Starting phenix.real_space_refine on Fri Sep 27 05:32:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0v_32926/09_2024/7x0v_32926.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0v_32926/09_2024/7x0v_32926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0v_32926/09_2024/7x0v_32926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0v_32926/09_2024/7x0v_32926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0v_32926/09_2024/7x0v_32926.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0v_32926/09_2024/7x0v_32926.cif" } resolution = 3.2 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 396 5.16 5 C 40592 2.51 5 N 11328 2.21 5 O 12572 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 183 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 65000 Number of models: 1 Model: "" Number of chains: 48 Chain: "K" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "J" Number of atoms: 4008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4008 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 511} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4037 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 16, 'TRANS': 509} Chain: "G" Number of atoms: 4094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4094 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "E" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4126 Classifications: {'peptide': 535} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 515} Chain: "I" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3935 Classifications: {'peptide': 521} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 505} Chain: "B" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3937 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 10, 'TRANS': 512} Chain: "A" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4077 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 14, 'TRANS': 522} Chain: "z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "P" Number of atoms: 4008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4008 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 511} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4037 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 16, 'TRANS': 509} Chain: "N" Number of atoms: 4094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4094 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "e" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4126 Classifications: {'peptide': 535} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 515} Chain: "a" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4077 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 14, 'TRANS': 522} Chain: "M" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3935 Classifications: {'peptide': 521} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 505} Chain: "L" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3937 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 10, 'TRANS': 512} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 32.00, per 1000 atoms: 0.49 Number of scatterers: 65000 At special positions: 0 Unit cell: (180.566, 184.52, 175.294, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 396 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12572 8.00 N 11328 7.00 C 40592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=22, symmetry=0 Number of additional bonds: simple=22, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.24 Conformation dependent library (CDL) restraints added in 6.7 seconds 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15736 Finding SS restraints... Secondary structure from input PDB file: 350 helices and 94 sheets defined 53.1% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.75 Creating SS restraints... Processing helix chain 'K' and resid 2 through 8 removed outlier: 3.774A pdb=" N THR K 6 " --> pdb=" O ALA K 2 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU K 7 " --> pdb=" O ALA K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 35 removed outlier: 3.778A pdb=" N LEU K 20 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA K 21 " --> pdb=" O GLN K 17 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL K 33 " --> pdb=" O GLY K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 66 Processing helix chain 'K' and resid 71 through 88 removed outlier: 3.517A pdb=" N ALA K 83 " --> pdb=" O LYS K 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP K 85 " --> pdb=" O ALA K 81 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR K 88 " --> pdb=" O GLN K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 103 removed outlier: 3.524A pdb=" N VAL K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE K 99 " --> pdb=" O ASN K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 111 removed outlier: 3.773A pdb=" N LEU K 108 " --> pdb=" O LYS K 104 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR K 109 " --> pdb=" O GLN K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 138 removed outlier: 3.833A pdb=" N ILE K 119 " --> pdb=" O HIS K 115 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA K 125 " --> pdb=" O GLU K 121 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS K 129 " --> pdb=" O ALA K 125 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU K 135 " --> pdb=" O LEU K 131 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU K 136 " --> pdb=" O GLN K 132 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS K 138 " --> pdb=" O LEU K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 158 removed outlier: 3.765A pdb=" N ASP K 150 " --> pdb=" O GLU K 146 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR K 158 " --> pdb=" O THR K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 178 removed outlier: 4.319A pdb=" N GLU K 170 " --> pdb=" O ASP K 166 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP K 174 " --> pdb=" O GLU K 170 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER K 175 " --> pdb=" O ALA K 171 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA K 178 " --> pdb=" O ASP K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 191 removed outlier: 3.611A pdb=" N MET K 190 " --> pdb=" O ASP K 187 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE K 191 " --> pdb=" O LEU K 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 187 through 191' Processing helix chain 'K' and resid 200 through 204 removed outlier: 4.026A pdb=" N THR K 204 " --> pdb=" O GLU K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 253 through 264 removed outlier: 3.734A pdb=" N GLU K 257 " --> pdb=" O ALA K 253 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS K 258 " --> pdb=" O GLU K 254 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG K 264 " --> pdb=" O VAL K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 280 removed outlier: 3.784A pdb=" N ARG K 270 " --> pdb=" O PHE K 266 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE K 274 " --> pdb=" O ARG K 270 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG K 279 " --> pdb=" O ILE K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 309 removed outlier: 3.561A pdb=" N LYS K 307 " --> pdb=" O ASP K 303 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU K 308 " --> pdb=" O ALA K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 329 removed outlier: 4.291A pdb=" N THR K 325 " --> pdb=" O MET K 321 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU K 326 " --> pdb=" O GLU K 322 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 344 Processing helix chain 'K' and resid 380 through 404 removed outlier: 3.503A pdb=" N LEU K 384 " --> pdb=" O ASN K 380 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR K 385 " --> pdb=" O LYS K 381 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP K 393 " --> pdb=" O ASP K 389 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA K 397 " --> pdb=" O ASP K 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 425 removed outlier: 3.552A pdb=" N ILE K 423 " --> pdb=" O ALA K 419 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS K 424 " --> pdb=" O GLU K 420 " (cutoff:3.500A) Processing helix chain 'K' and resid 426 through 429 removed outlier: 3.847A pdb=" N VAL K 429 " --> pdb=" O LYS K 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 426 through 429' Processing helix chain 'K' and resid 433 through 444 removed outlier: 3.828A pdb=" N VAL K 437 " --> pdb=" O ALA K 433 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN K 438 " --> pdb=" O GLN K 434 " (cutoff:3.500A) Processing helix chain 'K' and resid 445 through 455 removed outlier: 3.515A pdb=" N SER K 455 " --> pdb=" O LEU K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 472 removed outlier: 3.573A pdb=" N LEU K 463 " --> pdb=" O LEU K 459 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 489 through 493 removed outlier: 3.672A pdb=" N GLY K 493 " --> pdb=" O ALA K 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 489 through 493' Processing helix chain 'K' and resid 497 through 505 removed outlier: 3.621A pdb=" N LYS K 501 " --> pdb=" O ASN K 497 " (cutoff:3.500A) Processing helix chain 'K' and resid 506 through 516 Processing helix chain 'J' and resid 28 through 43 removed outlier: 3.593A pdb=" N GLU J 38 " --> pdb=" O GLN J 34 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 74 removed outlier: 3.634A pdb=" N ILE J 72 " --> pdb=" O ASP J 68 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU J 73 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 68 through 74' Processing helix chain 'J' and resid 80 through 97 removed outlier: 3.635A pdb=" N MET J 85 " --> pdb=" O PRO J 81 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE J 86 " --> pdb=" O ALA J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 120 removed outlier: 3.696A pdb=" N VAL J 104 " --> pdb=" O GLY J 100 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU J 105 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 143 removed outlier: 3.504A pdb=" N VAL J 128 " --> pdb=" O SER J 124 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU J 130 " --> pdb=" O SER J 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA J 135 " --> pdb=" O GLY J 131 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU J 141 " --> pdb=" O ARG J 137 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE J 142 " --> pdb=" O LYS J 138 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU J 143 " --> pdb=" O ALA J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 164 removed outlier: 4.215A pdb=" N SER J 162 " --> pdb=" O ASP J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 170 removed outlier: 3.570A pdb=" N ILE J 168 " --> pdb=" O LEU J 164 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER J 170 " --> pdb=" O THR J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 188 removed outlier: 3.639A pdb=" N ALA J 186 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL J 188 " --> pdb=" O ALA J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 200 No H-bonds generated for 'chain 'J' and resid 198 through 200' Processing helix chain 'J' and resid 211 through 215 Processing helix chain 'J' and resid 261 through 285 removed outlier: 3.558A pdb=" N ASN J 267 " --> pdb=" O GLU J 263 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE J 268 " --> pdb=" O GLU J 264 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER J 269 " --> pdb=" O LEU J 265 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS J 270 " --> pdb=" O MET J 266 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN J 279 " --> pdb=" O LEU J 275 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE J 283 " --> pdb=" O GLN J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 308 removed outlier: 3.526A pdb=" N TYR J 304 " --> pdb=" O MET J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 329 removed outlier: 3.533A pdb=" N LEU J 321 " --> pdb=" O SER J 317 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS J 326 " --> pdb=" O ARG J 322 " (cutoff:3.500A) Processing helix chain 'J' and resid 381 through 405 removed outlier: 3.511A pdb=" N MET J 385 " --> pdb=" O THR J 381 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP J 386 " --> pdb=" O ASP J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 413 through 429 removed outlier: 3.570A pdb=" N ILE J 417 " --> pdb=" O GLY J 413 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU J 418 " --> pdb=" O ALA J 414 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR J 424 " --> pdb=" O ALA J 420 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR J 429 " --> pdb=" O SER J 425 " (cutoff:3.500A) Processing helix chain 'J' and resid 434 through 445 removed outlier: 3.717A pdb=" N ILE J 438 " --> pdb=" O GLU J 434 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE J 445 " --> pdb=" O PHE J 441 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 456 removed outlier: 3.614A pdb=" N ARG J 450 " --> pdb=" O GLU J 446 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU J 452 " --> pdb=" O ILE J 448 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 470 removed outlier: 3.590A pdb=" N LYS J 466 " --> pdb=" O GLU J 462 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU J 467 " --> pdb=" O VAL J 463 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR J 468 " --> pdb=" O ILE J 464 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA J 469 " --> pdb=" O SER J 465 " (cutoff:3.500A) Processing helix chain 'J' and resid 491 through 496 removed outlier: 3.835A pdb=" N ALA J 495 " --> pdb=" O ASP J 491 " (cutoff:3.500A) Processing helix chain 'J' and resid 500 through 520 removed outlier: 3.511A pdb=" N ILE J 508 " --> pdb=" O LYS J 504 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS J 509 " --> pdb=" O TYR J 505 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 33 removed outlier: 3.557A pdb=" N VAL H 31 " --> pdb=" O SER H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 36 No H-bonds generated for 'chain 'H' and resid 34 through 36' Processing helix chain 'H' and resid 61 through 66 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.669A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 107 removed outlier: 3.673A pdb=" N LEU H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 removed outlier: 3.614A pdb=" N GLU H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 138 removed outlier: 3.621A pdb=" N LYS H 137 " --> pdb=" O VAL H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 163 removed outlier: 3.807A pdb=" N ARG H 152 " --> pdb=" O LYS H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 184 removed outlier: 4.034A pdb=" N LYS H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET H 178 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 259 through 282 removed outlier: 3.837A pdb=" N ALA H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL H 267 " --> pdb=" O TYR H 263 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP H 271 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 removed outlier: 3.531A pdb=" N PHE H 303 " --> pdb=" O ALA H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 315 through 327 removed outlier: 3.599A pdb=" N ARG H 321 " --> pdb=" O GLU H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 337 removed outlier: 4.107A pdb=" N ALA H 336 " --> pdb=" O SER H 333 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU H 337 " --> pdb=" O VAL H 