 (mm) cc_final: 0.7462 (mt) REVERT: F 45 ASP cc_start: 0.2173 (m-30) cc_final: 0.0936 (m-30) REVERT: F 64 ILE cc_start: 0.4978 (OUTLIER) cc_final: 0.4496 (mt) REVERT: F 88 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.5877 (tp30) REVERT: F 93 THR cc_start: 0.4910 (OUTLIER) cc_final: 0.4701 (t) REVERT: F 161 LYS cc_start: 0.2082 (OUTLIER) cc_final: 0.1508 (tptt) REVERT: F 187 LYS cc_start: 0.5243 (ptmm) cc_final: 0.4609 (mttt) REVERT: F 194 LYS cc_start: 0.3334 (OUTLIER) cc_final: 0.3068 (tttp) REVERT: F 210 LYS cc_start: 0.4251 (OUTLIER) cc_final: 0.3331 (tptt) REVERT: F 241 ILE cc_start: 0.4484 (OUTLIER) cc_final: 0.4190 (mm) REVERT: F 243 GLU cc_start: 0.3157 (OUTLIER) cc_final: 0.2236 (pt0) REVERT: F 249 GLU cc_start: 0.6187 (tp30) cc_final: 0.5351 (mm-30) REVERT: F 382 ARG cc_start: 0.4243 (OUTLIER) cc_final: 0.3810 (ptp-110) REVERT: F 413 MET cc_start: 0.5929 (pp-130) cc_final: 0.5716 (pp-130) REVERT: F 510 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6838 (tm) REVERT: F 513 ASP cc_start: 0.4601 (m-30) cc_final: 0.4151 (p0) REVERT: F 519 GLU cc_start: 0.3676 (OUTLIER) cc_final: 0.2576 (tt0) REVERT: F 527 MET cc_start: 0.3012 (OUTLIER) cc_final: 0.1433 (mtt) REVERT: F 530 MET cc_start: 0.4115 (OUTLIER) cc_final: 0.2846 (mmt) REVERT: G 64 ILE cc_start: 0.5112 (OUTLIER) cc_final: 0.4694 (mt) REVERT: G 72 HIS cc_start: 0.4433 (OUTLIER) cc_final: 0.4203 (t70) REVERT: G 88 GLU cc_start: 0.6109 (OUTLIER) cc_final: 0.4911 (tp30) REVERT: G 187 LYS cc_start: 0.5183 (ptmm) cc_final: 0.4672 (mttp) REVERT: G 241 ILE cc_start: 0.5375 (OUTLIER) cc_final: 0.5125 (mm) REVERT: G 243 GLU cc_start: 0.3745 (OUTLIER) cc_final: 0.3326 (pt0) REVERT: G 382 ARG cc_start: 0.4315 (OUTLIER) cc_final: 0.3919 (ptm160) REVERT: G 412 SER cc_start: 0.5405 (OUTLIER) cc_final: 0.4953 (p) REVERT: G 475 VAL cc_start: 0.7281 (t) cc_final: 0.7077 (p) REVERT: G 510 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6856 (tm) REVERT: G 513 ASP cc_start: 0.5298 (m-30) cc_final: 0.4437 (p0) REVERT: G 527 MET cc_start: 0.3749 (OUTLIER) cc_final: 0.3132 (ttt) REVERT: G 530 MET cc_start: 0.4572 (OUTLIER) cc_final: 0.3350 (mmt) REVERT: H 25 ILE cc_start: 0.7679 (mm) cc_final: 0.7439 (mt) REVERT: H 45 ASP cc_start: 0.2178 (m-30) cc_final: 0.0921 (m-30) REVERT: H 64 ILE cc_start: 0.4983 (OUTLIER) cc_final: 0.4493 (mt) REVERT: H 88 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5892 (tp30) REVERT: H 93 THR cc_start: 0.4905 (OUTLIER) cc_final: 0.4692 (t) REVERT: H 161 LYS cc_start: 0.2091 (OUTLIER) cc_final: 0.1516 (tptt) REVERT: H 187 LYS cc_start: 0.5238 (ptmm) cc_final: 0.4589 (mttt) REVERT: H 194 LYS cc_start: 0.3312 (OUTLIER) cc_final: 0.3056 (tttp) REVERT: H 210 LYS cc_start: 0.4255 (OUTLIER) cc_final: 0.3335 (tptt) REVERT: H 241 ILE cc_start: 0.4478 (OUTLIER) cc_final: 0.4184 (mm) REVERT: H 243 GLU cc_start: 0.3160 (OUTLIER) cc_final: 0.2242 (pt0) REVERT: H 249 GLU cc_start: 0.6208 (tp30) cc_final: 0.5358 (mm-30) REVERT: H 382 ARG cc_start: 0.4242 (OUTLIER) cc_final: 0.3814 (ptp-110) REVERT: H 413 MET cc_start: 0.5919 (pp-130) cc_final: 0.5698 (pp-130) REVERT: H 510 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6835 (tm) REVERT: H 513 ASP cc_start: 0.4576 (m-30) cc_final: 0.4117 (p0) REVERT: H 519 GLU cc_start: 0.3701 (OUTLIER) cc_final: 0.2621 (tt0) REVERT: H 527 MET cc_start: 0.3050 (OUTLIER) cc_final: 0.1456 (mtt) REVERT: H 530 MET cc_start: 0.4110 (OUTLIER) cc_final: 0.2855 (mmt) REVERT: I 25 ILE cc_start: 0.7703 (mm) cc_final: 0.7482 (mt) REVERT: I 45 ASP cc_start: 0.2190 (m-30) cc_final: 0.0944 (m-30) REVERT: I 64 ILE cc_start: 0.4976 (OUTLIER) cc_final: 0.4500 (mt) REVERT: I 88 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5878 (tp30) REVERT: I 93 THR cc_start: 0.4906 (OUTLIER) cc_final: 0.4699 (t) REVERT: I 161 LYS cc_start: 0.2085 (OUTLIER) cc_final: 0.1506 (tptt) REVERT: I 187 LYS cc_start: 0.5242 (ptmm) cc_final: 0.4608 (mttt) REVERT: I 194 LYS cc_start: 0.3339 (OUTLIER) cc_final: 0.3072 (tttp) REVERT: I 210 LYS cc_start: 0.4227 (OUTLIER) cc_final: 0.3306 (tptt) REVERT: I 241 ILE cc_start: 0.4487 (OUTLIER) cc_final: 0.4186 (mm) REVERT: I 243 GLU cc_start: 0.3173 (OUTLIER) cc_final: 0.2252 (pt0) REVERT: I 249 GLU cc_start: 0.6171 (tp30) cc_final: 0.5355 (mm-30) REVERT: I 382 ARG cc_start: 0.4240 (OUTLIER) cc_final: 0.3811 (ptp-110) REVERT: I 413 MET cc_start: 0.5949 (pp-130) cc_final: 0.5733 (pp-130) REVERT: I 510 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6788 (tm) REVERT: I 513 ASP cc_start: 0.4629 (m-30) cc_final: 0.4169 (p0) REVERT: I 519 GLU cc_start: 0.3684 (OUTLIER) cc_final: 0.2578 (tt0) REVERT: I 527 MET cc_start: 0.3017 (OUTLIER) cc_final: 0.1444 (mtt) REVERT: I 530 MET cc_start: 0.4107 (OUTLIER) cc_final: 0.2839 (mmt) REVERT: J 64 ILE cc_start: 0.5077 (OUTLIER) cc_final: 0.4675 (mt) REVERT: J 72 HIS cc_start: 0.4428 (OUTLIER) cc_final: 0.4204 (t70) REVERT: J 88 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.4902 (tp30) REVERT: J 187 LYS cc_start: 0.5194 (ptmm) cc_final: 0.4671 (mttp) REVERT: J 241 ILE cc_start: 0.5375 (OUTLIER) cc_final: 0.5114 (mm) REVERT: J 243 GLU cc_start: 0.3754 (OUTLIER) cc_final: 0.3331 (pt0) REVERT: J 382 ARG cc_start: 0.4310 (OUTLIER) cc_final: 0.3912 (ptm160) REVERT: J 412 SER cc_start: 0.5419 (OUTLIER) cc_final: 0.4944 (p) REVERT: J 475 VAL cc_start: 0.7287 (t) cc_final: 0.7078 (p) REVERT: J 510 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6852 (tm) REVERT: J 513 ASP cc_start: 0.5311 (m-30) cc_final: 0.4436 (p0) REVERT: J 527 MET cc_start: 0.3751 (OUTLIER) cc_final: 0.3141 (ttt) REVERT: J 530 MET cc_start: 0.4548 (OUTLIER) cc_final: 0.3313 (mmt) REVERT: K 25 ILE cc_start: 0.7699 (mm) cc_final: 0.7458 (mt) REVERT: K 45 ASP cc_start: 0.2196 (m-30) cc_final: 0.0947 (m-30) REVERT: K 64 ILE cc_start: 0.4956 (OUTLIER) cc_final: 0.4488 (mt) REVERT: K 88 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.5873 (tp30) REVERT: K 93 THR cc_start: 0.4903 (OUTLIER) cc_final: 0.4683 (t) REVERT: K 161 LYS cc_start: 0.2082 (OUTLIER) cc_final: 0.1503 (tptt) REVERT: K 187 LYS cc_start: 0.5239 (ptmm) cc_final: 0.4595 (mttt) REVERT: K 194 LYS cc_start: 0.3335 (OUTLIER) cc_final: 0.3070 (tttp) REVERT: K 210 LYS cc_start: 0.4224 (OUTLIER) cc_final: 0.3311 (tptt) REVERT: K 241 ILE cc_start: 0.4483 (OUTLIER) cc_final: 0.4183 (mm) REVERT: K 243 GLU cc_start: 0.3170 (OUTLIER) cc_final: 0.2252 (pt0) REVERT: K 249 GLU cc_start: 0.6164 (tp30) cc_final: 0.5349 (mm-30) REVERT: K 382 ARG cc_start: 0.4236 (OUTLIER) cc_final: 0.3807 (ptp-110) REVERT: K 413 MET cc_start: 0.5946 (pp-130) cc_final: 0.5731 (pp-130) REVERT: K 510 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6818 (tm) REVERT: K 513 ASP cc_start: 0.4602 (m-30) cc_final: 0.4149 (p0) REVERT: K 519 GLU cc_start: 0.3689 (OUTLIER) cc_final: 0.2584 (tt0) REVERT: K 527 MET cc_start: 0.3009 (OUTLIER) cc_final: 0.1446 (mtt) REVERT: K 530 MET cc_start: 0.4098 (OUTLIER) cc_final: 0.2835 (mmt) REVERT: L 64 ILE cc_start: 0.5073 (OUTLIER) cc_final: 0.4676 (mt) REVERT: L 72 HIS cc_start: 0.4435 (OUTLIER) cc_final: 0.4203 (t70) REVERT: L 88 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.4908 (tp30) REVERT: L 161 LYS cc_start: 0.3009 (OUTLIER) cc_final: 0.2809 (tptt) REVERT: L 187 LYS cc_start: 0.5187 (ptmm) cc_final: 0.4660 (mttp) REVERT: L 241 ILE cc_start: 0.5365 (OUTLIER) cc_final: 0.5106 (mm) REVERT: L 243 GLU cc_start: 0.3754 (OUTLIER) cc_final: 0.3328 (pt0) REVERT: L 382 ARG cc_start: 0.4307 (OUTLIER) cc_final: 0.3918 (ptm160) REVERT: L 412 SER cc_start: 0.5416 (OUTLIER) cc_final: 0.4949 (p) REVERT: L 475 VAL cc_start: 0.7289 (t) cc_final: 0.7081 (p) REVERT: L 510 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6853 (tm) REVERT: L 513 ASP cc_start: 0.5294 (m-30) cc_final: 0.4419 (p0) REVERT: L 527 MET cc_start: 0.3732 (OUTLIER) cc_final: 0.3133 (ttt) REVERT: L 530 MET cc_start: 0.4520 (OUTLIER) cc_final: 0.3298 (mmt) REVERT: M 25 ILE cc_start: 0.7696 (mm) cc_final: 0.7455 (mt) REVERT: M 45 ASP cc_start: 0.2206 (m-30) cc_final: 0.0953 (m-30) REVERT: M 64 ILE cc_start: 0.4970 (OUTLIER) cc_final: 0.4492 (mt) REVERT: M 88 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5882 (tp30) REVERT: M 93 THR cc_start: 0.4906 (OUTLIER) cc_final: 0.4680 (t) REVERT: M 161 LYS cc_start: 0.2071 (OUTLIER) cc_final: 0.1487 (tptt) REVERT: M 187 LYS cc_start: 0.5245 (ptmm) cc_final: 0.4600 (mttt) REVERT: M 194 LYS cc_start: 0.3317 (OUTLIER) cc_final: 0.3054 (tttp) REVERT: M 210 LYS cc_start: 0.4230 (OUTLIER) cc_final: 0.3320 (tptt) REVERT: M 241 ILE cc_start: 0.4477 (OUTLIER) cc_final: 0.4175 (mm) REVERT: M 243 GLU cc_start: 0.3164 (OUTLIER) cc_final: 0.2249 (pt0) REVERT: M 249 GLU cc_start: 0.6188 (tp30) cc_final: 0.5352 (mm-30) REVERT: M 382 ARG cc_start: 0.4233 (OUTLIER) cc_final: 0.3806 (ptp-110) REVERT: M 413 MET cc_start: 0.5936 (pp-130) cc_final: 0.5720 (pp-130) REVERT: M 510 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6805 (tm) REVERT: M 513 ASP cc_start: 0.4610 (m-30) cc_final: 0.4153 (p0) REVERT: M 519 GLU cc_start: 0.3685 (OUTLIER) cc_final: 0.2580 (tt0) REVERT: M 527 MET cc_start: 0.3026 (OUTLIER) cc_final: 0.1451 (mtt) REVERT: M 530 MET cc_start: 0.4085 (OUTLIER) cc_final: 0.2830 (mmt) REVERT: N 64 ILE cc_start: 0.5088 (OUTLIER) cc_final: 0.4689 (mt) REVERT: N 72 HIS cc_start: 0.4453 (OUTLIER) cc_final: 0.4195 (t70) REVERT: N 88 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.4918 (tp30) REVERT: N 187 LYS cc_start: 0.5182 (ptmm) cc_final: 0.4662 (mttp) REVERT: N 241 ILE cc_start: 0.5357 (OUTLIER) cc_final: 0.5109 (mm) REVERT: N 243 GLU cc_start: 0.3758 (OUTLIER) cc_final: 0.3334 (pt0) REVERT: N 382 ARG cc_start: 0.4300 (OUTLIER) cc_final: 0.3918 (ptm160) REVERT: N 412 SER cc_start: 0.5406 (OUTLIER) cc_final: 0.4948 (p) REVERT: N 510 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6892 (tm) REVERT: N 513 ASP cc_start: 0.5258 (m-30) cc_final: 0.4393 (p0) REVERT: N 527 MET cc_start: 0.3742 (OUTLIER) cc_final: 0.3130 (ttt) REVERT: N 530 MET cc_start: 0.4543 (OUTLIER) cc_final: 0.3306 (mmt) REVERT: O 25 ILE cc_start: 0.7699 (mm) cc_final: 0.7484 (mt) REVERT: O 45 ASP cc_start: 0.2204 (m-30) cc_final: 0.0936 (m-30) REVERT: O 64 ILE cc_start: 0.4979 (OUTLIER) cc_final: 0.4492 (mt) REVERT: O 88 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5891 (tp30) REVERT: O 93 THR cc_start: 0.4901 (OUTLIER) cc_final: 0.4684 (t) REVERT: O 161 LYS cc_start: 0.2087 (OUTLIER) cc_final: 0.1515 (tptt) REVERT: O 187 LYS cc_start: 0.5241 (ptmm) cc_final: 0.4595 (mttt) REVERT: O 194 LYS cc_start: 0.3316 (OUTLIER) cc_final: 0.3057 (tttp) REVERT: O 210 LYS cc_start: 0.4244 (OUTLIER) cc_final: 0.3316 (tptt) REVERT: O 241 ILE cc_start: 0.4481 (OUTLIER) cc_final: 0.4178 (mm) REVERT: O 243 GLU cc_start: 0.3168 (OUTLIER) cc_final: 0.2247 (pt0) REVERT: O 249 GLU cc_start: 0.6191 (tp30) cc_final: 0.5353 (mm-30) REVERT: O 382 ARG cc_start: 0.4239 (OUTLIER) cc_final: 0.3819 (ptp-110) REVERT: O 413 MET cc_start: 0.5935 (pp-130) cc_final: 0.5715 (pp-130) REVERT: O 510 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6820 (tm) REVERT: O 513 ASP cc_start: 0.4606 (m-30) cc_final: 0.4152 (p0) REVERT: O 519 GLU cc_start: 0.3696 (OUTLIER) cc_final: 0.2590 (tt0) REVERT: O 527 MET cc_start: 0.3051 (OUTLIER) cc_final: 0.1462 (mtt) REVERT: O 530 MET cc_start: 0.4083 (OUTLIER) cc_final: 0.2834 (mmt) REVERT: P 64 ILE cc_start: 0.5093 (OUTLIER) cc_final: 0.4683 (mt) REVERT: P 72 HIS cc_start: 0.4436 (OUTLIER) cc_final: 0.4196 (t70) REVERT: P 88 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.4930 (tp30) REVERT: P 187 LYS cc_start: 0.5187 (ptmm) cc_final: 0.4668 (mttp) REVERT: P 241 ILE cc_start: 0.5372 (OUTLIER) cc_final: 0.5121 (mm) REVERT: P 243 GLU cc_start: 0.3760 (OUTLIER) cc_final: 0.3334 (pt0) REVERT: P 382 ARG cc_start: 0.4310 (OUTLIER) cc_final: 0.3920 (ptm160) REVERT: P 412 SER cc_start: 0.5424 (OUTLIER) cc_final: 0.4964 (p) REVERT: P 510 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6854 (tm) REVERT: P 513 ASP cc_start: 0.5296 (m-30) cc_final: 0.4429 (p0) REVERT: P 527 MET cc_start: 0.3758 (OUTLIER) cc_final: 0.3140 (ttt) REVERT: P 530 MET cc_start: 0.4558 (OUTLIER) cc_final: 0.3327 (mmt) outliers start: 1632 outliers final: 750 residues processed: 2865 average time/residue: 0.6372 time to fit residues: 2999.0749 Evaluate side-chains 2233 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 934 poor density : 1299 time to evaluate : 5.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 716 optimal weight: 6.9990 chunk 642 optimal weight: 6.9990 chunk 356 optimal weight: 10.0000 chunk 219 optimal weight: 0.9980 chunk 433 optimal weight: 5.9990 chunk 343 optimal weight: 10.0000 chunk 664 optimal weight: 8.9990 chunk 257 optimal weight: 0.7980 chunk 404 optimal weight: 6.9990 chunk 494 optimal weight: 0.9990 chunk 770 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 114 ASN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN B 4 GLN ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN C 4 GLN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 GLN D 4 GLN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN ** D 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 ASN ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 GLN F 4 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 ASN ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 GLN ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 ASN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 500 GLN H 4 GLN ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 ASN ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 324 ASN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 ASN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 324 ASN ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 ASN ** J 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 500 GLN K 4 GLN ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 ASN ** K 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 324 ASN ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 ASN ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 500 GLN M 4 GLN ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 ASN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 324 ASN ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 ASN ** N 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 500 GLN O 4 GLN ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 ASN ** O 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 324 ASN ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 4 GLN P 114 ASN ** P 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 500 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4818 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 64112 Z= 0.349 Angle : 1.465 14.557 86240 Z= 0.766 Chirality : 0.070 0.350 10448 Planarity : 0.008 0.133 11216 Dihedral : 9.673 34.793 8928 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 37.15 Ramachandran Plot: Outliers : 5.86 % Allowed : 20.96 % Favored : 73.18 % Rotamer: Outliers : 1.42 % Allowed : 10.38 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.70 (0.07), residues: 8480 helix: -2.39 (0.07), residues: 3248 sheet: None (None), residues: 0 loop : -5.09 (0.06), residues: 5232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS M 463 PHE 0.018 0.003 PHE D 433 TYR 0.008 0.002 TYR D 418 ARG 0.006 0.001 ARG F 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2026 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1929 time to evaluate : 6.281 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: 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: 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 12 MET cc_start: 0.4540 (mpp) cc_final: 0.3795 (mmt) REVERT: A 48 LEU cc_start: 0.4628 (OUTLIER) cc_final: 0.4124 (pp) REVERT: A 68 MET cc_start: 0.2569 (mmm) cc_final: 0.2276 (mmm) REVERT: A 194 LYS cc_start: 0.4074 (pptt) cc_final: 0.3834 (ptpt) REVERT: A 269 LEU cc_start: 0.6983 (mm) cc_final: 0.6767 (tp) REVERT: A 415 LEU cc_start: 0.6444 (mt) cc_final: 0.5806 (mm) REVERT: A 433 PHE cc_start: 0.3035 (t80) cc_final: 0.2827 (t80) REVERT: A 442 ARG cc_start: 0.6438 (ttt180) cc_final: 0.6204 (ttt180) REVERT: A 451 ASP cc_start: 0.4547 (t0) cc_final: 0.4208 (t0) REVERT: A 475 VAL cc_start: 0.7088 (t) cc_final: 0.6876 (p) REVERT: A 527 MET cc_start: 0.3648 (ttt) cc_final: 0.3290 (ttt) REVERT: B 12 MET cc_start: 0.4254 (mmt) cc_final: 0.3939 (mmt) REVERT: B 23 MET cc_start: 0.4132 (tpt) cc_final: 0.3874 (ttt) REVERT: B 48 LEU cc_start: 0.4602 (OUTLIER) cc_final: 0.4066 (pp) REVERT: B 71 GLU cc_start: 0.4906 (mm-30) cc_final: 0.4295 (mm-30) REVERT: B 297 TYR cc_start: 0.3729 (m-80) cc_final: 0.3412 (m-80) REVERT: B 527 MET cc_start: 0.2430 (ttt) cc_final: 0.2053 (ttt) REVERT: C 12 MET cc_start: 0.4264 (mmt) cc_final: 0.3500 (mmt) REVERT: C 48 LEU cc_start: 0.4625 (OUTLIER) cc_final: 0.4167 (pp) REVERT: C 68 MET cc_start: 0.2543 (mmm) cc_final: 0.2203 (mmm) REVERT: C 194 LYS cc_start: 0.3976 (pptt) cc_final: 0.3716 (ptpt) REVERT: C 269 LEU cc_start: 0.7251 (mm) cc_final: 0.6962 (tp) REVERT: C 415 LEU cc_start: 0.6448 (mt) cc_final: 0.5822 (mm) REVERT: C 433 PHE cc_start: 0.3009 (t80) cc_final: 0.2770 (t80) REVERT: C 442 ARG cc_start: 0.6537 (ttt180) cc_final: 0.6314 (ttt180) REVERT: C 451 ASP cc_start: 0.4548 (t0) cc_final: 0.4219 (t0) REVERT: C 475 VAL cc_start: 0.7165 (t) cc_final: 0.6949 (p) REVERT: C 527 MET cc_start: 0.3955 (ttt) cc_final: 0.3573 (ttt) REVERT: D 12 MET cc_start: 0.4325 (mmt) cc_final: 0.3917 (mmt) REVERT: D 23 MET cc_start: 0.4219 (tpt) cc_final: 0.3977 (ttt) REVERT: D 48 LEU cc_start: 0.4619 (OUTLIER) cc_final: 0.4040 (pp) REVERT: D 71 GLU cc_start: 0.4867 (mm-30) cc_final: 0.4239 (mm-30) REVERT: D 297 TYR cc_start: 0.3727 (m-80) cc_final: 0.3416 (m-80) REVERT: D 527 MET cc_start: 0.2455 (ttt) cc_final: 0.2087 (ttt) REVERT: E 12 MET cc_start: 0.4291 (mmt) cc_final: 0.3531 (mmt) REVERT: E 48 LEU cc_start: 0.4567 (OUTLIER) cc_final: 0.4057 (pp) REVERT: E 68 MET cc_start: 0.2555 (mmm) cc_final: 0.2183 (mmm) REVERT: E 194 LYS cc_start: 0.3976 (pptt) cc_final: 0.3709 (ptpt) REVERT: E 269 LEU cc_start: 0.7264 (mm) cc_final: 0.6963 (tp) REVERT: E 415 LEU cc_start: 0.6452 (mt) cc_final: 0.5818 (mm) REVERT: E 433 PHE cc_start: 0.2993 (t80) cc_final: 