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 333 through 337' Processing helix chain 'H' and resid 378 through 402 removed outlier: 3.579A pdb=" N ILE H 395 " --> pdb=" O ASP H 391 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG H 398 " --> pdb=" O MET H 394 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE H 400 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS H 401 " --> pdb=" O ARG H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 425 removed outlier: 3.695A pdb=" N SER H 417 " --> pdb=" O GLU H 413 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG H 425 " --> pdb=" O ARG H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 441 removed outlier: 3.573A pdb=" N GLY H 436 " --> pdb=" O GLN H 432 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA H 437 " --> pdb=" O LEU H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 452 removed outlier: 3.543A pdb=" N LEU H 449 " --> pdb=" O ILE H 445 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS H 450 " --> pdb=" O PRO H 446 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN H 452 " --> pdb=" O GLN H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 471 removed outlier: 3.508A pdb=" N LEU H 461 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN H 462 " --> pdb=" O THR H 458 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS H 463 " --> pdb=" O ASN H 459 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA H 469 " --> pdb=" O ARG H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 514 removed outlier: 3.539A pdb=" N VAL H 514 " --> pdb=" O ALA H 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 removed outlier: 3.631A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 35 removed outlier: 3.916A pdb=" N ASN G 28 " --> pdb=" O SER G 24 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 68 removed outlier: 3.640A pdb=" N LEU G 67 " --> pdb=" O GLY G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 91 removed outlier: 3.581A pdb=" N SER G 79 " --> pdb=" O PRO G 75 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU G 82 " --> pdb=" O LYS G 78 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER G 84 " --> pdb=" O MET G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 108 removed outlier: 3.743A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 114 removed outlier: 3.874A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU G 114 " --> pdb=" O GLU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 138 removed outlier: 3.705A pdb=" N VAL G 122 " --> pdb=" O HIS G 118 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER G 135 " --> pdb=" O ASP G 131 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR G 136 " --> pdb=" O ASP G 132 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU G 137 " --> pdb=" O MET G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 161 removed outlier: 3.755A pdb=" N MET G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE G 155 " --> pdb=" O MET G 151 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 167 removed outlier: 3.627A pdb=" N SER G 166 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 163 through 167' Processing helix chain 'G' and resid 168 through 183 removed outlier: 4.225A pdb=" N ASN G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL G 180 " --> pdb=" O ALA G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 261 through 283 removed outlier: 4.566A pdb=" N THR G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU G 268 " --> pdb=" O PHE G 264 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU G 272 " --> pdb=" O LEU G 268 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE G 275 " --> pdb=" O GLU G 271 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE G 282 " --> pdb=" O LEU G 278 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE G 283 " --> pdb=" O CYS G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 307 removed outlier: 3.676A pdb=" N TYR G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG G 306 " --> pdb=" O HIS G 302 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 327 removed outlier: 3.822A pdb=" N ARG G 325 " --> pdb=" O ASN G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 338 removed outlier: 3.878A pdb=" N LEU G 338 " --> pdb=" O PRO G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 341 No H-bonds generated for 'chain 'G' and resid 339 through 341' Processing helix chain 'G' and resid 380 through 404 removed outlier: 3.674A pdb=" N GLU G 386 " --> pdb=" O GLU G 382 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL G 397 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS G 398 " --> pdb=" O ALA G 394 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL G 401 " --> pdb=" O VAL G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 426 removed outlier: 3.655A pdb=" N VAL G 418 " --> pdb=" O SER G 414 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA G 421 " --> pdb=" O ALA G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 427 through 429 No H-bonds generated for 'chain 'G' and resid 427 through 429' Processing helix chain 'G' and resid 433 through 444 removed outlier: 3.720A pdb=" N VAL G 440 " --> pdb=" O PRO G 436 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA G 441 " --> pdb=" O TYR G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 456 removed outlier: 3.600A pdb=" N LEU G 451 " --> pdb=" O ILE G 447 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE G 452 " --> pdb=" O PRO G 448 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N CYS G 455 " --> pdb=" O LEU G 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 470 removed outlier: 3.786A pdb=" N SER G 465 " --> pdb=" O ARG G 461 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS G 470 " --> pdb=" O LEU G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 494 Processing helix chain 'G' and resid 499 through 518 removed outlier: 3.580A pdb=" N GLU G 511 " --> pdb=" O LYS G 507 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA G 513 " --> pdb=" O ALA G 509 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG G 518 " --> pdb=" O VAL G 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 48 removed outlier: 3.979A pdb=" N LYS E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA E 38 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR E 48 " --> pdb=" O ASN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 78 removed outlier: 3.548A pdb=" N ILE E 75 " --> pdb=" O ASP E 71 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU E 76 " --> pdb=" O GLY E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 100 removed outlier: 3.601A pdb=" N MET E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 124 removed outlier: 3.540A pdb=" N VAL E 109 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 147 removed outlier: 3.518A pdb=" N GLN E 137 " --> pdb=" O ASP E 133 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP E 147 " --> pdb=" O ILE E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 172 removed outlier: 3.552A pdb=" N THR E 169 " --> pdb=" O GLN E 165 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR E 170 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 180 removed outlier: 3.519A pdb=" N HIS E 180 " --> pdb=" O ASN E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 removed outlier: 3.557A pdb=" N GLU E 185 " --> pdb=" O ARG E 181 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA E 187 " --> pdb=" O MET E 183 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR E 193 " --> pdb=" O ASN E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 220 Processing helix chain 'E' and resid 268 through 292 removed outlier: 3.560A pdb=" N GLU E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE E 290 " --> pdb=" O MET E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 315 removed outlier: 3.968A pdb=" N HIS E 310 " --> pdb=" O ASP E 306 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU E 311 " --> pdb=" O GLU E 307 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 313 " --> pdb=" O ASN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 335 removed outlier: 3.929A pdb=" N ILE E 328 " --> pdb=" O GLY E 324 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU E 329 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU E 330 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE E 331 " --> pdb=" O GLU E 327 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 351 removed outlier: 3.720A pdb=" N LEU E 351 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 413 removed outlier: 3.517A pdb=" N ILE E 393 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG E 408 " --> pdb=" O LEU E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 435 removed outlier: 3.628A pdb=" N ILE E 425 " --> pdb=" O GLY E 421 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA E 430 " --> pdb=" O SER E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 454 removed outlier: 3.535A pdb=" N GLU E 454 " --> pdb=" O ALA E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 464 removed outlier: 3.526A pdb=" N LEU E 460 " --> pdb=" O ILE E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 482 removed outlier: 4.313A pdb=" N GLU E 474 " --> pdb=" O GLN E 470 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU E 482 " --> pdb=" O ARG E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 503 Processing helix chain 'E' and resid 508 through 527 Processing helix chain 'I' and resid 32 through 48 Processing helix chain 'I' and resid 49 through 52 removed outlier: 3.864A pdb=" N LEU I 52 " --> pdb=" O ARG I 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 49 through 52' Processing helix chain 'I' and resid 73 through 82 removed outlier: 3.566A pdb=" N LEU I 78 " --> pdb=" O GLY I 74 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN I 80 " --> pdb=" O THR I 76 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 102 Processing helix chain 'I' and resid 107 through 124 removed outlier: 3.530A pdb=" N ASP I 118 " --> pdb=" O GLY I 114 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR I 121 " --> pdb=" O LEU I 117 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS I 122 " --> pdb=" O ASP I 118 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU I 123 " --> pdb=" O SER I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 152 removed outlier: 3.502A pdb=" N GLN I 138 " --> pdb=" O SER I 134 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU I 146 " --> pdb=" O GLU I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 172 removed outlier: 3.519A pdb=" N LEU I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR I 169 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER I 170 " --> pdb=" O SER I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 180 removed outlier: 3.681A pdb=" N SER I 177 " --> pdb=" O LYS I 174 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN I 178 " --> pdb=" O VAL I 175 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER I 180 " --> pdb=" O SER I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 190 removed outlier: 3.549A pdb=" N VAL I 188 " --> pdb=" O SER I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 206 No H-bonds generated for 'chain 'I' and resid 204 through 206' Processing helix chain 'I' and resid 217 through 221 Processing helix chain 'I' and resid 272 through 292 removed outlier: 3.629A pdb=" N LEU I 276 " --> pdb=" O MET I 272 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU I 278 " --> pdb=" O ARG I 274 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE I 283 " --> pdb=" O GLU I 279 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN I 285 " --> pdb=" O ALA I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 320 removed outlier: 3.580A pdb=" N HIS I 315 " --> pdb=" O ASP I 311 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE I 316 " --> pdb=" O LEU I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 340 Processing helix chain 'I' and resid 347 through 351 removed outlier: 3.531A pdb=" N PHE I 351 " --> pdb=" O ILE I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 352 through 356 removed outlier: 3.501A pdb=" N MET I 355 " --> pdb=" O THR I 352 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU I 356 " --> pdb=" O ALA I 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 352 through 356' Processing helix chain 'I' and resid 394 through 418 removed outlier: 3.737A pdb=" N ILE I 398 " --> pdb=" O ASN I 394 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU I 399 " --> pdb=" O LYS I 395 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL I 411 " --> pdb=" O ASP I 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE I 412 " --> pdb=" O ALA I 408 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS I 417 " --> pdb=" O ARG I 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 426 through 442 removed outlier: 3.837A pdb=" N ILE I 430 " --> pdb=" O GLY I 426 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU I 431 " --> pdb=" O ALA I 427 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU I 436 " --> pdb=" O LEU I 432 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR I 437 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR I 442 " --> pdb=" O GLU I 438 " (cutoff:3.500A) Processing helix chain 'I' and resid 446 through 457 removed outlier: 3.747A pdb=" N CYS I 450 " --> pdb=" O MET I 446 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG I 452 " --> pdb=" O SER I 448 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA I 453 " --> pdb=" O TYR I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 459 through 469 Processing helix chain 'I' and resid 472 through 487 removed outlier: 3.798A pdb=" N VAL I 477 " --> pdb=" O PRO I 473 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR I 478 " --> pdb=" O ILE I 474 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN I 486 " --> pdb=" O ASN I 482 " (cutoff:3.500A) Processing helix chain 'I' and resid 512 through 530 removed outlier: 3.627A pdb=" N ALA I 522 " --> pdb=" O ALA I 518 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER I 528 " --> pdb=" O GLU I 524 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU I 530 " --> pdb=" O VAL I 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 37 removed outlier: 3.637A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 43 removed outlier: 4.080A pdb=" N SER B 41 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 43 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 75 removed outlier: 3.916A pdb=" N ASN B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 removed outlier: 4.184A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 116 removed outlier: 3.515A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 144 removed outlier: 3.607A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 140 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 167 removed outlier: 3.726A pdb=" N PHE B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 178 through 189 removed outlier: 3.810A pdb=" N ALA B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 260 through 283 removed outlier: 3.894A pdb=" N VAL B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 265 " --> pdb=" O THR B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.740A pdb=" N LEU B 303 " --> pdb=" O TYR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 328 removed outlier: 3.515A pdb=" N ARG B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.856A pdb=" N VAL B 341 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 401 removed outlier: 3.611A pdb=" N ARG B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 426 removed outlier: 3.697A pdb=" N ASN B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 444 removed outlier: 4.239A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 455 removed outlier: 3.665A pdb=" N ILE B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 470 removed outlier: 3.708A pdb=" N VAL B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 removed outlier: 3.529A pdb=" N ALA B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 33 removed outlier: 4.089A pdb=" N ARG A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.845A pdb=" N LEU A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 86 removed outlier: 3.738A pdb=" N VAL A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 109 removed outlier: 3.618A pdb=" N ILE A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 133 removed outlier: 3.603A pdb=" N GLU A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 157 removed outlier: 4.176A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 177 removed outlier: 3.509A pdb=" N VAL A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.553A pdb=" N VAL A 195 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.637A pdb=" N SER A 208 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 259 through 278 removed outlier: 3.965A pdb=" N ILE A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 275 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.829A pdb=" N ARG A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.709A pdb=" N LEU A 345 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 405 removed outlier: 3.682A pdb=" N VAL A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 401 " --> pdb=" O CYS A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.750A pdb=" N ILE A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 446 removed outlier: 3.577A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.519A pdb=" N LEU A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 453 " --> pdb=" O PRO A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 477 removed outlier: 3.852A pdb=" N PHE A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 removed outlier: 4.452A pdb=" N TRP A 485 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 486 " --> pdb=" O LEU A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 486' Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.536A pdb=" N GLY A 502 " --> pdb=" O ASN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 525 removed outlier: 4.175A pdb=" N SER A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'z' and resid 3 through 8 removed outlier: 3.651A pdb=" N LEU z 7 " --> pdb=" O ALA z 3 " (cutoff:3.500A) Processing helix chain 'z' and resid 15 through 35 removed outlier: 3.726A pdb=" N LEU z 20 " --> pdb=" O ALA z 16 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA z 21 " --> pdb=" O GLN z 17 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL z 33 " --> pdb=" O GLY z 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 59 through 66 Processing helix chain 'z' and resid 71 through 88 removed outlier: 3.515A pdb=" N ALA z 83 " --> pdb=" O LYS z 79 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP z 85 " --> pdb=" O ALA z 81 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE z 87 " --> pdb=" O ALA z 83 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR z 88 " --> pdb=" O GLN z 84 " (cutoff:3.500A) Processing helix chain 'z' and resid 92 through 103 removed outlier: 3.598A pdb=" N VAL z 96 " --> pdb=" O THR z 92 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU z 97 " --> pdb=" O THR z 93 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE z 98 " --> pdb=" O SER z 94 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE z 99 " --> pdb=" O ASN z 95 " (cutoff:3.500A) Processing helix chain 'z' and resid 106 through 111 Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.774A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY z 122 " --> pdb=" O ILE z 118 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA z 125 " --> pdb=" O GLU z 121 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS z 129 " --> pdb=" O ALA z 125 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU z 135 " --> pdb=" O LEU z 131 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU z 136 " --> pdb=" O GLN z 132 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS z 138 " --> pdb=" O LEU z 134 " (cutoff:3.500A) Processing helix chain 'z' and resid 146 through 158 removed outlier: 3.680A pdb=" N ASP z 150 " --> pdb=" O GLU z 146 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER z 155 " --> pdb=" O VAL z 151 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 164 through 178 removed outlier: 4.081A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP z 174 " --> pdb=" O GLU z 170 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER z 175 " --> pdb=" O ALA z 171 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA z 178 " --> pdb=" O ASP z 174 " (cutoff:3.500A) Processing helix chain 'z' and resid 187 through 191 removed outlier: 3.613A pdb=" N MET z 190 " --> pdb=" O ASP z 187 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE z 191 " --> pdb=" O LEU z 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 187 through 191' Processing helix chain 'z' and resid 200 through 204 removed outlier: 3.540A pdb=" N ASP z 203 " --> pdb=" O SER z 200 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR z 204 " --> pdb=" O GLU z 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 200 through 204' Processing helix chain 'z' and resid 253 through 264 removed outlier: 3.816A pdb=" N GLU z 257 " --> pdb=" O ALA z 253 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS z 258 " --> pdb=" O GLU z 254 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU z 259 " --> pdb=" O GLU z 255 " (cutoff:3.500A) Processing helix chain 'z' and resid 264 through 276 removed outlier: 3.812A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE z 274 " --> pdb=" O ARG z 270 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 309 removed outlier: 3.601A pdb=" N LYS z 307 " --> pdb=" O ASP z 303 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 319 through 329 removed outlier: 4.289A pdb=" N THR z 325 " --> pdb=" O MET z 321 " (cutoff:3.500A) Processing helix chain 'z' and resid 340 through 344 removed outlier: 3.500A pdb=" N CYS z 343 " --> pdb=" O SER z 340 " (cutoff:3.500A) Processing helix chain 'z' and resid 380 through 404 removed outlier: 3.517A pdb=" N THR z 385 " --> pdb=" O LYS z 381 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP z 393 " --> pdb=" O ASP z 389 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG z 396 " --> pdb=" O ARG z 392 " (cutoff:3.500A) Processing helix chain 'z' and resid 414 through 424 removed outlier: 3.505A pdb=" N LEU z 422 " --> pdb=" O MET z 418 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE z 423 " --> pdb=" O ALA z 419 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS z 424 " --> pdb=" O GLU z 420 " (cutoff:3.500A) Processing helix chain 'z' and resid 425 through 429 removed outlier: 3.784A pdb=" N VAL z 429 " --> pdb=" O LYS z 426 " (cutoff:3.500A) Processing helix chain 'z' and resid 433 through 445 removed outlier: 3.876A pdb=" N VAL z 437 " --> pdb=" O ALA z 433 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN z 438 " --> pdb=" O GLN z 434 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU z 445 " --> pdb=" O ALA z 441 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 455 Processing helix chain 'z' and resid 459 through 472 removed outlier: 3.717A pdb=" N LEU z 463 " --> pdb=" O LEU z 459 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS z 465 " --> pdb=" O GLU z 461 " (cutoff:3.500A) Processing helix chain 'z' and resid 489 through 493 removed outlier: 3.683A pdb=" N GLY z 493 " --> pdb=" O ALA z 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 489 through 493' Processing helix chain 'z' and resid 497 through 516 removed outlier: 3.638A pdb=" N LYS z 501 " --> pdb=" O ASN z 497 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS z 508 " --> pdb=" O LEU z 504 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR z 509 " --> pdb=" O LEU z 505 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE z 515 " --> pdb=" O ILE z 511 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 43 removed outlier: 3.578A pdb=" N GLU P 38 " --> pdb=" O GLN P 34 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU P 39 " --> pdb=" O ALA P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 74 removed outlier: 3.561A pdb=" N ILE P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU P 73 " --> pdb=" O ALA P 69 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 68 through 74' Processing helix chain 'P' and resid 80 through 97 removed outlier: 3.716A pdb=" N MET P 85 " --> pdb=" O PRO P 81 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE P 86 " --> pdb=" O ALA P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 120 removed outlier: 3.600A pdb=" N VAL P 104 " --> pdb=" O GLY P 100 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU P 105 " --> pdb=" O THR P 101 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU P 117 " --> pdb=" O GLU P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 143 removed outlier: 3.533A pdb=" N ILE P 129 " --> pdb=" O VAL P 125 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU P 130 " --> pdb=" O SER P 126 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE P 134 " --> pdb=" O GLU P 130 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA P 135 " --> pdb=" O GLY P 131 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU P 141 " --> pdb=" O ARG P 137 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE P 142 " --> pdb=" O LYS P 138 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU P 143 " --> pdb=" O ALA P 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 164 Processing helix chain 'P' and resid 164 through 170 removed outlier: 3.524A pdb=" N ILE P 168 " --> pdb=" O LEU P 164 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER P 170 " --> pdb=" O THR P 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 188 removed outlier: 3.503A pdb=" N LYS P 181 " --> pdb=" O VAL P 177 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA P 186 " --> pdb=" O LEU P 182 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL P 188 " --> pdb=" O ALA P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 189 through 191 No H-bonds generated for 'chain 'P' and resid 189 through 191' Processing helix chain 'P' and resid 198 through 200 No H-bonds generated for 'chain 'P' and resid 198 through 200' Processing helix chain 'P' and resid 211 through 215 Processing helix chain 'P' and resid 261 through 285 removed outlier: 3.514A pdb=" N LEU P 265 " --> pdb=" O THR P 261 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE P 268 " --> pdb=" O GLU P 264 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER P 269 " --> pdb=" O LEU P 265 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS P 270 " --> pdb=" O MET P 266 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU P 273 " --> pdb=" O SER P 269 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN P 279 " --> pdb=" O LEU P 275 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE P 283 " --> pdb=" O GLN P 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 308 removed outlier: 3.523A pdb=" N TYR P 304 " --> pdb=" O MET P 300 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN P 306 " --> pdb=" O LEU P 302 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 329 removed outlier: 3.585A pdb=" N LEU P 321 " --> pdb=" O SER P 317 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG P 322 " --> pdb=" O LYS P 318 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG P 323 " --> pdb=" O TRP P 319 " (cutoff:3.500A) Processing helix chain 'P' and resid 381 through 405 removed outlier: 3.529A pdb=" N MET P 385 " --> pdb=" O THR P 381 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP P 387 " --> pdb=" O ASN P 383 " (cutoff:3.500A) Processing helix chain 'P' and resid 413 through 429 removed outlier: 3.621A pdb=" N ILE P 417 " --> pdb=" O GLY P 413 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU P 418 " --> pdb=" O ALA P 414 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE P 423 " --> pdb=" O LEU P 419 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR P 424 " --> pdb=" O ALA P 420 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR P 429 " --> pdb=" O SER P 425 " (cutoff:3.500A) Processing helix chain 'P' and resid 434 through 455 removed outlier: 3.648A pdb=" N ILE P 438 " --> pdb=" O GLU P 434 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE P 445 " --> pdb=" O PHE P 441 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE P 448 " --> pdb=" O ALA P 444 " (cutoff:3.500A) Proline residue: P 449 - end of helix removed outlier: 3.728A pdb=" N LEU P 452 " --> pdb=" O ILE P 448 " (cutoff:3.500A) Processing helix chain 'P' and resid 459 through 470 removed outlier: 3.522A pdb=" N LYS P 466 " --> pdb=" O GLU P 462 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR P 468 " --> pdb=" O ILE P 464 " (cutoff:3.500A) Processing helix chain 'P' and resid 491 through 496 removed outlier: 3.557A pdb=" N ALA P 495 " --> pdb=" O ASP P 491 " (cutoff:3.500A) Processing helix chain 'P' and resid 500 through 520 removed outlier: 3.501A pdb=" N ILE P 508 " --> pdb=" O LYS P 504 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS P 509 " --> pdb=" O TYR P 505 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 33 removed outlier: 3.549A pdb=" N VAL O 31 " --> pdb=" O SER O 27 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 36 No H-bonds generated for 'chain 'O' and resid 34 through 36' Processing helix chain 'O' and resid 61 through 66 Processing helix chain 'O' and resid 77 through 90 removed outlier: 3.614A pdb=" N ALA O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 107 removed outlier: 3.656A pdb=" N THR O 98 " --> pdb=" O THR O 94 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU O 105 " --> pdb=" O ALA O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 113 removed outlier: 3.616A pdb=" N GLU O 113 " --> pdb=" O LYS O 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 138 removed outlier: 3.810A pdb=" N LYS O 137 " --> pdb=" O VAL O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 163 removed outlier: 3.728A pdb=" N ARG O 152 " --> pdb=" O LYS O 148 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 185 removed outlier: 4.187A pdb=" N LYS O 177 " --> pdb=" O ALA O 173 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET O 178 " --> pdb=" O PHE O 174 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET O 185 " --> pdb=" O ASP O 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 204 through 208 removed outlier: 3.519A pdb=" N SER O 208 " --> pdb=" O LEU O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 259 through 282 removed outlier: 3.539A pdb=" N GLN O 264 " --> pdb=" O VAL O 260 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA O 265 " --> pdb=" O GLU O 261 