0.2761 (t80) REVERT: E 442 ARG cc_start: 0.6519 (ttt180) cc_final: 0.6301 (ttt180) REVERT: E 451 ASP cc_start: 0.4543 (t0) cc_final: 0.4223 (t0) REVERT: E 475 VAL cc_start: 0.7148 (t) cc_final: 0.6944 (p) REVERT: E 527 MET cc_start: 0.3830 (ttt) cc_final: 0.3431 (ttt) REVERT: F 12 MET cc_start: 0.4331 (mmt) cc_final: 0.3920 (mmt) REVERT: F 48 LEU cc_start: 0.4620 (OUTLIER) cc_final: 0.4007 (pp) REVERT: F 71 GLU cc_start: 0.4820 (mm-30) cc_final: 0.4221 (mm-30) REVERT: F 297 TYR cc_start: 0.3710 (m-80) cc_final: 0.3389 (m-80) REVERT: F 527 MET cc_start: 0.2476 (ttt) cc_final: 0.2105 (ttt) REVERT: G 12 MET cc_start: 0.4269 (mmt) cc_final: 0.3514 (mmt) REVERT: G 48 LEU cc_start: 0.4565 (OUTLIER) cc_final: 0.4046 (pp) REVERT: G 68 MET cc_start: 0.2570 (mmm) cc_final: 0.2170 (mmm) REVERT: G 194 LYS cc_start: 0.3932 (pptt) cc_final: 0.3674 (ptpt) REVERT: G 269 LEU cc_start: 0.7256 (mm) cc_final: 0.6944 (tp) REVERT: G 415 LEU cc_start: 0.6460 (mt) cc_final: 0.5831 (mm) REVERT: G 433 PHE cc_start: 0.3006 (t80) cc_final: 0.2791 (t80) REVERT: G 442 ARG cc_start: 0.6516 (ttt180) cc_final: 0.6311 (ttt180) REVERT: G 451 ASP cc_start: 0.4548 (t0) cc_final: 0.4219 (t0) REVERT: G 475 VAL cc_start: 0.7136 (t) cc_final: 0.6920 (p) REVERT: G 527 MET cc_start: 0.3841 (ttt) cc_final: 0.3438 (ttt) REVERT: H 12 MET cc_start: 0.4222 (mmt) cc_final: 0.3874 (mmt) REVERT: H 48 LEU cc_start: 0.4606 (OUTLIER) cc_final: 0.3986 (pp) REVERT: H 71 GLU cc_start: 0.4814 (mm-30) cc_final: 0.4220 (mm-30) REVERT: H 297 TYR cc_start: 0.3692 (m-80) cc_final: 0.3351 (m-80) REVERT: H 527 MET cc_start: 0.2498 (ttt) cc_final: 0.2076 (ttt) REVERT: I 12 MET cc_start: 0.4386 (mmt) cc_final: 0.3927 (mmt) REVERT: I 48 LEU cc_start: 0.4625 (OUTLIER) cc_final: 0.4029 (pp) REVERT: I 71 GLU cc_start: 0.4818 (mm-30) cc_final: 0.4207 (mm-30) REVERT: I 297 TYR cc_start: 0.3668 (m-80) cc_final: 0.3319 (m-80) REVERT: I 527 MET cc_start: 0.2522 (ttt) cc_final: 0.2140 (ttt) REVERT: J 12 MET cc_start: 0.4292 (mmt) cc_final: 0.3509 (mmt) REVERT: J 48 LEU cc_start: 0.4595 (OUTLIER) cc_final: 0.4056 (pp) REVERT: J 68 MET cc_start: 0.2557 (mmm) cc_final: 0.2172 (mmm) REVERT: J 194 LYS cc_start: 0.3946 (pptt) cc_final: 0.3685 (ptpt) REVERT: J 269 LEU cc_start: 0.7254 (mm) cc_final: 0.6948 (tp) REVERT: J 415 LEU cc_start: 0.6444 (mt) cc_final: 0.5831 (mm) REVERT: J 475 VAL cc_start: 0.7138 (t) cc_final: 0.6913 (p) REVERT: J 527 MET cc_start: 0.3838 (ttt) cc_final: 0.3440 (ttt) REVERT: K 12 MET cc_start: 0.4323 (mmt) cc_final: 0.3919 (mmt) REVERT: K 48 LEU cc_start: 0.4625 (OUTLIER) cc_final: 0.4040 (pp) REVERT: K 71 GLU cc_start: 0.4855 (mm-30) cc_final: 0.4263 (mm-30) REVERT: K 297 TYR cc_start: 0.3677 (m-80) cc_final: 0.3340 (m-80) REVERT: K 527 MET cc_start: 0.2503 (ttt) cc_final: 0.2086 (ttt) REVERT: L 12 MET cc_start: 0.4279 (mmt) cc_final: 0.3532 (mmt) REVERT: L 48 LEU cc_start: 0.4618 (OUTLIER) cc_final: 0.4077 (pp) REVERT: L 68 MET cc_start: 0.2522 (mmm) cc_final: 0.2129 (mmm) REVERT: L 194 LYS cc_start: 0.3993 (pptt) cc_final: 0.3710 (ptpt) REVERT: L 269 LEU cc_start: 0.7264 (mm) cc_final: 0.6956 (tp) REVERT: L 415 LEU cc_start: 0.6438 (mt) cc_final: 0.5832 (mm) REVERT: L 442 ARG cc_start: 0.6519 (ttt180) cc_final: 0.6319 (ttt180) REVERT: L 475 VAL cc_start: 0.7132 (t) cc_final: 0.6920 (p) REVERT: L 527 MET cc_start: 0.3831 (ttt) cc_final: 0.3435 (ttt) REVERT: M 12 MET cc_start: 0.4290 (mmt) cc_final: 0.3895 (mmt) REVERT: M 48 LEU cc_start: 0.4594 (OUTLIER) cc_final: 0.3986 (pp) REVERT: M 71 GLU cc_start: 0.4846 (mm-30) cc_final: 0.4250 (mm-30) REVERT: M 297 TYR cc_start: 0.3664 (m-80) cc_final: 0.3334 (m-80) REVERT: M 527 MET cc_start: 0.2467 (ttt) cc_final: 0.2052 (ttt) REVERT: N 12 MET cc_start: 0.4256 (mmt) cc_final: 0.3520 (mmt) REVERT: N 48 LEU cc_start: 0.4630 (OUTLIER) cc_final: 0.4097 (pp) REVERT: N 68 MET cc_start: 0.2527 (mmm) cc_final: 0.2155 (mmm) REVERT: N 194 LYS cc_start: 0.3984 (pptt) cc_final: 0.3708 (ptpt) REVERT: N 269 LEU cc_start: 0.7254 (mm) cc_final: 0.6938 (tp) REVERT: N 415 LEU cc_start: 0.6435 (mt) cc_final: 0.5817 (mm) REVERT: N 442 ARG cc_start: 0.6517 (ttt180) cc_final: 0.6315 (ttt180) REVERT: N 527 MET cc_start: 0.3827 (ttt) cc_final: 0.3435 (ttt) REVERT: O 12 MET cc_start: 0.4311 (mmt) cc_final: 0.3863 (mmt) REVERT: O 48 LEU cc_start: 0.4608 (OUTLIER) cc_final: 0.3989 (pp) REVERT: O 71 GLU cc_start: 0.4815 (mm-30) cc_final: 0.4240 (mm-30) REVERT: O 297 TYR cc_start: 0.3667 (m-80) cc_final: 0.3321 (m-80) REVERT: O 527 MET cc_start: 0.2473 (ttt) cc_final: 0.2075 (ttt) REVERT: P 12 MET cc_start: 0.4276 (mmt) cc_final: 0.3497 (mmt) REVERT: P 48 LEU cc_start: 0.4587 (OUTLIER) cc_final: 0.4044 (pp) REVERT: P 68 MET cc_start: 0.2572 (mmm) cc_final: 0.2161 (mmm) REVERT: P 194 LYS cc_start: 0.3951 (pptt) cc_final: 0.3686 (ptpt) REVERT: P 269 LEU cc_start: 0.7250 (mm) cc_final: 0.6934 (tp) REVERT: P 415 LEU cc_start: 0.6439 (mt) cc_final: 0.5835 (mm) REVERT: P 442 ARG cc_start: 0.6507 (ttt180) cc_final: 0.6293 (ttt180) REVERT: P 527 MET cc_start: 0.3835 (ttt) cc_final: 0.3475 (ttt) outliers start: 97 outliers final: 32 residues processed: 1969 average time/residue: 0.7125 time to fit residues: 2335.0136 Evaluate side-chains 1253 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1205 time to evaluate : 5.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 427 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 640 optimal weight: 5.9990 chunk 524 optimal weight: 0.4980 chunk 212 optimal weight: 0.0030 chunk 771 optimal weight: 20.0000 chunk 833 optimal weight: 10.0000 chunk 687 optimal weight: 6.9990 chunk 765 optimal weight: 4.9990 chunk 263 optimal weight: 0.9990 chunk 618 optimal weight: 0.2980 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 ASN ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 447 ASN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 497 GLN I 296 HIS I 447 ASN ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 HIS ** J 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 447 ASN ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 497 GLN ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 HIS ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 447 ASN ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 296 HIS ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN ** O 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 447 ASN ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 497 GLN ** P 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4741 moved from start: 0.6440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 64112 Z= 0.282 Angle : 1.296 17.082 86240 Z= 0.664 Chirality : 0.060 0.236 10448 Planarity : 0.009 0.171 11216 Dihedral : 9.258 32.560 8928 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 29.47 Ramachandran Plot: Outliers : 5.40 % Allowed : 19.23 % Favored : 75.37 % Rotamer: Outliers : 0.56 % Allowed : 10.80 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.53 (0.07), residues: 8480 helix: -2.16 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : -5.19 (0.05), residues: 4928 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 463 PHE 0.015 0.002 PHE P 285 TYR 0.010 0.001 TYR A 297 ARG 0.012 0.001 ARG F 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1585 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1547 time to evaluate : 5.424 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: 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 44 MET cc_start: 0.3282 (mmm) cc_final: 0.2627 (mmt) REVERT: A 513 ASP cc_start: 0.4679 (m-30) cc_final: 0.4086 (p0) REVERT: A 527 MET cc_start: 0.1954 (ttt) cc_final: 0.0413 (tpt) REVERT: B 46 LYS cc_start: 0.4703 (mmtt) cc_final: 0.4429 (mmmt) REVERT: B 331 ASP cc_start: 0.6748 (m-30) cc_final: 0.6428 (p0) REVERT: B 513 ASP cc_start: 0.4982 (m-30) cc_final: 0.4370 (p0) REVERT: B 527 MET cc_start: 0.1445 (ttt) cc_final: 0.1208 (tpt) REVERT: C 527 MET cc_start: 0.2075 (ttt) cc_final: 0.0852 (tpt) REVERT: D 331 ASP cc_start: 0.6739 (m-30) cc_final: 0.6440 (p0) REVERT: D 513 ASP cc_start: 0.4962 (m-30) cc_final: 0.4362 (p0) REVERT: E 44 MET cc_start: 0.3326 (mmm) cc_final: 0.2719 (mmt) REVERT: E 527 MET cc_start: 0.2046 (ttt) cc_final: 0.0836 (tpt) REVERT: F 331 ASP cc_start: 0.6748 (m-30) cc_final: 0.6432 (p0) REVERT: G 44 MET cc_start: 0.3291 (mmm) cc_final: 0.2701 (mmt) REVERT: G 527 MET cc_start: 0.2049 (ttt) cc_final: 0.0856 (tpt) REVERT: H 331 ASP cc_start: 0.6677 (m-30) cc_final: 0.6445 (p0) REVERT: I 331 ASP cc_start: 0.6743 (m-30) cc_final: 0.6420 (p0) REVERT: I 513 ASP cc_start: 0.4835 (m-30) cc_final: 0.4433 (p0) REVERT: J 44 MET cc_start: 0.3307 (mmm) cc_final: 0.2711 (mmt) REVERT: J 527 MET cc_start: 0.2111 (ttt) cc_final: 0.0421 (tpt) REVERT: K 331 ASP cc_start: 0.6726 (m-30) cc_final: 0.6429 (p0) REVERT: K 513 ASP cc_start: 0.4920 (m-30) cc_final: 0.4367 (p0) REVERT: L 527 MET cc_start: 0.2126 (ttt) cc_final: 0.0464 (tpt) REVERT: M 331 ASP cc_start: 0.6721 (m-30) cc_final: 0.6432 (p0) REVERT: M 513 ASP cc_start: 0.4774 (m-30) cc_final: 0.4192 (p0) REVERT: N 44 MET cc_start: 0.3255 (mmm) cc_final: 0.2718 (mmt) REVERT: N 527 MET cc_start: 0.2093 (ttt) cc_final: 0.0442 (tpt) REVERT: O 331 ASP cc_start: 0.6720 (m-30) cc_final: 0.6416 (p0) REVERT: O 513 ASP cc_start: 0.4893 (m-30) cc_final: 0.4391 (p0) REVERT: P 44 MET cc_start: 0.3283 (mmm) cc_final: 0.2720 (mmt) REVERT: P 527 MET cc_start: 0.2087 (ttt) cc_final: 0.0455 (tpt) outliers start: 38 outliers final: 1 residues processed: 1569 average time/residue: 0.6218 time to fit residues: 1633.5114 Evaluate side-chains 1140 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1139 time to evaluate : 5.