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL O 267 " --> pdb=" O TYR O 263 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU O 274 " --> pdb=" O GLU O 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 296 through 306 Processing helix chain 'O' and resid 315 through 327 removed outlier: 3.558A pdb=" N ARG O 321 " --> pdb=" O GLU O 317 " (cutoff:3.500A) Processing helix chain 'O' and resid 333 through 337 removed outlier: 3.908A pdb=" N ALA O 336 " --> pdb=" O SER O 333 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU O 337 " --> pdb=" O VAL O 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 333 through 337' Processing helix chain 'O' and resid 378 through 402 removed outlier: 3.539A pdb=" N ARG O 398 " --> pdb=" O MET O 394 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE O 400 " --> pdb=" O VAL O 396 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS O 401 " --> pdb=" O ARG O 397 " (cutoff:3.500A) Processing helix chain 'O' and resid 410 through 425 removed outlier: 3.739A pdb=" N SER O 417 " --> pdb=" O GLU O 413 " (cutoff:3.500A) Processing helix chain 'O' and resid 431 through 442 removed outlier: 3.620A pdb=" N GLY O 436 " --> pdb=" O GLN O 432 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA O 437 " --> pdb=" O LEU O 433 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU O 442 " --> pdb=" O TYR O 438 " (cutoff:3.500A) Processing helix chain 'O' and resid 444 through 452 removed outlier: 3.646A pdb=" N CYS O 450 " --> pdb=" O PRO O 446 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN O 452 " --> pdb=" O GLN O 448 " (cutoff:3.500A) Processing helix chain 'O' and resid 456 through 469 removed outlier: 3.513A pdb=" N LEU O 461 " --> pdb=" O ALA O 457 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN O 462 " --> pdb=" O THR O 458 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS O 463 " --> pdb=" O ASN O 459 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA O 469 " --> pdb=" O ARG O 465 " (cutoff:3.500A) Processing helix chain 'O' and resid 496 through 514 Processing helix chain 'N' and resid 19 through 24 removed outlier: 3.647A pdb=" N GLN N 23 " --> pdb=" O GLY N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 37 removed outlier: 3.800A pdb=" N ASN N 28 " --> pdb=" O SER N 24 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE N 33 " --> pdb=" O ALA N 29 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE N 37 " --> pdb=" O ILE N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 68 removed outlier: 3.627A pdb=" N LEU N 67 " --> pdb=" O GLY N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 91 removed outlier: 3.509A pdb=" N SER N 79 " --> pdb=" O PRO N 75 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET N 80 " --> pdb=" O ALA N 76 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU N 82 " --> pdb=" O LYS N 78 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER N 84 " --> pdb=" O MET N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 114 removed outlier: 3.966A pdb=" N HIS N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE N 112 " --> pdb=" O VAL N 108 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU N 114 " --> pdb=" O GLU N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 138 removed outlier: 3.608A pdb=" N VAL N 122 " --> pdb=" O HIS N 118 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP N 132 " --> pdb=" O LYS N 128 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER N 135 " --> pdb=" O ASP N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 161 removed outlier: 3.732A pdb=" N MET N 152 " --> pdb=" O ASP N 148 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN N 154 " --> pdb=" O ASP N 150 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE N 155 " --> pdb=" O MET N 151 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER N 159 " --> pdb=" O ILE N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 163 through 167 removed outlier: 3.619A pdb=" N SER N 166 " --> pdb=" O LYS N 163 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG N 167 " --> pdb=" O ALA N 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 163 through 167' Processing helix chain 'N' and resid 168 through 183 removed outlier: 4.349A pdb=" N ASN N 174 " --> pdb=" O SER N 170 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL N 180 " --> pdb=" O ALA N 176 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL N 183 " --> pdb=" O ALA N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 283 removed outlier: 4.454A pdb=" N THR N 265 " --> pdb=" O GLU N 261 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU N 272 " --> pdb=" O LEU N 268 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE N 275 " --> pdb=" O GLU N 271 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE N 283 " --> pdb=" O CYS N 279 " (cutoff:3.500A) Processing helix chain 'N' and resid 297 through 307 removed outlier: 3.640A pdb=" N TYR N 303 " --> pdb=" O LEU N 299 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG N 306 " --> pdb=" O HIS N 302 " (cutoff:3.500A) Processing helix chain 'N' and resid 316 through 327 removed outlier: 3.747A pdb=" N ARG N 325 " --> pdb=" O ASN N 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 334 through 338 removed outlier: 3.814A pdb=" N LEU N 338 " --> pdb=" O PRO N 335 " (cutoff:3.500A) Processing helix chain 'N' and resid 339 through 341 No H-bonds generated for 'chain 'N' and resid 339 through 341' Processing helix chain 'N' and resid 380 through 404 removed outlier: 3.686A pdb=" N GLU N 386 " --> pdb=" O GLU N 382 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL N 397 " --> pdb=" O ASP N 393 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS N 398 " --> pdb=" O ALA N 394 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL N 401 " --> pdb=" O VAL N 397 " (cutoff:3.500A) Processing helix chain 'N' and resid 412 through 426 removed outlier: 3.675A pdb=" N VAL N 418 " --> pdb=" O SER N 414 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA N 421 " --> pdb=" O ALA N 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 427 through 429 No H-bonds generated for 'chain 'N' and resid 427 through 429' Processing helix chain 'N' and resid 433 through 444 removed outlier: 3.731A pdb=" N VAL N 440 " --> pdb=" O PRO N 436 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA N 441 " --> pdb=" O TYR N 437 " (cutoff:3.500A) Processing helix chain 'N' and resid 445 through 456 removed outlier: 3.502A pdb=" N LEU N 451 " --> pdb=" O ILE N 447 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE N 452 " --> pdb=" O PRO N 448 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS N 455 " --> pdb=" O LEU N 451 " (cutoff:3.500A) Processing helix chain 'N' and resid 460 through 470 removed outlier: 3.936A pdb=" N SER N 465 " --> pdb=" O ARG N 461 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS N 470 " --> pdb=" O LEU N 466 " (cutoff:3.500A) Processing helix chain 'N' and resid 489 through 494 Processing helix chain 'N' and resid 499 through 518 removed outlier: 3.591A pdb=" N GLU N 511 " --> pdb=" O LYS N 507 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA N 513 " --> pdb=" O ALA N 509 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG N 518 " --> pdb=" O VAL N 514 " (cutoff:3.500A) Processing helix chain 'e' and resid 19 through 23 removed outlier: 3.578A pdb=" N LYS e 23 " --> pdb=" O GLN e 20 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 47 removed outlier: 3.620A pdb=" N HIS e 35 " --> pdb=" O ALA e 31 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA e 41 " --> pdb=" O MET e 37 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL e 42 " --> pdb=" O ALA e 38 " (cutoff:3.500A) Processing helix chain 'e' and resid 71 through 78 removed outlier: 3.722A pdb=" N LEU e 76 " --> pdb=" O GLY e 72 " (cutoff:3.500A) Processing helix chain 'e' and resid 83 through 100 removed outlier: 3.610A pdb=" N LEU e 88 " --> pdb=" O GLN e 84 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET e 89 " --> pdb=" O ILE e 85 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 124 removed outlier: 3.576A pdb=" N VAL e 109 " --> pdb=" O THR e 105 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN e 120 " --> pdb=" O GLU e 116 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU e 121 " --> pdb=" O GLU e 117 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG e 124 " --> pdb=" O GLN e 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 147 removed outlier: 3.532A pdb=" N GLN e 137 " --> pdb=" O ASP e 133 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL e 141 " --> pdb=" O GLN e 137 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP e 147 " --> pdb=" O ILE e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 160 through 172 removed outlier: 3.643A pdb=" N THR e 169 " --> pdb=" O GLN e 165 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR e 170 " --> pdb=" O THR e 166 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 180 removed outlier: 3.514A pdb=" N HIS e 180 " --> pdb=" O ASN e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 181 through 193 removed outlier: 3.637A pdb=" N GLU e 185 " --> pdb=" O ARG e 181 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA e 187 " --> pdb=" O MET e 183 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL e 191 " --> pdb=" O ALA e 187 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR e 193 " --> pdb=" O ASN e 189 " (cutoff:3.500A) Processing helix chain 'e' and resid 216 through 220 removed outlier: 3.510A pdb=" N THR e 220 " --> pdb=" O LEU e 217 " (cutoff:3.500A) Processing helix chain 'e' and resid 268 through 292 removed outlier: 3.518A pdb=" N GLU e 284 " --> pdb=" O LYS e 280 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE e 287 " --> pdb=" O PHE e 283 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE e 290 " --> pdb=" O MET e 286 " (cutoff:3.500A) Processing helix chain 'e' and resid 305 through 315 removed outlier: 3.879A pdb=" N HIS e 310 " --> pdb=" O ASP e 306 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU e 311 " --> pdb=" O GLU e 307 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU e 312 " --> pdb=" O ALA e 308 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU e 313 " --> pdb=" O ASN e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 324 through 335 removed outlier: 3.931A pdb=" N ILE e 328 " --> pdb=" O GLY e 324 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU e 329 " --> pdb=" O GLY e 325 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU e 330 " --> pdb=" O PRO e 326 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE e 333 " --> pdb=" O GLU e 329 " (cutoff:3.500A) Processing helix chain 'e' and resid 389 through 413 removed outlier: 3.524A pdb=" N GLU e 395 " --> pdb=" O MET e 391 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP e 402 " --> pdb=" O ARG e 398 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE e 407 " --> pdb=" O ALA e 403 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG e 408 " --> pdb=" O LEU e 404 " (cutoff:3.500A) Processing helix chain 'e' and resid 421 through 435 Processing helix chain 'e' and resid 442 through 454 removed outlier: 3.539A pdb=" N GLU e 454 " --> pdb=" O ALA e 450 " (cutoff:3.500A) Processing helix chain 'e' and resid 454 through 464 Processing helix chain 'e' and resid 467 through 482 removed outlier: 3.576A pdb=" N THR e 473 " --> pdb=" O ILE e 469 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU e 474 " --> pdb=" O GLN e 470 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN e 479 " --> pdb=" O VAL e 475 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL e 480 " --> pdb=" O ARG e 476 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU e 482 " --> pdb=" O ARG e 478 " (cutoff:3.500A) Processing helix chain 'e' and resid 498 through 503 Processing helix chain 'e' and resid 508 through 527 Processing helix chain 'a' and resid 14 through 33 removed outlier: 4.167A pdb=" N ARG a 18 " --> pdb=" O GLY a 14 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL a 22 " --> pdb=" O ARG a 18 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE a 31 " --> pdb=" O SER a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 57 through 65 removed outlier: 3.504A pdb=" N ILE a 61 " --> pdb=" O ASP a 57 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU a 62 " --> pdb=" O GLY a 58 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU a 64 " --> pdb=" O THR a 60 " (cutoff:3.500A) Processing helix chain 'a' and resid 69 through 86 removed outlier: 3.701A pdb=" N VAL a 74 " --> pdb=" O PRO a 70 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP a 80 " --> pdb=" O CYS a 76 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP a 83 " --> pdb=" O ALA a 79 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS a 84 " --> pdb=" O ASP a 80 " (cutoff:3.500A) Processing helix chain 'a' and resid 91 through 109 removed outlier: 3.542A pdb=" N ILE a 95 " --> pdb=" O THR a 91 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU a 101 " --> pdb=" O ALA a 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU a 106 " --> pdb=" O LYS a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 133 removed outlier: 3.596A pdb=" N VAL a 117 " --> pdb=" O HIS a 113 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU a 127 " --> pdb=" O LEU a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 157 removed outlier: 3.685A pdb=" N SER a 155 " --> pdb=" O ALA a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 166 through 177 removed outlier: 3.506A pdb=" N VAL a 172 " --> pdb=" O PHE a 168 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA a 175 " --> pdb=" O MET a 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 191 through 195 removed outlier: 3.598A pdb=" N VAL a 195 " --> pdb=" O VAL a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 204 through 208 removed outlier: 3.612A pdb=" N SER a 208 " --> pdb=" O GLN a 205 " (cutoff:3.500A) Processing helix chain 'a' and resid 256 through 258 No H-bonds generated for 'chain 'a' and resid 256 through 258' Processing helix chain 'a' and resid 259 through 278 removed outlier: 3.933A pdb=" N ILE a 263 " --> pdb=" O LYS a 259 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG a 274 " --> pdb=" O ILE a 270 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE a 275 " --> pdb=" O THR a 271 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS a 277 " --> pdb=" O GLU a 273 " (cutoff:3.500A) Processing helix chain 'a' and resid 297 through 304 removed outlier: 3.527A pdb=" N ALA a 303 " --> pdb=" O TYR a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 312 through 324 removed outlier: 3.566A pdb=" N LYS a 317 " --> pdb=" O LYS a 313 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG a 318 " --> pdb=" O ARG a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 345 removed outlier: 3.747A pdb=" N LEU a 345 " --> pdb=" O ALA a 342 " (cutoff:3.500A) Processing helix chain 'a' and resid 381 through 405 removed outlier: 3.600A pdb=" N VAL a 398 " --> pdb=" O ASP a 394 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL a 399 " --> pdb=" O ALA a 395 " (cutoff:3.500A) Processing helix chain 'a' and resid 413 through 430 removed outlier: 3.548A pdb=" N ALA a 418 " --> pdb=" O ALA a 414 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE a 421 " --> pdb=" O ALA a 417 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET a 430 " --> pdb=" O TYR a 426 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 446 Processing helix chain 'a' and resid 446 through 456 removed outlier: 3.629A pdb=" N LEU a 452 " --> pdb=" O ILE a 448 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA a 453 " --> pdb=" O PRO a 449 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL a 454 " --> pdb=" O ASN a 450 " (cutoff:3.500A) Processing helix chain 'a' and resid 462 through 477 removed outlier: 3.813A pdb=" N PHE a 470 " --> pdb=" O LYS a 466 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS a 471 " --> pdb=" O LEU a 467 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU a 473 " --> pdb=" O ALA a 469 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN a 475 " --> pdb=" O HIS a 471 " (cutoff:3.500A) Processing helix chain 'a' and resid 497 through 502 Processing helix chain 'a' and resid 507 through 525 removed outlier: 4.160A pdb=" N SER a 513 " --> pdb=" O VAL a 509 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR a 523 " --> pdb=" O GLU a 519 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE a 524 " --> pdb=" O ALA a 520 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 48 Processing helix chain 'M' and resid 49 through 52 removed outlier: 3.803A pdb=" N LEU M 52 " --> pdb=" O ARG M 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 49 through 52' Processing helix chain 'M' and resid 73 through 82 removed outlier: 3.549A pdb=" N LEU M 78 " --> pdb=" O GLY M 74 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN M 80 " --> pdb=" O THR M 76 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN M 82 " --> pdb=" O LEU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 102 Processing helix chain 'M' and resid 107 through 125 removed outlier: 3.531A pdb=" N ASP M 118 " --> pdb=" O GLY M 114 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR M 121 " --> pdb=" O LEU M 117 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS M 122 " --> pdb=" O ASP M 118 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU M 123 " --> pdb=" O SER M 119 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN M 125 " --> pdb=" O THR M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 152 removed outlier: 3.986A pdb=" N GLU M 146 " --> pdb=" O GLU M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 172 removed outlier: 3.562A pdb=" N LEU M 163 " --> pdb=" O ASP M 159 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER M 170 " --> pdb=" O SER M 166 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU M 171 " --> pdb=" O ALA M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 180 removed outlier: 3.695A pdb=" N SER M 177 " --> pdb=" O LYS M 174 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN M 178 " --> pdb=" O VAL M 175 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER M 180 " --> pdb=" O SER M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 193 removed outlier: 3.564A pdb=" N VAL M 188 " --> pdb=" O SER M 184 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL M 191 " --> pdb=" O SER M 187 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS M 193 " --> pdb=" O ASN M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 206 No H-bonds generated for 'chain 'M' and resid 204 through 206' Processing helix chain 'M' and resid 217 through 221 Processing helix chain 'M' and resid 272 through 292 removed outlier: 3.666A pdb=" N LEU M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU M 278 " --> pdb=" O ARG M 274 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE M 283 " --> pdb=" O GLU M 279 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 320 removed outlier: 3.544A pdb=" N HIS M 315 " --> pdb=" O ASP M 311 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE M 316 " --> pdb=" O LEU M 312 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 340 Processing helix chain 'M' and resid 347 through 351 removed outlier: 3.519A pdb=" N PHE M 351 " --> pdb=" O ILE M 348 " (cutoff:3.500A) Processing helix chain 'M' and resid 352 through 356 Processing helix chain 'M' and resid 394 through 418 removed outlier: 3.731A pdb=" N ILE M 398 " --> pdb=" O ASN M 394 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU M 399 " --> pdb=" O LYS M 395 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL M 411 " --> pdb=" O ASP M 407 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE M 412 " --> pdb=" O ALA M 408 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS M 417 " --> pdb=" O ARG M 413 " (cutoff:3.500A) Processing helix chain 'M' and resid 426 through 442 removed outlier: 3.802A pdb=" N ILE M 430 " --> pdb=" O GLY M 426 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU M 431 " --> pdb=" O ALA M 427 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU M 436 " --> pdb=" O LEU M 432 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR M 437 " --> pdb=" O ALA M 433 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR M 442 " --> pdb=" O GLU M 438 " (cutoff:3.500A) Processing helix chain 'M' and resid 447 through 457 removed outlier: 3.710A pdb=" N ARG M 452 " --> pdb=" O SER M 448 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA M 453 " --> pdb=" O TYR M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 459 through 469 Processing helix chain 'M' and resid 472 through 487 removed outlier: 3.887A pdb=" N VAL M 477 " --> pdb=" O PRO M 473 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR M 478 " --> pdb=" O ILE M 474 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN M 486 " --> pdb=" O ASN M 482 " (cutoff:3.500A) Processing helix chain 'M' and resid 512 through 530 removed outlier: 3.714A pdb=" N ALA M 522 " --> pdb=" O ALA M 518 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER M 528 " --> pdb=" O GLU M 524 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU M 530 " --> pdb=" O VAL M 526 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 37 removed outlier: 3.643A pdb=" N ILE L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 43 removed outlier: 4.068A pdb=" N SER L 41 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU L 43 " --> pdb=" O LYS L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 75 removed outlier: 3.939A pdb=" N ASN L 73 " --> pdb=" O THR L 69 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 95 removed outlier: 4.199A pdb=" N LEU L 84 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 116 removed outlier: 3.518A pdb=" N THR L 103 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 144 removed outlier: 3.645A pdb=" N GLU L 132 " --> pdb=" O ALA L 128 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU L 139 " --> pdb=" O LYS L 135 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA L 140 " --> pdb=" O ALA L 136 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU L 141 " --> pdb=" O ALA L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 167 removed outlier: 3.616A pdb=" N PHE L 155 " --> pdb=" O ASP L 151 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN L 157 " --> pdb=" O VAL L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 170 No H-bonds generated for 'chain 'L' and resid 168 through 170' Processing helix chain 'L' and resid 178 through 189 removed outlier: 3.805A pdb=" N ALA L 186 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL L 187 " --> pdb=" O ALA L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 212 Processing helix chain 'L' and resid 261 through 283 removed outlier: 3.566A pdb=" N ALA L 265 " --> pdb=" O THR L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 284 through 286 No H-bonds generated for 'chain 'L' and resid 284 through 286' Processing helix chain 'L' and resid 297 through 307 removed outlier: 3.879A pdb=" N LEU L 303 " --> pdb=" O TYR L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 318 through 328 removed outlier: 3.542A pdb=" N ARG L 322 " --> pdb=" O ALA L 318 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY L 328 " --> pdb=" O ALA L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 337 through 341 removed outlier: 3.829A pdb=" N VAL L 341 " --> pdb=" O PRO L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 401 removed outlier: 3.602A pdb=" N ARG L 388 " --> pdb=" O ASP L 384 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL L 396 " --> pdb=" O ASP L 392 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 426 removed outlier: 3.702A pdb=" N ASN L 426 " --> pdb=" O THR L 422 " (cutoff:3.500A) Processing helix chain 'L' and resid 429 through 444 removed outlier: 4.207A pdb=" N VAL L 434 " --> pdb=" O GLY L 430 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALA L 435 " --> pdb=" O LYS L 431 " (cutoff:3.500A) Processing helix chain 'L' and resid 444 through 455 removed outlier: 3.644A pdb=" N ILE L 450 " --> pdb=" O LEU L 446 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA L 454 " --> pdb=" O ILE L 450 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY L 455 " --> pdb=" O ALA L 451 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 470 removed outlier: 3.700A pdb=" N VAL L 462 " --> pdb=" O SER L 458 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA L 463 " --> pdb=" O ALA L 459 " (cutoff:3.500A) Processing helix chain 'L' and resid 488 through 492 Processing helix chain 'L' and resid 497 through 516 removed outlier: 3.510A pdb=" N ALA L 507 " --> pdb=" O VAL L 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.866A pdb=" N MET K 44 " --> pdb=" O GLN J 523 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ILE J 525 " --> pdb=" O MET K 44 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N MET K 46 " --> pdb=" O ILE J 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 192 through 195 removed outlier: 6.509A pdb=" N GLU K 192 " --> pdb=" O LEU K 374 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE K 376 " --> pdb=" O GLU K 192 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N MET K 194 " --> pdb=" O ILE K 376 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER K 205 " --> pdb=" O LEU K 375 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 210 through 212 removed outlier: 3.716A pdb=" N LEU K 349 " --> pdb=" O GLU K 364 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY K 348 " --> pdb=" O ASP K 227 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY K 288 " --> pdb=" O ASP K 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 408 through 409 Processing sheet with id=AA5, first strand: chain 'K' and resid 477 through 478 Processing sheet with id=AA6, first strand: chain 'K' and resid 522 through 523 Processing sheet with id=AA7, first strand: chain 'J' and resid 63 through 66 removed outlier: 3.561A pdb=" N THR J 66 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ASN J 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU H 518 " --> pdb=" O ASN J 53 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR H 519 " --> pdb=" O SER H 16 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP H 14 " --> pdb=" O LYS H 521 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 149 through 150 removed outlier: 4.146A pdb=" N CYS J 149 " --> pdb=" O LEU J 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 202 through 208 removed outlier: 6.501A pdb=" N ARG J 203 " --> pdb=" O ILE J 375 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU J 377 " --> pdb=" O ARG J 203 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N CYS J 205 " --> pdb=" O LEU J 377 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLY J 379 " --> pdb=" O CYS J 205 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE J 207 " --> pdb=" O GLY J 379 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 222 through 223 removed outlier: 3.643A pdb=" N VAL J 361 " --> pdb=" O PHE J 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 311 through 314 Processing sheet with id=AB3, first strand: chain 'J' and resid 257 through 259 removed outlier: 6.786A pdb=" N VAL J 257 " --> pdb=" O GLU H 254 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 56 through 59 removed outlier: 7.498A pdb=" N ASP H 46 " --> pdb=" O ASP E 529 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE E 531 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU H 48 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.154A pdb=" N GLY H 196 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU H 374 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS H 198 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLY H 376 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL H 200 " --> pdb=" O GLY H 376 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN H 209 " --> pdb=" O ILE H 373 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 215 through 216 removed outlier: 3.626A pdb=" N PHE H 216 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN H 359 " --> pdb=" O PHE H 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU H 349 " --> pdb=" O PHE H 360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 309 through 311 removed outlier: 5.923A pdb=" N ALA H 238 " --> pdb=" O SER H 290 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLN H 331 " --> pdb=" O ILE H 237 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU H 239 " --> pdb=" O GLN H 331 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 405 through 407 Processing sheet with id=AB9, first strand: chain 'H' and resid 475 through 477 Processing sheet with id=AC1, first strand: chain 'G' and resid 15 through 18 removed outlier: 3.736A pdb=" N SER G 524 " --> pdb=" O LYS G 15 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 17 " --> pdb=" O ILE G 522 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASP A 42 " --> pdb=" O ILE G 519 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP G 521 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY G 525 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AC3, first strand: chain 'G' and resid 184 through 185 removed outlier: 3.540A pdb=" N PHE G 185 " --> pdb=" O GLU G 192 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU G 192 " --> pdb=" O PHE G 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 200 through 205 removed outlier: 3.728A pdb=" N GLY G 378 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS G 213 " --> pdb=" O LEU G 375 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 218 through 220 Processing sheet with id=AC6, first strand: chain 'G' and resid 310 through 312 removed outlier: 6.549A pdb=" N VAL G 290 " --> pdb=" O ILE G 312 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE G 238 " --> pdb=" O GLY G 344 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 255 through 256 removed outlier: 7.758A pdb=" N GLN A 251 " --> pdb=" O ASN I 262 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE I 264 " --> pdb=" O GLN A 251 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL A 253 " --> pdb=" O ILE I 264 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL I 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP I 261 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL B 258 " --> pdb=" O ASP I 261 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN I 263 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU E 264 " --> pdb=" O ARG B 255 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ARG B 257 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 66 through 69 removed outlier: 