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 762 optimal weight: 2.9990 chunk 580 optimal weight: 8.9990 chunk 400 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 368 optimal weight: 5.9990 chunk 518 optimal weight: 8.9990 chunk 774 optimal weight: 9.9990 chunk 819 optimal weight: 5.9990 chunk 404 optimal weight: 0.8980 chunk 733 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 296 HIS ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 GLN ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN G 222 GLN ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 222 GLN ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN I 222 GLN ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 HIS ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 497 GLN J 222 GLN ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN ** K 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 222 GLN ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 222 GLN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 497 GLN N 222 GLN ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN O 222 GLN ** O 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 222 GLN ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4849 moved from start: 0.7124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 64112 Z= 0.290 Angle : 1.222 14.465 86240 Z= 0.628 Chirality : 0.058 0.246 10448 Planarity : 0.008 0.154 11216 Dihedral : 8.954 31.459 8928 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 30.67 Ramachandran Plot: Outliers : 5.19 % Allowed : 19.98 % Favored : 74.83 % Rotamer: Outliers : 0.22 % Allowed : 7.87 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.19 (0.07), residues: 8480 helix: -1.88 (0.08), residues: 3568 sheet: None (None), residues: 0 loop : -5.00 (0.06), residues: 4912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS J 296 PHE 0.014 0.002 PHE P 355 TYR 0.009 0.003 TYR H 15 ARG 0.010 0.001 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1424 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1409 time to evaluate : 5.396 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: 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 44 MET cc_start: 0.2148 (mmm) cc_final: 0.1660 (mmt) REVERT: A 66 ARG cc_start: 0.7675 (mmt180) cc_final: 0.7141 (mmp80) REVERT: A 314 MET cc_start: 0.5154 (mpp) cc_final: 0.4688 (mpp) REVERT: A 510 LEU cc_start: 0.6720 (pp) cc_final: 0.6451 (pp) REVERT: B 513 ASP cc_start: 0.5040 (m-30) cc_final: 0.4417 (p0) REVERT: B 527 MET cc_start: 0.2339 (ttt) cc_final: 0.1709 (tpt) REVERT: B 530 MET cc_start: 0.3848 (mmt) cc_final: 0.2015 (mtt) REVERT: C 66 ARG cc_start: 0.7644 (mmt180) cc_final: 0.7121 (mmp80) REVERT: C 314 MET cc_start: 0.5105 (mpp) cc_final: 0.4698 (mpp) REVERT: C 510 LEU cc_start: 0.7213 (pp) cc_final: 0.6984 (pp) REVERT: C 513 ASP cc_start: 0.4695 (m-30) cc_final: 0.4410 (m-30) REVERT: D 513 ASP cc_start: 0.5270 (m-30) cc_final: 0.4584 (p0) REVERT: D 527 MET cc_start: 0.1237 (tpt) cc_final: 0.1035 (tpt) REVERT: D 530 MET cc_start: 0.4233 (mmt) cc_final: 0.2048 (mtt) REVERT: E 44 MET cc_start: 0.2129 (mmm) cc_final: 0.1677 (mmt) REVERT: E 66 ARG cc_start: 0.7660 (mmt180) cc_final: 0.7106 (mmp80) REVERT: E 314 MET cc_start: 0.5126 (mpp) cc_final: 0.4686 (mpp) REVERT: E 510 LEU cc_start: 0.7204 (pp) cc_final: 0.6956 (pp) REVERT: E 513 ASP cc_start: 0.4656 (m-30) cc_final: 0.4415 (m-30) REVERT: F 46 LYS cc_start: 0.4879 (mmtt) cc_final: 0.4667 (mmmt) REVERT: F 527 MET cc_start: 0.1238 (tpt) cc_final: 0.0970 (tpt) REVERT: F 530 MET cc_start: 0.3999 (mmt) cc_final: 0.2111 (mtt) REVERT: G 44 MET cc_start: 0.1780 (mmm) cc_final: 0.1345 (mmt) REVERT: G 66 ARG cc_start: 0.7637 (mmt180) cc_final: 0.7099 (mmp80) REVERT: G 314 MET cc_start: 0.5134 (mpp) cc_final: 0.4691 (mpp) REVERT: G 510 LEU cc_start: 0.7232 (pp) cc_final: 0.6976 (pp) REVERT: G 513 ASP cc_start: 0.4683 (m-30) cc_final: 0.4439 (m-30) REVERT: H 46 LYS cc_start: 0.4932 (mmtt) cc_final: 0.4678 (mmmt) REVERT: H 330 LYS cc_start: 0.5317 (pptt) cc_final: 0.4958 (pttm) REVERT: H 527 MET cc_start: 0.1211 (tpt) cc_final: 0.1001 (tpt) REVERT: H 530 MET cc_start: 0.4264 (mmt) cc_final: 0.2231 (mtt) REVERT: I 46 LYS cc_start: 0.4916 (mmtt) cc_final: 0.4706 (mmmt) REVERT: I 451 ASP cc_start: 0.5745 (t0) cc_final: 0.5536 (t0) REVERT: I 527 MET cc_start: 0.1383 (tpt) cc_final: 0.1152 (tpt) REVERT: I 530 MET cc_start: 0.4120 (mmt) cc_final: 0.2182 (mtt) REVERT: J 44 MET cc_start: 0.2168 (mmm) cc_final: 0.1754 (mmt) REVERT: J 66 ARG cc_start: 0.7663 (mmt180) cc_final: 0.7111 (mmp80) REVERT: J 314 MET cc_start: 0.5052 (mpp) cc_final: 0.4628 (mpp) REVERT: J 425 ARG cc_start: 0.4526 (tmt170) cc_final: 0.4284 (ttt-90) REVERT: K 330 LYS cc_start: 0.5393 (pptt) cc_final: 0.5022 (pttm) REVERT: K 513 ASP cc_start: 0.4981 (m-30) cc_final: 0.4608 (p0) REVERT: K 527 MET cc_start: 0.1368 (tpt) cc_final: 0.1142 (tpt) REVERT: K 530 MET cc_start: 0.4151 (mmt) cc_final: 0.2216 (mtt) REVERT: L 66 ARG cc_start: 0.7661 (mmt180) cc_final: 0.7114 (mmp80) REVERT: L 314 MET cc_start: 0.5056 (mpp) cc_final: 0.4633 (mpp) REVERT: M 330 LYS cc_start: 0.5392 (pptt) cc_final: 0.5022 (pttm) REVERT: M 513 ASP cc_start: 0.4900 (m-30) cc_final: 0.4506 (p0) REVERT: M 514 ASP cc_start: 0.3770 (p0) cc_final: 0.3520 (m-30) REVERT: M 527 MET cc_start: 0.1360 (tpt) cc_final: 0.1128 (tpt) REVERT: M 530 MET cc_start: 0.4182 (mmt) cc_final: 0.2239 (mtt) REVERT: N 44 MET cc_start: 0.2124 (mmm) cc_final: 0.1778 (mmt) REVERT: N 66 ARG cc_start: 0.7649 (mmt180) cc_final: 0.7119 (mmp80) REVERT: N 314 MET cc_start: 0.5091 (mpp) cc_final: 0.4629 (mpp) REVERT: O 46 LYS cc_start: 0.4890 (mmtt) cc_final: 0.4659 (mmmt) REVERT: O 330 LYS cc_start: 0.5395 (pptt) cc_final: 0.5024 (pttm) REVERT: O 513 ASP cc_start: 0.5011 (m-30) cc_final: 0.4590 (p0) REVERT: O 527 MET cc_start: 0.1350 (tpt) cc_final: 0.1071 (tpt) REVERT: O 530 MET cc_start: 0.4084 (mmt) cc_final: 0.2104 (mtt) REVERT: P 44 MET cc_start: 0.1802 (mmm) cc_final: 0.1377 (mmt) REVERT: P 66 ARG cc_start: 0.7694 (mmt180) cc_final: 0.7127 (mmp80) REVERT: P 314 MET cc_start: 0.5085 (mpp) cc_final: 0.4604 (mpp) outliers start: 15 outliers final: 0 residues processed: 1424 average time/residue: 0.6658 time to fit residues: 1606.1348 Evaluate side-chains 1072 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1072 time to evaluate : 5.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 682 optimal weight: 6.9990 chunk 465 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 610 optimal weight: 9.9990 chunk 338 optimal weight: 5.9990 chunk 699 optimal weight: 0.8980 chunk 566 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 418 optimal weight: 6.9990 chunk 735 optimal weight: 20.0000 chunk 206 optimal weight: 0.4980 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 287 GLN ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 GLN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 GLN ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 497 GLN K 287 GLN ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 497 GLN M 287 GLN ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 497 GLN O 287 GLN ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 497 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4919 moved from start: 0.7631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 64112 Z= 0.293 Angle : 1.206 18.889 86240 Z= 0.610 Chirality : 0.058 0.263 10448 Planarity : 0.009 0.173 11216 Dihedral : 8.942 32.465 8928 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 28.95 Ramachandran Plot: Outliers : 4.55 % Allowed : 19.81 % Favored : 75.64 % Rotamer: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 6.82 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.07), residues: 8480 helix: -1.74 (0.08), residues: 3456 sheet: None (None), residues: 0 loop : -4.82 (0.06), residues: 5024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS N 375 PHE 0.013 0.002 PHE B 433 TYR 0.011 0.002 TYR B 418 ARG 0.010 0.001 ARG I 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1386 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1386 time to evaluate : 5.479 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: 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 44 MET cc_start: 0.2378 (mmm) cc_final: 0.2085 (mmt) REVERT: A 77 MET cc_start: 0.5419 (mmt) cc_final: 0.4397 (tmm) REVERT: A 307 ARG cc_start: 0.4398 (mtp85) cc_final: 0.4128 (mtp180) REVERT: A 507 GLU cc_start: 0.6167 (mm-30) cc_final: 0.5936 (mm-30) REVERT: A 510 LEU cc_start: 0.6652 (pp) cc_final: 0.6067 (pp) REVERT: B 513 ASP cc_start: 