6.290A pdb=" N ASP E 56 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN B 519 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B 17 " --> pdb=" O LYS B 522 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 207 through 213 removed outlier: 6.669A pdb=" N LYS E 208 " --> pdb=" O ILE E 383 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE E 385 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU E 210 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N GLY E 387 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LYS E 212 " --> pdb=" O GLY E 387 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS E 221 " --> pdb=" O PHE E 384 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 240 through 241 removed outlier: 3.702A pdb=" N GLN E 358 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET E 369 " --> pdb=" O ILE E 360 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 319 through 320 removed outlier: 6.955A pdb=" N ALA E 298 " --> pdb=" O VAL E 320 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 416 through 418 Processing sheet with id=AD4, first strand: chain 'I' and resid 69 through 71 Processing sheet with id=AD5, first strand: chain 'I' and resid 153 through 154 Processing sheet with id=AD6, first strand: chain 'I' and resid 208 through 212 removed outlier: 6.458A pdb=" N LYS I 209 " --> pdb=" O ILE I 388 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL I 390 " --> pdb=" O LYS I 209 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL I 211 " --> pdb=" O VAL I 390 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'I' and resid 240 through 244 removed outlier: 6.581A pdb=" N ARG I 240 " --> pdb=" O GLU I 363 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU I 363 " --> pdb=" O ARG I 240 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLU I 242 " --> pdb=" O LEU I 361 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU I 361 " --> pdb=" O GLU I 242 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU I 363 " --> pdb=" O LYS I 375 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU I 373 " --> pdb=" O VAL I 365 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 246 through 249 removed outlier: 3.704A pdb=" N ASP I 327 " --> pdb=" O ILE I 300 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 491 through 494 Processing sheet with id=AE1, first strand: chain 'I' and resid 532 through 537 removed outlier: 4.675A pdb=" N ILE I 532 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE B 51 " --> pdb=" O ILE I 532 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASP I 534 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU B 53 " --> pdb=" O ASP I 534 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL I 536 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS B 50 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 52 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 199 through 205 removed outlier: 3.668A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 213 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AE4, first strand: chain 'B' and resid 237 through 240 removed outlier: 6.499A pdb=" N PHE B 290 " --> pdb=" O ILE B 312 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 406 through 408 Processing sheet with id=AE6, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AE7, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.793A pdb=" N GLN A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 197 through 201 removed outlier: 6.555A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N GLY A 379 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA A 200 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 213 through 216 removed outlier: 3.989A pdb=" N LEU A 361 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLU A 349 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 234 through 237 removed outlier: 6.247A pdb=" N ILE A 286 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 408 through 410 Processing sheet with id=AF3, first strand: chain 'z' and resid 54 through 57 removed outlier: 6.701A pdb=" N MET z 44 " --> pdb=" O GLN P 523 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE P 525 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N MET z 46 " --> pdb=" O ILE P 525 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'z' and resid 192 through 195 removed outlier: 6.605A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER z 205 " --> pdb=" O LEU z 375 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'z' and resid 210 through 212 removed outlier: 3.616A pdb=" N LEU z 349 " --> pdb=" O GLU z 364 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY z 348 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLY z 288 " --> pdb=" O VAL z 225 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP z 227 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL z 290 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'z' and resid 408 through 409 Processing sheet with id=AF7, first strand: chain 'z' and resid 477 through 478 Processing sheet with id=AF8, first strand: chain 'z' and resid 522 through 523 Processing sheet with id=AF9, first strand: chain 'P' and resid 63 through 66 removed outlier: 3.503A pdb=" N THR P 66 " --> pdb=" O LYS P 54 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASN P 53 " --> pdb=" O VAL O 516 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU O 518 " --> pdb=" O ASN P 53 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR O 519 " --> pdb=" O SER O 16 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER O 16 " --> pdb=" O THR O 519 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS O 521 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP O 14 " --> pdb=" O LYS O 521 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 149 through 150 removed outlier: 4.328A pdb=" N CYS P 149 " --> pdb=" O LEU P 408 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 202 through 208 removed outlier: 3.595A pdb=" N ARG P 203 " --> pdb=" O SER P 373 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY P 379 " --> pdb=" O ILE P 207 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 222 through 223 removed outlier: 3.717A pdb=" N VAL P 361 " --> pdb=" O PHE P 223 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 311 through 314 Processing sheet with id=AG5, first strand: chain 'P' and resid 257 through 259 removed outlier: 6.532A pdb=" N VAL P 257 " --> pdb=" O GLU O 254 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'O' and resid 56 through 59 removed outlier: 7.665A pdb=" N ASP O 46 " --> pdb=" O ASP e 529 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE e 531 " --> pdb=" O ASP O 46 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU O 48 " --> pdb=" O ILE e 531 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 195 through 201 removed outlier: 3.511A pdb=" N GLY O 376 " --> pdb=" O VAL O 200 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 215 through 216 removed outlier: 3.521A pdb=" N PHE O 216 " --> pdb=" O ASN O 359 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU O 349 " --> pdb=" O PHE O 360 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 237 through 240 Processing sheet with id=AH1, first strand: chain 'O' and resid 405 through 407 Processing sheet with id=AH2, first strand: chain 'O' and resid 475 through 477 Processing sheet with id=AH3, first strand: chain 'N' and resid 15 through 18 removed outlier: 3.795A pdb=" N SER N 524 " --> pdb=" O LYS N 15 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU N 17 " --> pdb=" O ILE N 522 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY N 525 " --> pdb=" O VAL a 46 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 142 through 143 Processing sheet with id=AH5, first strand: chain 'N' and resid 184 through 185 Processing sheet with id=AH6, first strand: chain 'N' and resid 199 through 205 removed outlier: 3.582A pdb=" N ARG N 200 " --> pdb=" O CYS N 372 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY N 378 " --> pdb=" O ILE N 204 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR N 373 " --> pdb=" O LEU N 215 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'N' and resid 218 through 220 Processing sheet with id=AH8, first strand: chain 'N' and resid 310 through 312 removed outlier: 6.595A pdb=" N VAL N 290 " --> pdb=" O ILE N 312 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE N 238 " --> pdb=" O GLY N 344 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 255 through 256 removed outlier: 6.724A pdb=" N ASP M 261 " --> pdb=" O VAL L 256 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL L 258 " --> pdb=" O ASP M 261 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN M 263 " --> pdb=" O VAL L 258 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU e 264 " --> pdb=" O ARG L 255 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG L 257 " --> pdb=" O LEU e 264 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'e' and resid 66 through 69 removed outlier: 6.321A pdb=" N ASP e 56 " --> pdb=" O VAL L 517 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN L 519 " --> pdb=" O ASP e 56 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP L 17 " --> pdb=" O LYS L 522 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'e' and resid 207 through 213 removed outlier: 6.582A pdb=" N LYS e 208 " --> pdb=" O ILE e 383 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE e 385 " --> pdb=" O LYS e 208 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU e 210 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLY e 387 " --> pdb=" O GLU e 210 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LYS e 212 " --> pdb=" O GLY e 387 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS e 221 " --> pdb=" O PHE e 384 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'e' and resid 240 through 241 removed outlier: 3.591A pdb=" N GLN e 358 " --> pdb=" O VAL e 371 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET e 369 " --> pdb=" O ILE e 360 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'e' and resid 319 through 320 removed outlier: 6.952A pdb=" N ALA e 298 " --> pdb=" O VAL e 320 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU e 297 " --> pdb=" O LYS e 245 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'e' and resid 416 through 418 Processing sheet with id=AI6, first strand: chain 'a' and resid 10 through 12 removed outlier: 7.213A pdb=" N ASP a 529 " --> pdb=" O MET M 60 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N GLN M 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE a 531 " --> pdb=" O GLN M 62 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'a' and resid 181 through 183 removed outlier: 3.788A pdb=" N GLN a 187 " --> pdb=" O ASP a 183 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'a' and resid 197 through 201 removed outlier: 6.419A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLY a 379 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA a 200 " --> pdb=" O GLY a 379 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'a' and resid 213 through 216 removed outlier: 3.958A pdb=" N LEU a 361 " --> pdb=" O GLU a 354 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU a 349 " --> pdb=" O ASN a 231 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'a' and resid 234 through 237 removed outlier: 6.133A pdb=" N ILE a 286 " --> pdb=" O VAL a 308 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'a' and resid 408 through 410 Processing sheet with id=AJ3, first strand: chain 'M' and resid 153 through 154 Processing sheet with id=AJ4, first strand: chain 'M' and resid 208 through 212 removed outlier: 6.476A pdb=" N LYS M 209 " --> pdb=" O ILE M 388 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL M 390 " --> pdb=" O LYS M 209 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL M 211 " --> pdb=" O VAL M 390 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'M' and resid 240 through 244 removed outlier: 6.516A pdb=" N GLU M 360 " --> pdb=" O LYS M 243 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU M 363 " --> pdb=" O LYS M 375 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU M 373 " --> pdb=" O VAL M 365 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'M' and resid 323 through 328 removed outlier: 3.667A pdb=" N ASP M 327 " --> pdb=" O ILE M 300 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N VAL M 345 " --> pdb=" O ILE M 246 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU M 248 " --> pdb=" O VAL M 345 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'M' and resid 491 through 494 Processing sheet with id=AJ8, first strand: chain 'M' and resid 532 through 537 removed outlier: 4.594A pdb=" N ILE M 532 " --> pdb=" O ASP L 49 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE L 51 " --> pdb=" O ILE M 532 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ASP M 534 " --> pdb=" O ILE L 51 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU L 53 " --> pdb=" O ASP M 534 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL M 536 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS L 50 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR L 64 " --> pdb=" O LYS L 50 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU L 52 " --> pdb=" O MET L 62 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'L' and resid 199 through 205 removed outlier: 3.680A pdb=" N GLY L 377 " --> pdb=" O LYS L 204 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR L 372 " --> pdb=" O ASP L 215 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR L 213 " --> pdb=" O VAL L 374 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'L' and resid 219 through 220 Processing sheet with id=AK2, first strand: chain 'L' and resid 237 through 240 removed outlier: 6.536A pdb=" N PHE L 290 " --> pdb=" O ILE L 312 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'L' and resid 406 through 408 Processing sheet with id=AK4, first strand: chain 'L' and resid 476 through 479 2872 hydrogen bonds defined for protein. 8274 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: 29.26 Time building geometry restraints manager: 14.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 8981 1.24 - 1.38: 14308 1.38 - 1.53: 31314 1.53 - 1.67: 10423 1.67 - 1.81: 706 Bond restraints: 65732 Sorted by residual: bond pdb=" CA THR M 106 " pdb=" C THR M 106 " ideal model delta sigma weight residual 1.523 1.359 0.164 1.34e-02 5.57e+03 1.51e+02 bond pdb=" CA THR I 106 " pdb=" C THR I 106 " ideal model delta sigma weight residual 1.519 1.378 0.141 1.19e-02 7.06e+03 1.40e+02 bond pdb=" CA THR O 94 " pdb=" C THR O 94 " ideal model delta sigma weight residual 1.523 1.366 0.157 1.34e-02 5.57e+03 1.37e+02 bond pdb=" CA ASN P 102 " pdb=" C ASN P 102 " ideal model delta sigma weight residual 1.521 1.376 0.145 1.27e-02 6.20e+03 1.30e+02 bond pdb=" C THR M 106 " pdb=" O THR M 106 " ideal model delta sigma weight residual 1.235 1.097 0.138 1.26e-02 6.30e+03 1.21e+02 ... (remaining 65727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 88324 3.28 - 6.55: 390 6.55 - 9.83: 36 9.83 - 13.10: 10 13.10 - 16.38: 4 Bond angle restraints: 88764 Sorted by residual: angle pdb=" O GLY A 87 " pdb=" C GLY A 87 " pdb=" N ASP A 88 " ideal model delta sigma weight residual 122.77 114.20 8.57 9.40e-01 1.13e+00 8.32e+01 angle pdb=" C GLY M 105 " pdb=" N THR M 106 " pdb=" CA THR M 106 " ideal model delta sigma weight residual 121.54 105.16 16.38 1.91e+00 2.74e-01 7.35e+01 angle pdb=" CA GLY A 87 " pdb=" C GLY A 87 " pdb=" N ASP A 88 " ideal model delta sigma weight residual 117.63 126.48 -8.85 1.17e+00 7.31e-01 5.72e+01 angle pdb=" C GLY O 93 " pdb=" N THR O 94 " pdb=" CA THR O 94 " ideal model delta sigma weight residual 121.54 108.26 13.28 1.91e+00 2.74e-01 4.83e+01 angle pdb=" N ASN P 102 " pdb=" CA ASN P 102 " pdb=" C ASN P 102 " ideal model delta sigma weight residual 113.97 105.73 8.24 1.28e+00 6.10e-01 4.14e+01 ... (remaining 88759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.97: 39833 27.97 - 55.94: 785 55.94 - 83.91: 32 83.91 - 111.88: 6 111.88 - 139.85: 22 Dihedral angle restraints: 40678 sinusoidal: 16386 harmonic: 24292 Sorted by residual: dihedral pdb=" CA THR a 90 " pdb=" C THR a 90 " pdb=" N THR a 91 " pdb=" CA THR a 91 " ideal model delta harmonic sigma weight residual 180.00 124.86 55.14 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" C5' ADP P 601 " pdb=" O5' ADP P 601 " pdb=" PA ADP P 601 " pdb=" O2A ADP P 601 " ideal model delta sinusoidal sigma weight residual -60.00 79.85 -139.85 1 2.00e+01 2.50e-03 4.23e+01 dihedral pdb=" C5' ADP M 601 " pdb=" O5' ADP M 601 " pdb=" PA ADP M 601 " pdb=" O2A ADP M 601 " ideal model delta sinusoidal sigma weight residual -60.00 79.85 -139.85 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 40675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 10580 0.216 - 0.432: 6 0.432 - 0.648: 2 0.648 - 0.864: 3 0.864 - 1.080: 1 Chirality restraints: 10592 Sorted by residual: chirality pdb=" CA THR M 106 " pdb=" N THR M 106 " pdb=" C THR M 106 " pdb=" CB THR M 106 " both_signs ideal model delta sigma weight residual False 2.53 1.45 1.08 2.00e-01 2.50e+01 2.92e+01 chirality pdb=" CA THR I 106 " pdb=" N THR I 106 " pdb=" C THR I 106 " pdb=" CB THR I 106 " both_signs ideal model delta sigma weight residual False 2.53 1.69 0.84 2.00e-01 2.50e+01 1.76e+01 chirality pdb=" CA THR O 94 " pdb=" N THR O 94 " pdb=" C THR O 94 " pdb=" CB THR O 94 " both_signs ideal model delta sigma weight residual False 2.53 1.71 0.82 2.00e-01 2.50e+01 1.66e+01 ... (remaining 10589 not shown) Planarity restraints: 11328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY O 93 " 0.039 2.00e-02 2.50e+03 8.10e-02 6.56e+01 pdb=" C GLY O 93 " -0.140 2.00e-02 2.50e+03 pdb=" O GLY O 93 " 0.054 2.00e-02 2.50e+03 pdb=" N THR O 94 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 105 " 0.033 2.00e-02 2.50e+03 6.81e-02 4.63e+01 pdb=" C GLY M 105 " -0.118 2.00e-02 2.50e+03 pdb=" O GLY M 105 " 0.045 2.00e-02 2.50e+03 pdb=" N THR M 106 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR P 101 " 0.031 2.00e-02 2.50e+03 6.10e-02 3.72e+01 pdb=" C THR P 101 " -0.106 2.00e-02 2.50e+03 pdb=" O THR P 101 " 0.039 2.00e-02 2.50e+03 pdb=" N ASN P 102 " 0.036 2.00e-02 2.50e+03 ... (remaining 11325 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.79: 45 1.79 - 2.57: 763 2.57 - 3.35: 74861 3.35 - 4.12: 156140 4.12 - 4.90: 287600 Nonbonded interactions: 519409 Sorted by model distance: nonbonded pdb=" OD2 ASP e 71 " pdb=" O HOH e 701 " model vdw 1.018 3.040 nonbonded pdb=" OD1 ASP z 90 " pdb="MG MG z 602 " model vdw 1.042 2.170 nonbonded pdb=" OD2 ASP M 73 " pdb=" O HOH M 701 " model vdw 1.056 3.040 nonbonded pdb=" OD1 ASP L 66 " pdb=" F2 AF3 L 603 " model vdw 1.071 2.990 nonbonded pdb=" OG1 THR G 95 " pdb=" F3 AF3 G 603 " model vdw 1.098 2.990 ... (remaining 519404 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 'a' } ncs_group { reference = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'G' selection = chain 'N' } ncs_group { reference = (chain 'H' and resid 1 through 526) selection = (chain 'O' and resid 1 through 526) } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 2.000 Check model and map are aligned: 0.380 Set scattering table: 0.490 Process input model: 122.920 Find NCS groups from input model: 5.160 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 : 0.005 0.261 65732 Z= 0.301 Angle : 0.610 16.380 88764 Z= 0.337 Chirality : 0.047 1.080 10592 Planarity : 0.005 0.081 11328 Dihedral : 10.889 139.846 24942 Min Nonbonded Distance : 1.018 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.88 % Favored : 95.10 % Rotamer: Outliers : 3.50 % Allowed : 5.51 % Favored : 90.99 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.42 % Twisted General : 0.02 % 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: -5.90 (0.06), residues: 8408 helix: -4.90 (0.02), residues: 4004 sheet: -2.17 (0.14), residues: 1024 loop : -2.92 (0.08), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 302 HIS 0.003 0.001 HIS J 80 PHE 0.015 0.001 PHE a 239 TYR 0.008 0.001 TYR G 437 ARG 0.013 0.000 ARG z 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2953 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 2707 time to evaluate : 5.835 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: K 44 MET cc_start: 0.8132 (mmm) cc_final: 0.7703 (mmt) REVERT: K 63 LEU cc_start: 0.8158 (mt) cc_final: 0.7948 (mp) REVERT: K 157 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7861 (mtt180) REVERT: K 250 TYR cc_start: 0.8371 (p90) cc_final: 0.8086 (p90) REVERT: J 321 LEU cc_start: 0.8742 (tp) cc_final: 0.8527 (tp) REVERT: J 418 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7427 (mm-30) REVERT: J 426 TYR cc_start: 0.6019 (m-80) cc_final: 0.5818 (m-80) REVERT: J 463 VAL cc_start: 0.8458 (t) cc_final: 0.8215 (t) REVERT: H 16 SER cc_start: 0.7510 (t) cc_final: 0.7193 (m) REVERT: H 29 CYS cc_start: 0.6893 (m) cc_final: 0.6689 (m) REVERT: H 279 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6367 (mm-30) REVERT: H 323 MET cc_start: 0.7843 (ttp) cc_final: 0.7638 (ttm) REVERT: H 481 ASN cc_start: 0.6669 (m-40) cc_final: 0.6262 (m-40) REVERT: G 130 LEU cc_start: 0.8977 (tp) cc_final: 0.8766 (tp) REVERT: G 278 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7964 (mt) REVERT: G 331 ILE cc_start: 0.8575 (mt) cc_final: 0.8075 (mt) REVERT: G 416 MET cc_start: 0.8047 (mmp) cc_final: 0.7653 (mmm) REVERT: E 360 ILE cc_start: 0.7417 (mm) cc_final: 0.7153 (tp) REVERT: E 369 MET cc_start: 0.5659 (mmm) cc_final: 0.5382 (mmt) REVERT: E 392 ILE cc_start: 0.8932 (tp) cc_final: 0.8662 (tp) REVERT: E 447 ARG cc_start: 0.7739 (mtt-85) cc_final: 0.7524 (mtt-85) REVERT: I 28 ASP cc_start: 0.4827 (OUTLIER) cc_final: 0.4626 (t70) REVERT: I 42 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7036 (mmmt) REVERT: I 67 ASP cc_start: 0.6974 (t70) cc_final: 0.6739 (t70) REVERT: I 397 VAL cc_start: 0.8890 (t) cc_final: 0.8663 (p) REVERT: B 50 LYS cc_start: 0.8320 (mttm) cc_final: 0.7921 (mttp) REVERT: B 208 SER cc_start: 0.8263 (p) cc_final: 0.8046 (p) REVERT: B 415 MET cc_start: 0.8650 (mmm) cc_final: 0.8383 (mmm) REVERT: B 445 MET cc_start: 0.8053 (mmm) cc_final: 0.7805 (mmt) REVERT: A 54 ILE cc_start: 0.8455 (mt) cc_final: 0.8140 (mt) REVERT: A 55 THR cc_start: 0.8704 (t) cc_final: 0.8245 (p) REVERT: z 79 LYS cc_start: 0.7777 (mttt) cc_final: 0.7544 (mmtm) REVERT: z 385 THR cc_start: 0.6983 (p) cc_final: 0.6698 (p) REVERT: z 389 ASP cc_start: 0.6567 (m-30) cc_final: 0.6348 (m-30) REVERT: z 520 GLU cc_start: 0.5997 (OUTLIER) cc_final: 0.5678 (tt0) REVERT: P 71 THR cc_start: 0.8426 (p) cc_final: 0.7638 (m) REVERT: P 117 GLU cc_start: 0.6055 (mt-10) cc_final: 0.5836 (mt-10) REVERT: P 173 TYR cc_start: 0.8370 (t80) cc_final: 0.7734 (t80) REVERT: P 311 MET cc_start: 0.7866 (ttp) cc_final: 0.7461 (ttm) REVERT: P 461 ASN cc_start: 0.7002 (m-40) cc_final: 0.6696 (m110) REVERT: P 506 TRP cc_start: 0.8177 (m100) cc_final: 0.7975 (m100) REVERT: O 382 MET cc_start: 0.7929 (mtm) cc_final: 0.7535 (mtm) REVERT: N 50 LEU cc_start: 0.8942 (mt) cc_final: 0.8613 (mp) REVERT: N 88 ASP cc_start: 0.6188 (t70) cc_final: 0.5969 (t0) REVERT: N 460 ILE cc_start: 0.7906 (mm) cc_final: 0.7446 (mm) REVERT: a 20 GLN cc_start: 0.7716 (mt0) cc_final: 0.7508 (mt0) REVERT: a 30 ASN cc_start: 0.8334 (m-40) cc_final: 0.8067 (m-40) REVERT: a 244 THR cc_start: 0.7441 (m) cc_final: 0.7094 (t) REVERT: a 534 HIS cc_start: 0.7340 (m-70) cc_final: 0.7002 (m-70) REVERT: M 312 LEU cc_start: 0.8214 (tp) cc_final: 0.7895 (tt) REVERT: L 365 VAL cc_start: 0.8379 (m) cc_final: 0.7946 (m) outliers start: 246 outliers final: 47 residues processed: 2850 average time/residue: 0.6643 time to fit residues: 3062.2447 Evaluate side-chains 1427 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1375 time to evaluate : 5.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain G residue 12 GLN Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 42 LYS Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 292 ILE Chi-restraints excluded: chain z residue 477 VAL Chi-restraints excluded: chain z residue 520 GLU Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 251 THR Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 389 LEU Chi-restraints excluded: chain O residue 516 VAL Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 522 VAL Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 64 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 705 optimal weight: 10.0000 chunk 633 optimal weight: 0.9990 chunk 351 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 427 optimal weight: 0.8980 chunk 338 optimal weight: 6.9990 chunk 655 optimal weight: 5.9990 chunk 253 optimal weight: 0.8980 chunk 398 optimal weight: 0.9980 chunk 487 optimal weight: 7.9990 chunk 759 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 214 HIS K 368 ASN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN J 79 GLN J 219 HIS J 279 GLN J 303 HIS J 306 ASN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 523 GLN H 30 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 GLN H 201 GLN H 234 ASN H 283 HIS H 301 GLN H 331 GLN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN H 470 GLN G 64 ASN G 226 HIS G 390 ASN G 442 GLN G 454 ASN E 20 GLN E 137 GLN ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN E 377 ASN E 493 HIS E 501 GLN I 129 HIS I 263 GLN I 394 ASN I 486 GLN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS A 251 GLN A 284 ASN A 492 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 37 ASN ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 105 GLN z 293 ASN z 294 GLN z 346 HIS z 497 ASN ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN P 41 GLN P 303 HIS P 422 GLN ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 GLN O 21 GLN O 117 HIS O 264 GLN O 501 ASN N 73 GLN ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 GLN N 390 ASN ** e 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN a 251 GLN a 284 ASN a 482 ASN a 498 ASN M 82 GLN M 347 HIS M 486 GLN L 73 ASN L 148 HIS L 502 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 65732 Z= 0.243 Angle : 0.681 14.531 88764 Z= 0.343 Chirality : 0.045 0.254 10592 Planarity : 0.005 0.069 11328 Dihedral : 7.938 160.568 9230 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.25 % Allowed : 14.07 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.36 (0.08), residues: 8408 helix: -2.14 (0.06), residues: 4096 sheet: -1.64 (0.16), residues: 984 loop : -2.32 (0.09), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 506 HIS 0.016 0.001 HIS H 283 PHE 0.019 0.001 PHE O 216 TYR 0.023 0.001 TYR z 353 ARG 0.008 0.001 ARG G 518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1675 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1446 time to evaluate : 6.640 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: K 63 LEU cc_start: 0.8595 (mt) cc_final: 0.8308 (mp) REVERT: K 399 LYS cc_start: 0.8750 (tmmt) cc_final: 0.8307 (tttm) REVERT: K 520 GLU cc_start: 0.7118 (tp30) cc_final: 0.6889 (tp30) REVERT: J 446 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: H 16 SER cc_start: 0.8430 (t) cc_final: 0.8015 (m) REVERT: H 394 MET cc_start: 0.8017 (mmm) cc_final: 0.7817 (mmm) REVERT: G 52 ASP cc_start: 0.6652 (m-30) cc_final: 0.6313 (m-30) REVERT: G 168 TRP cc_start: 0.8397 (m-90) cc_final: 0.8178 (m-90) REVERT: G 331 ILE cc_start: 0.8572 (mt) cc_final: 0.8109 (mt) REVERT: E 237 MET cc_start: 0.7771 (tpp) cc_final: 0.6556 (mmt) REVERT: I 42 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7151 (tptm) REVERT: B 62 MET cc_start: 0.7743 (tmm) cc_final: 0.7399 (ppp) REVERT: A 201 HIS cc_start: 0.7253 (p-80) cc_final: 0.6642 (p90) REVERT: A 295 MET cc_start: 0.7745 (tmm) cc_final: 0.7472 (ttp) REVERT: z 44 MET cc_start: 0.7438 (mmm) cc_final: 0.7083 (mtp) REVERT: z 56 LEU cc_start: 0.8636 (tp) cc_final: 0.8378 (tp) REVERT: z 442 ASP cc_start: 0.7453 (m-30) cc_final: 0.6948 (m-30) REVERT: z 520 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.6056 (tm-30) REVERT: z 522 MET cc_start: 0.7832 (ptt) cc_final: 0.7396 (ptt) REVERT: P 71 THR cc_start: 0.8457 (p) cc_final: 0.8241 (t) REVERT: P 169 MET cc_start: 0.7832 (ptp) cc_final: 0.7616 (ptm) REVERT: P 173 TYR cc_start: 0.8563 (t80) cc_final: 0.7811 (t80) REVERT: P 311 MET cc_start: 0.8023 (ttp) cc_final: 0.7598 (ttm) REVERT: P 385 MET cc_start: 0.8147 (mtm) cc_final: 0.7947 (mtm) REVERT: O 78 THR cc_start: 0.8972 (m) cc_final: 0.8710 (m) REVERT: O 382 MET cc_start: 0.7941 (mtm) cc_final: 0.7719 (mtp) REVERT: O 414 MET cc_start: 0.7524 (mmm) cc_final: 0.7299 (mmm) REVERT: N 88 ASP cc_start: 0.7204 (t70) cc_final: 0.6803 (t0) REVERT: N 395 MET cc_start: 0.8221 (mtm) cc_final: 0.7988 (mtm) REVERT: N 506 TYR cc_start: 0.8447 (m-10) cc_final: 0.8053 (m-10) REVERT: e 292 GLU cc_start: 0.7091 (pp20) cc_final: 0.6865 (pp20) REVERT: e 418 TYR cc_start: 0.7886 (m-80) cc_final: 0.7624 (m-80) REVERT: a 44 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7461 (mtp) REVERT: a 271 THR cc_start: 0.7088 (m) cc_final: 0.6710 (p) REVERT: a 534 HIS cc_start: 0.7314 (m-70) cc_final: 0.7081 (m-70) REVERT: M 400 GLU cc_start: 0.7423 (tp30) cc_final: 0.6360 (tp30) REVERT: M 403 ARG cc_start: 0.7360 (mtm110) cc_final: 0.6497 (mtm110) REVERT: M 530 LEU cc_start: 0.8597 (mt) cc_final: 0.8277 (mt) REVERT: L 481 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6382 (ptp-110) outliers start: 229 outliers final: 126 residues processed: 1603 average time/residue: 0.6422 time to fit residues: 1725.6461 Evaluate side-chains 1227 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1096 time to evaluate : 5.