0.4785 (m-30) cc_final: 0.4302 (p0) REVERT: B 527 MET cc_start: 0.2142 (ttt) cc_final: 0.1253 (tpp) REVERT: B 530 MET cc_start: 0.4113 (mmt) cc_final: 0.2222 (mtt) REVERT: C 77 MET cc_start: 0.5389 (mmt) cc_final: 0.4225 (tmm) REVERT: C 307 ARG cc_start: 0.4419 (mtp85) cc_final: 0.4076 (mtp180) REVERT: C 507 GLU cc_start: 0.5937 (mm-30) cc_final: 0.5651 (mm-30) REVERT: C 510 LEU cc_start: 0.6686 (pp) cc_final: 0.6353 (tp) REVERT: C 527 MET cc_start: 0.2934 (ttt) cc_final: 0.2311 (tpp) REVERT: C 530 MET cc_start: 0.4401 (mmt) cc_final: 0.3888 (mmt) REVERT: D 170 LEU cc_start: 0.6259 (pp) cc_final: 0.6003 (pp) REVERT: D 513 ASP cc_start: 0.4802 (m-30) cc_final: 0.4471 (p0) REVERT: D 530 MET cc_start: 0.4004 (mmt) cc_final: 0.2043 (mtt) REVERT: E 44 MET cc_start: 0.2016 (mmm) cc_final: 0.1740 (mmt) REVERT: E 77 MET cc_start: 0.5432 (mmt) cc_final: 0.4254 (tmm) REVERT: E 268 MET cc_start: 0.6639 (ttt) cc_final: 0.6434 (ttm) REVERT: E 507 GLU cc_start: 0.5931 (mm-30) cc_final: 0.5669 (mm-30) REVERT: E 510 LEU cc_start: 0.6657 (pp) cc_final: 0.6314 (tp) REVERT: E 527 MET cc_start: 0.2650 (ttt) cc_final: 0.2128 (tpp) REVERT: E 530 MET cc_start: 0.4697 (mmt) cc_final: 0.4201 (mmt) REVERT: F 68 MET cc_start: 0.2255 (mmm) cc_final: 0.1788 (mmm) REVERT: F 170 LEU cc_start: 0.6276 (pp) cc_final: 0.6013 (pp) REVERT: F 530 MET cc_start: 0.4225 (mmt) cc_final: 0.2221 (mtt) REVERT: G 44 MET cc_start: 0.2434 (mmm) cc_final: 0.2051 (mmt) REVERT: G 77 MET cc_start: 0.5377 (mmt) cc_final: 0.4217 (tmm) REVERT: G 507 GLU cc_start: 0.5967 (mm-30) cc_final: 0.5677 (mm-30) REVERT: G 510 LEU cc_start: 0.6674 (pp) cc_final: 0.6330 (tp) REVERT: G 527 MET cc_start: 0.3010 (ttt) cc_final: 0.2294 (tpp) REVERT: G 530 MET cc_start: 0.4454 (mmt) cc_final: 0.4141 (mmt) REVERT: H 68 MET cc_start: 0.2186 (mmm) cc_final: 0.1771 (mmm) REVERT: H 170 LEU cc_start: 0.6231 (pp) cc_final: 0.5968 (pp) REVERT: H 530 MET cc_start: 0.4112 (mmt) cc_final: 0.2182 (mtp) REVERT: I 1 MET cc_start: 0.1767 (pmm) cc_final: 0.1002 (pmm) REVERT: I 170 LEU cc_start: 0.6269 (pp) cc_final: 0.5985 (pp) REVERT: I 530 MET cc_start: 0.4077 (mmt) cc_final: 0.2206 (mtt) REVERT: J 77 MET cc_start: 0.5353 (mmt) cc_final: 0.4303 (tmm) REVERT: J 249 GLU cc_start: 0.5613 (mm-30) cc_final: 0.5358 (mm-30) REVERT: J 268 MET cc_start: 0.6773 (ttt) cc_final: 0.6543 (ttm) REVERT: J 507 GLU cc_start: 0.5972 (mm-30) cc_final: 0.5650 (mm-30) REVERT: J 510 LEU cc_start: 0.7353 (pp) cc_final: 0.6900 (pp) REVERT: J 527 MET cc_start: 0.2986 (ttt) cc_final: 0.2404 (tpp) REVERT: J 530 MET cc_start: 0.3843 (mmt) cc_final: 0.3354 (mmt) REVERT: K 170 LEU cc_start: 0.6280 (pp) cc_final: 0.5994 (pp) REVERT: K 530 MET cc_start: 0.4178 (mmt) cc_final: 0.2130 (mtp) REVERT: L 77 MET cc_start: 0.5375 (mmt) cc_final: 0.4350 (tmm) REVERT: L 249 GLU cc_start: 0.5636 (mm-30) cc_final: 0.5371 (mm-30) REVERT: L 268 MET cc_start: 0.6772 (ttt) cc_final: 0.6562 (ttm) REVERT: L 507 GLU cc_start: 0.6014 (mm-30) cc_final: 0.5814 (mm-30) REVERT: L 510 LEU cc_start: 0.7339 (pp) cc_final: 0.6834 (pp) REVERT: L 527 MET cc_start: 0.3012 (ttt) cc_final: 0.2389 (tpp) REVERT: L 530 MET cc_start: 0.3818 (mmt) cc_final: 0.3393 (mmt) REVERT: M 68 MET cc_start: 0.2153 (mmm) cc_final: 0.1687 (mmm) REVERT: M 170 LEU cc_start: 0.6291 (pp) cc_final: 0.6002 (pp) REVERT: M 530 MET cc_start: 0.4157 (mmt) cc_final: 0.2170 (mtp) REVERT: N 77 MET cc_start: 0.5360 (mmt) cc_final: 0.4210 (tmm) REVERT: N 249 GLU cc_start: 0.5618 (mm-30) cc_final: 0.5365 (mm-30) REVERT: N 268 MET cc_start: 0.6734 (ttt) cc_final: 0.6524 (ttm) REVERT: N 507 GLU cc_start: 0.6006 (mm-30) cc_final: 0.5734 (mm-30) REVERT: N 510 LEU cc_start: 0.7353 (pp) cc_final: 0.6914 (pp) REVERT: N 527 MET cc_start: 0.3084 (ttt) cc_final: 0.2539 (tpp) REVERT: O 170 LEU cc_start: 0.6260 (pp) cc_final: 0.5990 (pp) REVERT: O 527 MET cc_start: 0.1496 (tpt) cc_final: 0.1238 (tpt) REVERT: O 530 MET cc_start: 0.4149 (mmt) cc_final: 0.2165 (mtp) REVERT: P 44 MET cc_start: 0.2534 (mmm) cc_final: 0.2135 (mmt) REVERT: P 77 MET cc_start: 0.5440 (mmt) cc_final: 0.4267 (tmm) REVERT: P 249 GLU cc_start: 0.5632 (mm-30) cc_final: 0.5375 (mm-30) REVERT: P 268 MET cc_start: 0.6683 (ttt) cc_final: 0.6460 (ttm) REVERT: P 507 GLU cc_start: 0.6040 (mm-30) cc_final: 0.5786 (mm-30) REVERT: P 510 LEU cc_start: 0.7346 (pp) cc_final: 0.6918 (pp) REVERT: P 527 MET cc_start: 0.3083 (ttt) cc_final: 0.2551 (tpp) outliers start: 0 outliers final: 0 residues processed: 1386 average time/residue: 0.6537 time to fit residues: 1503.2625 Evaluate side-chains 1075 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1075 time to evaluate : 5.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 275 optimal weight: 0.2980 chunk 738 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 481 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 820 optimal weight: 5.9990 chunk 681 optimal weight: 0.0020 chunk 379 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 271 optimal weight: 0.9990 chunk 430 optimal weight: 0.0970 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN B 287 GLN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 HIS ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 ASN ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 HIS ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 HIS ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 236 ASN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 ASN ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 236 ASN ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 236 ASN ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 236 ASN ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 296 HIS ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4688 moved from start: 0.8419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 64112 Z= 0.236 Angle : 1.104 15.898 86240 Z= 0.555 Chirality : 0.053 0.236 10448 Planarity : 0.007 0.148 11216 Dihedral : 8.310 31.303 8928 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 4.47 % Allowed : 17.98 % Favored : 77.55 % Rotamer: Outliers : 0.01 % Allowed : 5.12 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 1.70 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.77 (0.07), residues: 8480 helix: -1.47 (0.08), residues: 3440 sheet: None (None), residues: 0 loop : -4.75 (0.06), residues: 5040 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 375 PHE 0.017 0.002 PHE H 433 TYR 0.017 0.001 TYR G 15 ARG 0.006 0.001 ARG M 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1493 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1492 time to evaluate : 5.463 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: A 68 MET cc_start: 0.4639 (tpp) cc_final: 0.4105 (tpp) REVERT: A 77 MET cc_start: 0.5302 (mmt) cc_final: 0.4745 (tmm) REVERT: A 170 LEU cc_start: 0.7083 (pp) cc_final: 0.6835 (pp) REVERT: A 173 ILE cc_start: 0.6837 (mm) cc_final: 0.6489 (mm) REVERT: A 267 LYS cc_start: 0.7725 (tmtt) cc_final: 0.7521 (tmtt) REVERT: A 510 LEU cc_start: 0.6775 (pp) cc_final: 0.6454 (pp) REVERT: A 527 MET cc_start: 0.1968 (ttt) cc_final: 0.1493 (tpp) REVERT: B 79 ILE cc_start: 0.7505 (mt) cc_final: 0.6989 (tt) REVERT: B 513 ASP cc_start: 0.4852 (m-30) cc_final: 0.4378 (p0) REVERT: B 527 MET cc_start: 0.2298 (ttt) cc_final: 0.1712 (tpp) REVERT: B 530 MET cc_start: 0.4229 (mmt) cc_final: 0.2062 (mtp) REVERT: C 507 GLU cc_start: 0.5645 (mm-30) cc_final: 0.5362 (mm-30) REVERT: C 527 MET cc_start: 0.1822 (ttt) cc_final: 0.1500 (tpp) REVERT: C 530 MET cc_start: 0.3991 (mmt) cc_final: 0.2409 (mtt) REVERT: D 513 ASP cc_start: 0.5080 (m-30) cc_final: 0.4394 (p0) REVERT: D 530 MET cc_start: 0.3972 (mmt) cc_final: 0.2028 (mtp) REVERT: E 44 MET cc_start: 0.1703 (mmm) cc_final: 0.1178 (mmt) REVERT: E 149 ILE cc_start: 0.5445 (mp) cc_final: 0.5239 (mt) REVERT: E 173 ILE cc_start: 0.6251 (mm) cc_final: 0.6004 (mm) REVERT: E 507 GLU cc_start: 0.5611 (mm-30) cc_final: 0.5360 (mm-30) REVERT: E 527 MET cc_start: 0.1909 (ttt) cc_final: 0.1598 (tpp) REVERT: F 1 MET cc_start: 0.0133 (ptt) cc_final: -0.0277 (ptp) REVERT: F 435 ASP cc_start: 0.4471 (m-30) cc_final: 0.3677 (m-30) REVERT: F 451 ASP cc_start: 0.5029 (t0) cc_final: 0.4815 (t0) REVERT: F 530 MET cc_start: 0.4331 (mmt) cc_final: 0.2203 (mtp) REVERT: G 44 MET cc_start: 0.1593 (mmm) cc_final: 0.1160 (mmt) REVERT: G 149 ILE cc_start: 0.5560 (mp) cc_final: 0.5348 (mt) REVERT: G 173 ILE cc_start: 0.6249 (mm) cc_final: 0.5990 (mm) REVERT: G 267 LYS cc_start: 0.7546 (tmtt) cc_final: 0.7336 (tmtt) REVERT: G 507 GLU cc_start: 0.5580 (mm-30) cc_final: 0.5336 (mm-30) REVERT: G 527 MET cc_start: 0.1869 (ttt) cc_final: 0.1581 (tpp) REVERT: H 530 MET cc_start: 0.4045 (mmt) cc_final: 0.1997 (mtp) REVERT: I 1 MET cc_start: 0.0841 (pmm) cc_final: 0.0583 (pmm) REVERT: I 108 GLU cc_start: 0.3425 (tt0) cc_final: 0.3221 (tt0) REVERT: I 435 ASP cc_start: 0.4493 (m-30) cc_final: 0.3807 (m-30) REVERT: I 451 ASP cc_start: 0.4906 (t0) cc_final: 0.4678 (t0) REVERT: I 530 MET cc_start: 0.4197 (mmt) cc_final: 0.2258 (mtp) REVERT: J 97 VAL cc_start: 0.6348 (t) cc_final: 0.6086 (t) REVERT: J 173 ILE cc_start: 0.6284 (mm) cc_final: 0.6051 (mm) REVERT: J 510 LEU cc_start: 0.6760 (pp) cc_final: 0.6353 (pp) REVERT: J 527 MET cc_start: 0.1751 (ttt) cc_final: 0.1410 (tpp) REVERT: J 530 MET cc_start: 0.3941 (mmt) cc_final: 0.2624 (mtt) REVERT: K 71 GLU cc_start: 0.5587 (pm20) cc_final: 0.4001 (pt0) REVERT: K 435 ASP cc_start: 0.4491 (m-30) cc_final: 0.3723 (m-30) REVERT: K 451 ASP cc_start: 0.4863 (t0) cc_final: 0.4657 (t0) REVERT: K 530 MET cc_start: 0.4093 (mmt) cc_final: 0.2013 (mtp) REVERT: L 149 ILE cc_start: 0.5459 (mp) cc_final: 0.5239 (mt) REVERT: L 173 ILE cc_start: 0.6247 (mm) cc_final: 0.5998 (mm) REVERT: L 510 LEU cc_start: 0.6737 (pp) cc_final: 0.6360 (pp) REVERT: L 527 MET cc_start: 0.1881 (ttt) cc_final: 0.1477 (tpp) REVERT: L 530 MET cc_start: 0.3810 (mmt) cc_final: 0.2476 (mtt) REVERT: M 1 MET cc_start: -0.0823 (ptm) cc_final: -0.1278 (ptm) REVERT: M 435 ASP cc_start: 0.4506 (m-30) cc_final: 0.3750 (m-30) REVERT: M 451 ASP cc_start: 0.5048 (t0) cc_final: 0.4795 (t0) REVERT: M 530 MET cc_start: 0.3999 (mmt) cc_final: 0.1990 (mtp) REVERT: N 510 LEU cc_start: 0.6887 (pp) cc_final: 0.6508 (pp) REVERT: O 1 MET cc_start: 0.0793 (ppp) cc_final: 0.0465 (ppp) REVERT: O 435 ASP cc_start: 0.4494 (m-30) cc_final: 0.3805 (m-30) REVERT: O 530 MET cc_start: 0.3986 (mmt) cc_final: 0.2036 (mtp) REVERT: P 44 MET cc_start: 0.1716 (mmm) cc_final: 0.1187 (mmt) REVERT: P 68 MET cc_start: 0.4558 (tpp) cc_final: 0.4264 (tpp) REVERT: P 149 ILE cc_start: 0.5543 (mp) cc_final: 0.5341 (mt) REVERT: P 170 LEU cc_start: 0.6384 (pp) cc_final: 0.6179 (pp) REVERT: P 173 ILE cc_start: 0.6236 (mm) cc_final: 0.5998 (mm) REVERT: P 510 LEU cc_start: 0.6839 (pp) cc_final: 0.6506 (pp) REVERT: P 527 MET cc_start: 0.1896 (ttt) cc_final: 0.1573 (tpp) outliers start: 1 outliers final: 0 residues processed: 1493 average time/residue: 0.6351 time to fit residues: 1577.1209 Evaluate side-chains 1086 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1086 time to evaluate : 5.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 791 optimal weight: 10.0000 chunk 92 optimal weight: 0.0060 chunk 467 optimal weight: 20.0000 chunk 599 optimal weight: 9.9990 chunk 464 optimal weight: 2.9990 chunk 690 optimal weight: 9.9990 chunk 458 optimal weight: 0.2980 chunk 817 optimal weight: 2.9990 chunk 511 optimal weight: 10.0000 chunk 498 optimal weight: 9.9990 chunk 377 optimal weight: 3.9990 overall best weight: 2.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 HIS H 447 ASN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 HIS ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 HIS ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4770 moved from start: 0.8762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 64112 Z= 0.240 Angle : 1.111 21.858 86240 Z= 0.555 Chirality : 0.054 0.251 10448 Planarity : 0.008 0.181 11216 Dihedral : 8.205 35.947 8928 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 24.86 Ramachandran Plot: Outliers : 4.14 % Allowed : 19.23 % Favored : 76.63 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.08), residues: 8480 helix: -1.39 (0.08), residues: 3472 sheet: None (None), residues: 0 loop : -4.64 (0.06), residues: 5008 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 463 PHE 0.013 0.002 PHE M 433 TYR 0.010 0.002 TYR A 15 ARG 0.014 0.001 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1349 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1349 time to evaluate : 6.106 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: symmetry clash REVERT: A 44 MET cc_start: 0.1747 (mmm) cc_final: 0.1220 (mmt) REVERT: A 156 THR cc_start: 0.4808 (p) cc_final: 0.4302 (m) REVERT: A 493 ARG cc_start: 0.5804 (mmm-85) cc_final: 0.5528 (mmm160) REVERT: A 510 LEU cc_start: 0.6298 (pp) cc_final: 0.6010 (pp) REVERT: B 47 MET cc_start: 0.4268 (tpp) cc_final: 0.3941 (tpt) REVERT: B 71 GLU cc_start: 0.5635 (pm20) cc_final: 0.5435 (pm20) REVERT: B 79 ILE cc_start: 0.7541 (mt) cc_final: 0.7150 (tt) REVERT: B 267 LYS cc_start: 0.6914 (tptt) cc_final: 0.6701 (tptm) REVERT: B 513 ASP cc_start: 0.4719 (m-30) cc_final: 0.4204 (p0) REVERT: B 527 MET cc_start: 0.2250 (ttt) cc_final: 0.1032 (mpp) REVERT: B 530 MET cc_start: 0.4109 (mmt) cc_final: 0.1863 (mtp) REVERT: C 527 MET cc_start: 0.1982 (ttt) cc_final: 0.1653 (tpp) REVERT: C 530 MET cc_start: 0.4113 (mmt) cc_final: 0.2486 (mtp) REVERT: D 267 LYS cc_start: 0.7089 (tptt) cc_final: 0.6871 (tptm) REVERT: D 374 GLU cc_start: 0.7511 (tt0) cc_final: 0.7248 (tt0) REVERT: D 513 ASP cc_start: 0.4805 (m-30) cc_final: 0.4033 (p0) REVERT: D 530 MET cc_start: 0.4121 (mmt) cc_final: 0.1836 (mtp) REVERT: E 44 MET cc_start: 0.1745 (mmm) cc_final: 0.1235 (mmt) REVERT: E 265 GLU cc_start: 0.4954 (tp30) cc_final: 0.4598 (tp30) REVERT: E 267 LYS cc_start: 0.7727 (tmtt) cc_final: 0.7322 (tmtt) REVERT: E 527 MET cc_start: 0.2032 (ttt) cc_final: 0.1612 (tpp) REVERT: E 530 MET cc_start: 0.4055 (mmt) cc_final: 0.2467 (mtp) REVERT: F 267 LYS cc_start: 0.7152 (tptt) cc_final: 0.6891 (tptm) REVERT: F 374 GLU cc_start: 0.7483 (tt0) cc_final: 0.7220 (tt0) REVERT: F 530 MET cc_start: 0.4214 (mmt) cc_final: 0.2013 (mtp) REVERT: G 44 MET cc_start: 0.1512 (mmm) cc_final: 0.1017 (mmt) REVERT: G 265 GLU cc_start: 0.4757 (tp30) cc_final: 0.4329 (tp30) REVERT: G 527 MET cc_start: 0.2055 (ttt) cc_final: 0.1647 (tpp) REVERT: G 530 MET cc_start: 0.4457 (mmt) cc_final: 0.2867 (mtp) REVERT: H 374 GLU cc_start: 0.7535 (tt0) cc_final: 0.7238 (tt0) REVERT: H 530 MET cc_start: 0.4066 (mmt) cc_final: 0.2029 (mtp) REVERT: I 46 LYS cc_start: 0.4757 (mmtt) cc_final: 0.4544 (tptp) REVERT: I 267 LYS cc_start: 0.7130 (tptt) cc_final: 0.6913 (tptm) REVERT: I 374 GLU cc_start: 0.7516 (tt0) cc_final: 0.7242 (tt0) REVERT: I 513 ASP cc_start: 0.4608 (p0) cc_final: 0.4202 (p0) REVERT: I 530 MET cc_start: 0.4153 (mmt) cc_final: 0.2007 (mtp) REVERT: J 251 ARG cc_start: 0.3673 (ptt90) cc_final: 0.3416 (ptt90) REVERT: J 267 LYS cc_start: 0.7718 (tmtt) cc_final: 0.7429 (tmtt) REVERT: J 268 MET cc_start: 0.6703 (ttm) cc_final: 0.6355 (ttm) REVERT: J 440 ILE cc_start: 0.5914 (mm) cc_final: 0.5298 (mm) REVERT: J 527 MET cc_start: 0.1918 (ttt) cc_final: 0.1649 (tpp) REVERT: J 530 MET cc_start: 0.4450 (mmt) cc_final: 0.2872 (mtp) REVERT: K 267 LYS cc_start: 0.7107 (tptt) cc_final: 0.6888 (tptm) REVERT: K 374 GLU cc_start: 0.7527 (tt0) cc_final: 0.7250 (tt0) REVERT: K 530 MET cc_start: 0.4178 (mmt) cc_final: 0.1836 (mtp) REVERT: L 251 ARG cc_start: 0.3695 (ptt90) cc_final: 0.3435 (ptt90) REVERT: L 268 MET cc_start: 0.6729 (ttm) cc_final: 0.6401 (ttm) REVERT: L 527 MET cc_start: 0.2013 (ttt) cc_final: 0.1620 (tpp) REVERT: L 530 MET cc_start: 0.4321 (mmt) cc_final: 0.2875 (mtp) REVERT: M 267 LYS cc_start: 0.7028 (tptt) cc_final: 0.6812 (tptm) REVERT: M 374 GLU cc_start: 0.7544 (tt0) cc_final: 0.7242 (tt0) REVERT: M 530 MET cc_start: 0.4145 (mmt) cc_final: 0.1867 (mtp) REVERT: N 16 MET cc_start: 0.5563 (tpp) cc_final: 0.5123 (tpp) REVERT: N 251 ARG cc_start: 0.3677 (ptt90) cc_final: 0.3442 (ptt90) REVERT: N 268 MET cc_start: 0.6705 (ttm) cc_final: 0.6381 (ttm) REVERT: O 267 LYS cc_start: 0.7145 (tptt) cc_final: 0.6887 (tptm) REVERT: O 374 GLU cc_start: 0.7574 (tt0) cc_final: 0.7255 (tt0) REVERT: O 530 MET cc_start: 0.4258 (mmt) cc_final: 0.2047 (mtp) REVERT: P 44 MET cc_start: 0.1522 (mmm) cc_final: 0.1040 (mmt) REVERT: P 251 ARG cc_start: 0.3696 (ptt90) cc_final: 0.3452 (ptt90) REVERT: P 265 GLU cc_start: 0.4943 (tp30) cc_final: 0.4500 (tp30) REVERT: P 267 LYS cc_start: 0.7703 (tmtt) cc_final: 0.7230 (tmtt) REVERT: P 493 ARG cc_start: 0.5900 (mmm-85) cc_final: 0.5646 (mmm160) outliers start: 0 outliers final: 0 residues processed: 1349 average time/residue: 0.6190 time to fit residues: 1401.0198 Evaluate side-chains 1027 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1027 time to evaluate : 5.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 505 optimal weight: 9.9990 chunk 326 optimal weight: 5.9990 chunk 488 optimal weight: 10.0000 chunk 246 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 158 optimal weight: 0.0370 chunk 519 optimal weight: 8.9990 chunk 556 optimal weight: 9.9990 chunk 404 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 642 optimal weight: 8.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4855 moved from start: 0.8988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 64112 Z= 0.257 Angle : 1.110 15.724 86240 Z= 0.559 Chirality : 0.054 0.250 10448 Planarity : 0.007 0.159 11216 Dihedral : 8.263 33.689 8928 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 25.31 Ramachandran Plot: Outliers : 3.96 % Allowed : 20.34 % Favored : 75.70 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 7.95 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.08), residues: 8480 helix: -1.36 (0.08), residues: 3488 sheet: None (None), residues: 0 loop : -4.60 (0.07), residues: 4992 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 463 PHE 0.020 0.002 PHE M 433 TYR 0.020 0.002 TYR J 15 ARG 0.008 0.001 ARG O 493 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1297 time to evaluate : 5.520 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: A 14 ARG cc_start: 0.6750 (mpp-170) cc_final: 0.5516 (mtm-85) REVERT: A 156 THR cc_start: 0.4952 (p) cc_final: 0.4655 (m) REVERT: A 265 GLU cc_start: 0.5210 (tp30) cc_final: 0.4957 (tp30) REVERT: A 314 MET cc_start: 0.5497 (mpp) cc_final: 0.4698 (mpp) REVERT: A 368 LEU cc_start: 0.4594 (pp) cc_final: 0.4392 (pp) REVERT: A 530 MET cc_start: 0.4781 (mmt) cc_final: 0.4207 (mtt) REVERT: B 251 ARG cc_start: 0.4548 (ptt90) cc_final: 0.4337 (ptt-90) REVERT: B 267 LYS cc_start: 0.7134 (tptt) cc_final: 0.6718 (tptm) REVERT: B 513 ASP cc_start: 0.4259 (m-30) cc_final: 0.3670 (p0) REVERT: B 527 MET cc_start: 0.2035 (ttt) cc_final: 0.0890 (mpp) REVERT: B 530 MET cc_start: 0.4306 (mmt) cc_final: 0.2053 (mtp) REVERT: C 156 THR cc_start: 0.4881 (p) cc_final: 0.4340 (m) REVERT: C 314 MET cc_start: 0.5424 (mpp) cc_final: 0.4636 (mpp) REVERT: C 527 MET cc_start: 0.2134 (ttt) cc_final: 0.1658 (tpp) REVERT: C 530 MET cc_start: 0.4881 (mmt) cc_final: 0.3229 (mtt) REVERT: D 267 LYS cc_start: 0.7075 (tptt) cc_final: 0.6777 (tptm) REVERT: D 513 ASP cc_start: 0.4571 (m-30) cc_final: 0.4006 (p0) REVERT: D 530 MET cc_start: 0.4310 (mmt) cc_final: 0.1869 (mtp) REVERT: E 156 THR cc_start: 0.4884 (p) cc_final: 0.4261 (m) REVERT: E 314 MET cc_start: 0.5458 (mpp) cc_final: 0.4686 (mpp) REVERT: E 527 MET cc_start: 0.2046 (ttt) cc_final: 0.1725 (tpp) REVERT: E 530 MET cc_start: 0.4519 (mmt) cc_final: 0.2745 (mtp) REVERT: F 1 MET cc_start: 0.0111 (ptt) cc_final: -0.0115 (ptm) REVERT: F 267 LYS cc_start: 0.7179 (tptt) cc_final: 0.6858 (tptm) REVERT: F 435 ASP cc_start: 0.3754 (m-30) cc_final: 0.3127 (m-30) REVERT: F 447 ASN cc_start: 0.6775 (t0) cc_final: 0.6540 (t0) REVERT: F 530 MET cc_start: 0.4463 (mmt) cc_final: 0.1930 (mtp) REVERT: G 44 MET cc_start: 0.2009 (mmm) cc_final: 0.1668 (mmt) REVERT: G 156 THR cc_start: 0.4892 (p) cc_final: 0.4298 (m) REVERT: G 267 LYS cc_start: 0.7764 (tmtt) cc_final: 0.7522 (tmtt) REVERT: G 314 MET cc_start: 0.5459 (mpp) cc_final: 0.4677 (mpp) REVERT: G 527 MET cc_start: 0.2250 (ttt) cc_final: 0.1659 (tpp) REVERT: G 530 MET cc_start: 0.4582 (mmt) cc_final: 0.3129 (mtt) REVERT: H 435 ASP cc_start: 0.4105 (m-30) cc_final: 0.3143 (m-30) REVERT: H 530 MET cc_start: 0.4602 (mmt) cc_final: 0.2142 (mtp) REVERT: I 435 ASP cc_start: 0.3784 (m-30) cc_final: 0.3259 (m-30) REVERT: I 512 ILE cc_start: 0.5194 (mm) cc_final: 0.4676 (mm) REVERT: I 530 MET cc_start: 0.4443 (mmt) cc_final: 0.2009 (mtp) REVERT: J 156 THR cc_start: 0.4826 (p) cc_final: 0.4568 (m) REVERT: J 527 MET cc_start: 0.1953 (ttt) cc_final: 0.1580 (tpp) REVERT: J 530 MET cc_start: 0.4647 (mmt) cc_final: 0.3108 (mtt) REVERT: K 70 VAL cc_start: 0.5941 (p) cc_final: 0.5718 (t) REVERT: K 267 LYS cc_start: 0.7144 (tptt) cc_final: 0.6846 (tptm) REVERT: K 530 MET cc_start: 0.4590 (mmt) cc_final: 0.2058 (mtp) REVERT: L 156 THR cc_start: 0.4799 (p) cc_final: 0.4541 (m) REVERT: L 527 MET cc_start: 0.1998 (ttt) cc_final: 0.1578 (tpp) REVERT: L 530 MET cc_start: 0.4421 (mmt) cc_final: 0.2886 (mtt) REVERT: M 44 MET cc_start: 0.2453 (pmm) cc_final: 0.1539 (pmm) REVERT: M 70 VAL cc_start: 0.5861 (p) cc_final: 0.5612 (t) REVERT: M 267 LYS cc_start: 0.7097 (tptt) cc_final: 0.6690 (tptm) REVERT: M 527 MET cc_start: 0.4226 (mpp) cc_final: 0.4002 (mpp) REVERT: M 530 MET cc_start: 0.4565 (mmt) cc_final: 0.2083 (mtp) REVERT: N 156 THR cc_start: 0.4808 (p) cc_final: 0.4501 (m) REVERT: N 314 MET cc_start: 0.5577 (mpp) cc_final: 0.5334 (mpp) REVERT: N 530 MET cc_start: 0.4376 (mmt) cc_final: 0.2913 (mtt) REVERT: O 267 LYS cc_start: 0.7085 (tptt) cc_final: 0.6702 (tptm) REVERT: O 435 ASP cc_start: 0.3742 (m-30) cc_final: 0.3020 (m-30) REVERT: O 530 MET cc_start: 0.4690 (mmt) cc_final: 0.2217 (mtp) REVERT: P 44 MET cc_start: 0.1726 (mmm) cc_final: 0.1131 (mmt) REVERT: P 156 THR cc_start: 0.4844 (p) cc_final: 0.4227 (m) REVERT: P 314 MET cc_start: 0.5341 (mpp) cc_final: 0.4595 (mpp) REVERT: P 530 MET cc_start: 0.4288 (mmt) cc_final: 0.3005 (mtt) outliers start: 0 outliers final: 0 residues processed: 1297 average time/residue: 0.7069 time to fit residues: 1545.7917 Evaluate side-chains 1009 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1009 time to evaluate : 5.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 743 optimal weight: 0.9980 chunk 783 optimal weight: 6.9990 chunk 714 optimal weight: 7.9990 chunk 761 optimal weight: 5.9990 chunk 782 optimal weight: 6.9990 chunk 458 optimal weight: 5.9990 chunk 331 optimal weight: 20.0000 chunk 598 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 chunk 688 optimal weight: 7.9990 chunk 720 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 ASN ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 236 ASN ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 GLN ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 ASN ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 236 ASN ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 447 ASN ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4979 moved from start: 0.9109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 64112 Z= 0.320 Angle : 1.180 15.741 86240 Z= 0.598 Chirality : 0.057 0.346 10448 Planarity : 0.008 0.148 11216 Dihedral : 8.596 33.595 8928 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 28.86 Ramachandran Plot: Outliers : 3.80 % Allowed : 21.33 % Favored : 74.87 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.08), residues: 8480 helix: -1.34 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : -4.43 (0.07), residues: 5216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS H 463 PHE 0.019 0.002 PHE B 433 TYR 0.019 0.003 TYR G 15 ARG 0.008 0.001 ARG F 493 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1250 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1250 time to evaluate : 5.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6798 (mpp-170) cc_final: 0.5640 (mtm-85) REVERT: A 156 THR cc_start: 0.5248 (p) cc_final: 0.4683 (m) REVERT: A 268 MET cc_start: 0.6783 (ttt) cc_final: 0.6557 (ttm) REVERT: A 314 MET cc_start: 0.5805 (mpp) cc_final: 0.5498 (mpp) REVERT: A 530 MET cc_start: 0.4446 (mmt) cc_final: 0.4132 (mtt) REVERT: B 16 MET cc_start: 0.6586 (tpp) cc_final: 0.6254 (tpt) REVERT: B 46 LYS cc_start: 0.5687 (tptt) cc_final: 0.5344 (tptm) REVERT: B 156 THR cc_start: 0.5513 (p) cc_final: 0.5241 (m) REVERT: B 513 ASP cc_start: 0.4628 (m-30) cc_final: 0.4349 (p0) REVERT: B 527 MET cc_start: 0.2526 (ttt) cc_final: 0.1087 (mpp) REVERT: B 530 MET cc_start: 0.4826 (mmt) cc_final: 0.2324 (mtp) REVERT: C 156 THR cc_start: 0.4983 (p) cc_final: 0.4520 (m) REVERT: C 267 LYS cc_start: 0.7158 (tptt) cc_final: 0.6702 (tptt) REVERT: C 314 MET cc_start: 0.5885 (mpp) cc_final: 0.4895 (mpp) REVERT: C 527 MET cc_start: 0.2684 (ttt) cc_final: 0.2398 (tpp) REVERT: C 530 MET cc_start: 0.4852 (mmt) cc_final: 0.3044 (mtp) REVERT: D 156 THR cc_start: 0.4975 (p) cc_final: 0.4641 (m) REVERT: D 513 ASP cc_start: 0.4632 (m-30) cc_final: 0.4118 (p0) REVERT: D 530 MET cc_start: 0.4866 (mmt) cc_final: 0.2494 (mtp) REVERT: E 156 THR cc_start: 0.5190 (p) cc_final: 0.4569 (m) REVERT: E 267 LYS cc_start: 0.7401 (tptt) cc_final: 0.7045 (tptt) REVERT: E 314 MET cc_start: 0.5914 (mpp) cc_final: 0.4900 (mpp) REVERT: E 530 MET cc_start: 0.4652 (mmt) cc_final: 0.3067 (mtt) REVERT: F 435 ASP cc_start: 0.3884 (m-30) cc_final: 0.3383 (m-30) REVERT: F 530 MET cc_start: 0.5069 (mmt) cc_final: 0.2607 (mtp) REVERT: G 156 THR cc_start: 0.5184 (p) cc_final: 0.4565 (m) REVERT: G 251 ARG cc_start: 0.3646 (ptt90) cc_final: 0.3391 (ptt90) REVERT: G 268 MET cc_start: 0.6608 (ttm) cc_final: 0.6392 (ttm) REVERT: G 314 MET cc_start: 0.5915 (mpp) cc_final: 0.4957 (mpp) REVERT: G 527 MET cc_start: 0.2619 (ttt) cc_final: 0.2344 (tpp) REVERT: G 530 MET cc_start: 0.4847 (mmt) cc_final: 0.3192 (mtp) REVERT: H 1 MET cc_start: 0.0794 (ptt) cc_final: 0.0518 (ptm) REVERT: H 435 ASP cc_start: 0.4610 (m-30) cc_final: 0.3934 (m-30) REVERT: H 530 MET cc_start: 0.5145 (mmt) cc_final: 0.2637 (mtp) REVERT: I 16 MET cc_start: 0.5891 (tpp) cc_final: 0.5620 (tpp) REVERT: I 394 THR cc_start: 0.6845 (p) cc_final: 0.6517 (m) REVERT: I 435 ASP cc_start: 0.3944 (m-30) cc_final: 0.3565 (m-30) REVERT: I 530 MET cc_start: 0.4982 (mmt) cc_final: 0.2558 (mtp) REVERT: J 156 THR cc_start: 0.5027 (p) cc_final: 0.4485 (m) REVERT: J 314 MET cc_start: 0.5743 (mpp) cc_final: 0.5379 (mpp) REVERT: J 514 ASP cc_start: 0.4272 (p0) cc_final: 0.3922 (m-30) REVERT: J 530 MET cc_start: 0.4860 (mmt) cc_final: 0.3260 (mtp) REVERT: K 156 THR cc_start: 0.4914 (p) cc_final: 0.4620 (m) REVERT: K 435 ASP cc_start: 0.4416 (m-30) cc_final: 0.3798 (m-30) REVERT: K 530 MET cc_start: 0.5151 (mmt) cc_final: 0.2843 (mtm) REVERT: L 80 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6211 (mt-10) REVERT: L 156 THR cc_start: 0.5059 (p) cc_final: 0.4565 (m) REVERT: L 314 MET cc_start: 0.5741 (mpp) cc_final: 0.5318 (mpp) REVERT: L 530 MET cc_start: 0.4689 (mmt) cc_final: 0.2901 (mtp) REVERT: M 44 MET cc_start: 0.3080 (pmm) cc_final: 0.2140 (pmm) REVERT: M 64 ILE cc_start: 0.5655 (tt) cc_final: 0.5307 (mt) REVERT: M 156 THR cc_start: 0.4948 (p) cc_final: 0.4670 (m) REVERT: M 527 MET cc_start: 0.4857 (mpp) cc_final: 0.4436 (mpp) REVERT: M 530 MET cc_start: 0.5094 (mmt) cc_final: 0.2868 (mtm) REVERT: N 80 GLU cc_start: 0.6425 (mt-10) cc_final: 0.6215 (mt-10) REVERT: N 156 THR cc_start: 0.5030 (p) cc_final: 0.4393 (m) REVERT: N 530 MET cc_start: 0.4473 (mmt) cc_final: 0.3018 (mtp) REVERT: O 78 LEU cc_start: 0.6118 (pp) cc_final: 0.5892 (pp) REVERT: O 394 THR cc_start: 0.6795 (p) cc_final: 0.6476 (m) REVERT: O 435 ASP cc_start: 0.3865 (m-30) cc_final: 0.3386 (m-30) REVERT: O 530 MET cc_start: 0.5126 (mmt) cc_final: 0.2981 (mtm) REVERT: P 44 MET cc_start: 0.1752 (mmm) cc_final: 0.1241 (mmt) REVERT: P 80 GLU cc_start: 0.6518 (mt-10) cc_final: 0.6272 (mt-10) REVERT: P 156 THR cc_start: 0.5098 (p) cc_final: 0.4557 (m) REVERT: P 267 LYS cc_start: 0.7271 (tptt) cc_final: 0.6892 (tptt) REVERT: P 314 MET cc_start: 0.5818 (mpp) cc_final: 0.4937 (mpp) REVERT: P 530 MET cc_start: 0.4171 (mmt) cc_final: 0.2897 (mtt) outliers start: 0 outliers final: 0 residues processed: 1250 average time/residue: 0.6297 time to fit residues: 1302.0019 Evaluate side-chains 995 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 995 time to evaluate : 5.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 758 optimal weight: 0.9990 chunk 500 optimal weight: 0.7980 chunk 805 optimal weight: 0.9990 chunk 491 optimal weight: 20.0000 chunk 382 optimal weight: 20.0000 chunk 559 optimal weight: 20.0000 chunk 844 optimal weight: 4.9990 chunk 777 optimal weight: 20.0000 chunk 672 optimal weight: 0.3980 chunk 69 optimal weight: 10.0000 chunk 519 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 222 GLN ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4828 moved from start: 0.9443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 64112 Z= 0.245 Angle : 1.105 16.189 86240 Z= 0.554 Chirality : 0.054 0.365 10448 Planarity : 0.007 0.139 11216 Dihedral : 8.205 32.608 8928 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 24.59 Ramachandran Plot: Outliers : 3.35 % Allowed : 19.79 % Favored : 76.86 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 7.39 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.66 (0.08), residues: 8480 helix: -1.43 (0.08), residues: 3472 sheet: None (None), residues: 0 loop : -4.66 (0.06), residues: 5008 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS M 463 PHE 0.012 0.002 PHE B 285 TYR 0.011 0.002 TYR M 297 ARG 0.017 0.001 ARG I 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1236 time to evaluate : 5.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.5253 (p) cc_final: 0.4724 (m) REVERT: A 314 MET cc_start: 0.5687 (mpp) cc_final: 0.4843 (mpp) REVERT: A 335 GLN cc_start: 0.6672 (mm-40) cc_final: 0.6399 (mm110) REVERT: A 530 MET cc_start: 0.4474 (mmt) cc_final: 0.3035 (mtt) REVERT: B 22 ARG cc_start: 0.4458 (mtp180) cc_final: 0.4062 (mtp180) REVERT: B 513 ASP cc_start: 0.4623 (m-30) cc_final: 0.3681 (p0) REVERT: B 527 MET cc_start: 0.2115 (ttt) cc_final: 0.0583 (mpp) REVERT: B 530 MET cc_start: 0.5006 (mmt) cc_final: 0.2588 (mtp) REVERT: C 156 THR cc_start: 0.5170 (p) cc_final: 0.4676 (m) REVERT: C 267 LYS cc_start: 0.7497 (tptt) cc_final: 0.6956 (tptt) REVERT: C 314 MET cc_start: 0.6136 (mpp) cc_final: 0.5291 (mpp) REVERT: C 527 MET cc_start: 0.2581 (ttt) cc_final: 0.2036 (tpp) REVERT: C 530 MET cc_start: 0.4693 (mmt) cc_final: 0.3163 (mtp) REVERT: D 44 MET cc_start: 0.1638 (pmm) cc_final: 0.0915 (pmm) REVERT: D 46 LYS cc_start: 0.4364 (mmtt) cc_final: 0.3972 (mmmt) REVERT: D 267 LYS cc_start: 0.7291 (tptt) cc_final: 0.6863 (tptm) REVERT: D 513 ASP cc_start: 0.4376 (m-30) cc_final: 0.3863 (p0) REVERT: D 530 MET cc_start: 0.4945 (mmt) cc_final: 0.2481 (mtm) REVERT: E 1 MET cc_start: 0.2071 (ptp) cc_final: 0.1856 (ptp) REVERT: E 156 THR cc_start: 0.5217 (p) cc_final: 0.4609 (m) REVERT: E 267 LYS cc_start: 0.7484 (tptt) cc_final: 0.6894 (tptt) REVERT: E 314 MET cc_start: 0.6125 (mpp) cc_final: 0.5286 (mpp) REVERT: E 527 MET cc_start: 0.2015 (ttt) cc_final: 0.1814 (tpp) REVERT: E 530 MET cc_start: 0.4726 (mmt) cc_final: 0.3077 (mtp) REVERT: F 435 ASP cc_start: 0.4308 (m-30) cc_final: 0.3920 (m-30) REVERT: F 530 MET cc_start: 0.5177 (mmt) cc_final: 0.2773 (mtm) REVERT: G 14 ARG cc_start: 0.6630 (mpp-170) cc_final: 0.5973 (mpp-170) REVERT: G 44 MET cc_start: 0.1872 (mmm) cc_final: 0.1413 (mmt) REVERT: G 71 GLU cc_start: 0.4225 (tm-30) cc_final: 0.3959 (tt0) REVERT: G 156 THR cc_start: 0.5192 (p) cc_final: 0.4617 (m) REVERT: G 314 MET cc_start: 0.6222 (mpp) cc_final: 0.5340 (mpp) REVERT: G 527 MET cc_start: 0.2874 (ttt) cc_final: 0.2143 (tpp) REVERT: G 530 MET cc_start: 0.4356 (mmt) cc_final: 0.3748 (mtp) REVERT: H 435 ASP cc_start: 0.4127 (m-30) cc_final: 0.3569 (m-30) REVERT: H 530 MET cc_start: 0.5242 (mmt) cc_final: 0.2777 (mtp) REVERT: I 12 MET cc_start: 0.5659 (mmt) cc_final: 0.5396 (mpp) REVERT: I 44 MET cc_start: 0.1406 (pmm) cc_final: 0.0858 (pmm) REVERT: I 78 LEU cc_start: 0.5722 (pp) cc_final: 0.5288 (pp) REVERT: I 394 THR cc_start: 0.6858 (p) cc_final: 0.6602 (m) REVERT: I 435 ASP cc_start: 0.4443 (m-30) cc_final: 0.4086 (m-30) REVERT: I 530 MET cc_start: 0.5067 (mmt) cc_final: 0.2917 (mtp) REVERT: J 156 THR cc_start: 0.5205 (p) cc_final: 0.4638 (m) REVERT: J 267 LYS cc_start: 0.7489 (tptp) cc_final: 0.7122 (tptt) REVERT: J 527 MET cc_start: 0.2157 (ttt) cc_final: 0.1733 (tpp) REVERT: J 530 MET cc_start: 0.4592 (mmt) cc_final: 0.3173 (mtt) REVERT: K 44 MET cc_start: 0.1555 (pmm) cc_final: 0.1010 (pmm) REVERT: K 307 ARG cc_start: 0.4354 (mmp-170) cc_final: 0.3994 (mmp-170) REVERT: K 435 ASP cc_start: 0.4224 (m-30) cc_final: 0.3607 (m-30) REVERT: K 530 MET cc_start: 0.4903 (mmt) cc_final: 0.2643 (mtm) REVERT: L 156 THR cc_start: 0.4831 (p) cc_final: 0.4269 (m) REVERT: L 267 LYS cc_start: 0.7492 (tptp) cc_final: 0.7095 (tptt) REVERT: L 291 ASP cc_start: 0.3981 (m-30) cc_final: 0.3752 (m-30) REVERT: L 527 MET cc_start: 0.2337 (ttt) cc_final: 0.1849 (tpp) REVERT: L 530 MET cc_start: 0.4494 (mmt) cc_final: 0.2997 (mtp) REVERT: M 307 ARG cc_start: 0.4444 (mmp-170) cc_final: 0.4081 (mmp-170) REVERT: M 527 MET cc_start: 0.4636 (mpp) cc_final: 0.4280 (mpp) REVERT: M 530 MET cc_start: 0.4754 (mmt) cc_final: 0.2657 (mtp) REVERT: N 156 THR cc_start: 0.5152 (p) cc_final: 0.4619 (m) REVERT: N 267 LYS cc_start: 0.7446 (tptp) cc_final: 0.7085 (tptt) REVERT: N 291 ASP cc_start: 0.4068 (m-30) cc_final: 0.3822 (m-30) REVERT: O 78 LEU cc_start: 0.6346 (pp) cc_final: 0.6089 (pp) REVERT: O 394 THR cc_start: 0.6817 (p) cc_final: 0.6505 (m) REVERT: O 435 ASP cc_start: 0.3661 (m-30) cc_final: 0.3261 (m-30) REVERT: O 530 MET cc_start: 0.5390 (mmt) cc_final: 0.3130 (mtm) REVERT: P 44 MET cc_start: 0.1119 (mmm) cc_final: 0.0675 (mmt) REVERT: P 156 THR cc_start: 0.5189 (p) cc_final: 0.4568 (m) REVERT: P 267 LYS cc_start: 0.7184 (tptt) cc_final: 0.6645 (tptt) REVERT: P 314 MET cc_start: 0.6144 (mpp) cc_final: 0.5301 (mpp) REVERT: P 493 ARG cc_start: 0.5664 (mmm-85) cc_final: 0.5350 (mmm160) REVERT: P 530 MET cc_start: 0.4256 (mmt) cc_final: 0.2966 (mtm) outliers start: 0 outliers final: 0 residues processed: 1236 average time/residue: 0.6144 time to fit residues: 1267.2539 Evaluate side-chains 991 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 991 time to evaluate : 5.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 412 optimal weight: 5.9990 chunk 534 optimal weight: 0.8980 chunk 716 optimal weight: 0.8980 chunk 206 optimal weight: 20.0000 chunk 620 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 673 optimal weight: 0.0570 chunk 281 optimal weight: 4.9990 chunk 691 optimal weight: 8.9990 chunk 85 optimal weight: 0.0970 overall best weight: 1.1898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 236 ASN A 295 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 GLN ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.195844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.181355 restraints weight = 176572.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.183505 restraints weight = 129900.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.185331 restraints weight = 100256.234| |-----------------------------------------------------------------------------| r_work (final): 0.4623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5490 moved from start: 0.9827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 64112 Z= 0.234 Angle : 1.083 18.240 86240 Z= 0.539 Chirality : 0.054 0.395 10448 Planarity : 0.007 0.168 11216 Dihedral : 7.819 33.419 8928 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 3.18 % Allowed : 19.42 % Favored : 77.39 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 3.41 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.08), residues: 8480 helix: -1.38 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : -4.72 (0.06), residues: 4928 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS M 463 PHE 0.010 0.001 PHE H 261 TYR 0.012 0.001 TYR G 297 ARG 0.008 0.001 ARG O 14 =============================================================================== Job complete usr+sys time: 21975.57 seconds wall clock time: 377 minutes 49.50 seconds (22669.50 seconds total)