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 324 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain J residue 359 GLN Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 446 GLU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 243 GLU Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 382 MET Chi-restraints excluded: chain G residue 226 HIS Chi-restraints excluded: chain G residue 263 ASP Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain I residue 42 LYS Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 235 ASN Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 447 GLU Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 504 LEU Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 108 LEU Chi-restraints excluded: chain z residue 176 ILE Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 435 LEU Chi-restraints excluded: chain z residue 506 HIS Chi-restraints excluded: chain z residue 520 GLU Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 191 PHE Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 253 THR Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 373 SER Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain O residue 17 GLN Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 178 MET Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 400 ILE Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain O residue 516 VAL Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 57 ILE Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 388 GLU Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 163 LEU Chi-restraints excluded: chain e residue 179 CYS Chi-restraints excluded: chain e residue 217 LEU Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 250 THR Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 399 SER Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 355 ARG Chi-restraints excluded: chain a residue 376 ILE Chi-restraints excluded: chain a residue 447 VAL Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 125 GLN Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 336 ILE Chi-restraints excluded: chain M residue 374 LEU Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 474 THR Chi-restraints excluded: chain L residue 481 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 421 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 631 optimal weight: 4.9990 chunk 516 optimal weight: 0.9980 chunk 209 optimal weight: 0.3980 chunk 760 optimal weight: 0.7980 chunk 821 optimal weight: 7.9990 chunk 677 optimal weight: 0.9980 chunk 754 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 610 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 293 ASN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 506 HIS J 41 GLN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 GLN H 359 ASN ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN E 433 GLN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN A 500 GLN z 65 HIS z 245 ASN P 34 GLN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 501 ASN e 180 HIS ** e 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN ** e 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 501 GLN e 514 GLN a 56 ASN a 251 GLN M 25 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 65732 Z= 0.193 Angle : 0.621 26.920 88764 Z= 0.304 Chirality : 0.043 0.221 10592 Planarity : 0.004 0.054 11328 Dihedral : 7.395 159.903 9187 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.98 % Allowed : 15.77 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.92 (0.09), residues: 8408 helix: -0.57 (0.08), residues: 4128 sheet: -1.40 (0.16), residues: 1020 loop : -2.05 (0.10), residues: 3260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 506 HIS 0.007 0.001 HIS E 262 PHE 0.015 0.001 PHE O 216 TYR 0.018 0.001 TYR M 282 ARG 0.014 0.001 ARG L 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1398 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1188 time to evaluate : 6.032 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: K 399 LYS cc_start: 0.8629 (tmmt) cc_final: 0.8188 (tttp) REVERT: J 76 LEU cc_start: 0.8746 (mt) cc_final: 0.8478 (mp) REVERT: H 17 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: H 77 LYS cc_start: 0.8644 (mttt) cc_final: 0.8255 (mtpp) REVERT: H 394 MET cc_start: 0.8102 (mmm) cc_final: 0.7889 (mmm) REVERT: G 242 ASP cc_start: 0.7049 (m-30) cc_final: 0.6816 (m-30) REVERT: G 331 ILE cc_start: 0.8493 (mt) cc_final: 0.8240 (mt) REVERT: E 288 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: E 451 ASP cc_start: 0.7894 (m-30) cc_final: 0.7676 (m-30) REVERT: E 503 HIS cc_start: 0.7791 (m-70) cc_final: 0.7511 (m-70) REVERT: I 323 MET cc_start: 0.8143 (ttm) cc_final: 0.7816 (mtp) REVERT: A 295 MET cc_start: 0.7733 (tmm) cc_final: 0.7499 (ttp) REVERT: z 44 MET cc_start: 0.7352 (mmm) cc_final: 0.6991 (mtp) REVERT: z 56 LEU cc_start: 0.8543 (tp) cc_final: 0.8286 (tp) REVERT: z 442 ASP cc_start: 0.7344 (m-30) cc_final: 0.6755 (m-30) REVERT: P 163 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8399 (tt) REVERT: P 169 MET cc_start: 0.7850 (ptp) cc_final: 0.7609 (ptm) REVERT: P 296 LYS cc_start: 0.7992 (tppt) cc_final: 0.7787 (tptt) REVERT: P 311 MET cc_start: 0.7987 (ttp) cc_final: 0.7675 (ttm) REVERT: P 521 VAL cc_start: 0.8723 (t) cc_final: 0.8514 (m) REVERT: O 78 THR cc_start: 0.9029 (m) cc_final: 0.8732 (m) REVERT: O 382 MET cc_start: 0.8055 (mtm) cc_final: 0.7708 (mtp) REVERT: O 432 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7543 (tp40) REVERT: N 47 MET cc_start: 0.7859 (mmm) cc_final: 0.7647 (mmm) REVERT: N 88 ASP cc_start: 0.7559 (t70) cc_final: 0.7285 (t0) REVERT: N 362 PHE cc_start: 0.8354 (m-80) cc_final: 0.8052 (m-10) REVERT: e 129 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8532 (mp) REVERT: a 271 THR cc_start: 0.7128 (m) cc_final: 0.6653 (p) REVERT: a 534 HIS cc_start: 0.7226 (m-70) cc_final: 0.6981 (m-70) REVERT: M 312 LEU cc_start: 0.8834 (tp) cc_final: 0.8574 (tp) REVERT: M 530 LEU cc_start: 0.8533 (mt) cc_final: 0.8301 (mt) REVERT: L 60 SER cc_start: 0.8106 (m) cc_final: 0.7693 (p) outliers start: 210 outliers final: 138 residues processed: 1337 average time/residue: 0.6031 time to fit residues: 1387.6869 Evaluate side-chains 1164 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1021 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 324 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 382 MET Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 263 ASP Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 235 ASN Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 65 HIS Chi-restraints excluded: chain z residue 108 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 176 ILE Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 391 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 435 LEU Chi-restraints excluded: chain z residue 506 HIS Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 163 LEU Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 253 THR Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 400 ILE Chi-restraints excluded: chain O residue 432 GLN Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain O residue 516 VAL Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 388 GLU Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 129 ILE Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 170 THR Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 251 CYS Chi-restraints excluded: chain e residue 264 LEU Chi-restraints excluded: chain e residue 330 LEU Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain a residue 56 ASN Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 355 ARG Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 125 GLN Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 336 ILE Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 534 ASP Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 333 SER Chi-restraints excluded: chain L residue 346 CYS Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 474 THR Chi-restraints excluded: chain L residue 480 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 751 optimal weight: 4.9990 chunk 571 optimal weight: 4.9990 chunk 394 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 362 optimal weight: 0.8980 chunk 510 optimal weight: 0.9990 chunk 763 optimal weight: 0.9990 chunk 808 optimal weight: 9.9990 chunk 398 optimal weight: 8.9990 chunk 723 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 ASN K 386 GLN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 503 GLN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 GLN ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 320 ASN P 34 GLN ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 GLN O 448 GLN O 501 ASN O 522 ASN N 302 HIS N 400 ASN ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN ** e 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 501 GLN M 484 HIS L 73 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 65732 Z= 0.179 Angle : 0.601 27.377 88764 Z= 0.292 Chirality : 0.043 0.236 10592 Planarity : 0.003 0.049 11328 Dihedral : 7.131 159.138 9174 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.01 % Allowed : 16.67 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.13 (0.09), residues: 8408 helix: 0.23 (0.08), residues: 4128 sheet: -1.22 (0.16), residues: 976 loop : -1.82 (0.10), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 435 HIS 0.021 0.001 HIS z 65 PHE 0.027 0.001 PHE P 445 TYR 0.020 0.001 TYR K 239 ARG 0.008 0.000 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1315 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1103 time to evaluate : 5.923 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: K 399 LYS cc_start: 0.8709 (tmmt) cc_final: 0.8246 (tttp) REVERT: J 138 LYS cc_start: 0.6728 (mttt) cc_final: 0.6477 (tttt) REVERT: J 302 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8503 (tt) REVERT: H 77 LYS cc_start: 0.8659 (mttt) cc_final: 0.8304 (mtpp) REVERT: H 394 MET cc_start: 0.8173 (mmm) cc_final: 0.7946 (mmm) REVERT: G 331 ILE cc_start: 0.8608 (mt) cc_final: 0.8264 (mt) REVERT: G 511 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: E 288 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: E 503 HIS cc_start: 0.7796 (m-70) cc_final: 0.7497 (m-70) REVERT: I 323 MET cc_start: 0.8164 (ttm) cc_final: 0.7797 (mtp) REVERT: B 432 GLU cc_start: 0.6357 (mp0) cc_final: 0.6006 (mp0) REVERT: z 44 MET cc_start: 0.7399 (mmm) cc_final: 0.7066 (mtp) REVERT: z 56 LEU cc_start: 0.8573 (tp) cc_final: 0.8349 (tp) REVERT: z 442 ASP cc_start: 0.7320 (m-30) cc_final: 0.6697 (m-30) REVERT: P 61 GLU cc_start: 0.6563 (mp0) cc_final: 0.6330 (mp0) REVERT: P 196 HIS cc_start: 0.6193 (m-70) cc_final: 0.5908 (m170) REVERT: O 78 THR cc_start: 0.8994 (m) cc_final: 0.8721 (m) REVERT: O 382 MET cc_start: 0.8028 (mtm) cc_final: 0.7712 (mtp) REVERT: O 432 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7623 (tp40) REVERT: O 442 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8778 (mp) REVERT: N 47 MET cc_start: 0.7802 (mmm) cc_final: 0.7550 (mmm) REVERT: N 88 ASP cc_start: 0.7570 (t70) cc_final: 0.7156 (t70) REVERT: N 429 MET cc_start: 0.8074 (mmm) cc_final: 0.7855 (mmt) REVERT: e 129 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8599 (mp) REVERT: a 271 THR cc_start: 0.7187 (m) cc_final: 0.6681 (p) REVERT: a 295 MET cc_start: 0.7773 (tmm) cc_final: 0.7539 (tmm) REVERT: a 309 ARG cc_start: 0.8124 (ptt180) cc_final: 0.7874 (ptm160) REVERT: a 534 HIS cc_start: 0.7349 (m-70) cc_final: 0.7131 (m-70) REVERT: M 312 LEU cc_start: 0.8862 (tp) cc_final: 0.8613 (tp) REVERT: L 49 ASP cc_start: 0.7584 (m-30) cc_final: 0.7276 (m-30) REVERT: L 60 SER cc_start: 0.8222 (m) cc_final: 0.7819 (p) outliers start: 212 outliers final: 138 residues processed: 1246 average time/residue: 0.5827 time to fit residues: 1252.4676 Evaluate side-chains 1142 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 998 time to evaluate : 5.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 324 LEU Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 479 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 382 MET Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 511 GLU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 235 ASN Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 108 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 176 ILE Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 506 HIS Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 251 THR Chi-restraints excluded: chain P residue 253 THR Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain O residue 17 GLN Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 323 MET Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 432 GLN Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain O residue 516 VAL Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 195 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 521 ASP Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 129 ILE Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 264 LEU Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 330 LEU Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 399 SER Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 56 ASN Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 149 ILE Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 355 ARG Chi-restraints excluded: chain a residue 523 THR Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 336 ILE Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 333 SER Chi-restraints excluded: chain L residue 346 CYS Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 379 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 673 optimal weight: 0.9980 chunk 458 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 601 optimal weight: 0.0970 chunk 333 optimal weight: 9.9990 chunk 689 optimal weight: 0.8980 chunk 558 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 412 optimal weight: 6.9990 chunk 725 optimal weight: 4.9990 chunk 203 optimal weight: 0.9980 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 382 HIS ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN z 161 HIS P 34 GLN P 80 HIS P 102 ASN ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 GLN O 151 GLN O 233 HIS O 501 ASN ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN ** e 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 520 GLN a 56 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 65732 Z= 0.190 Angle : 0.596 11.552 88764 Z= 0.289 Chirality : 0.043 0.231 10592 Planarity : 0.003 0.042 11328 Dihedral : 7.012 159.137 9171 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.11 % Allowed : 17.15 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -0.68 (0.09), residues: 8408 helix: 0.69 (0.08), residues: 4152 sheet: -1.07 (0.16), residues: 996 loop : -1.71 (0.10), residues: 3260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 506 HIS 0.006 0.001 HIS E 262 PHE 0.016 0.001 PHE E 232 TYR 0.019 0.001 TYR z 351 ARG 0.010 0.000 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1046 time to evaluate : 5.878 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: K 44 MET cc_start: 0.7758 (mtt) cc_final: 0.7555 (mtt) REVERT: K 399 LYS cc_start: 0.8718 (tmmt) cc_final: 0.8251 (tttp) REVERT: J 121 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7624 (tp) REVERT: J 302 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8563 (tt) REVERT: H 17 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: H 394 MET cc_start: 0.8116 (mmm) cc_final: 0.7896 (mmm) REVERT: G 511 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: E 78 MET cc_start: 0.7920 (mtp) cc_final: 0.7683 (mtm) REVERT: E 458 MET cc_start: 0.8134 (mtm) cc_final: 0.7894 (mtm) REVERT: I 70 ILE cc_start: 0.8370 (mp) cc_final: 0.8168 (mp) REVERT: I 323 MET cc_start: 0.8188 (ttm) cc_final: 0.7778 (mtp) REVERT: B 432 GLU cc_start: 0.6380 (mp0) cc_final: 0.6030 (mp0) REVERT: A 44 MET cc_start: 0.8324 (mtm) cc_final: 0.8050 (mtm) REVERT: z 44 MET cc_start: 0.7584 (mmm) cc_final: 0.7209 (mtp) REVERT: z 442 ASP cc_start: 0.7336 (m-30) cc_final: 0.6722 (m-30) REVERT: P 196 HIS cc_start: 0.6035 (m-70) cc_final: 0.5759 (m170) REVERT: P 461 ASN cc_start: 0.7523 (m-40) cc_final: 0.7179 (m110) REVERT: P 521 VAL cc_start: 0.8785 (t) cc_final: 0.8535 (m) REVERT: O 1 MET cc_start: 0.6014 (ptm) cc_final: 0.5664 (ttp) REVERT: O 78 THR cc_start: 0.9047 (m) cc_final: 0.8772 (m) REVERT: O 382 MET cc_start: 0.8003 (mtm) cc_final: 0.7729 (mtp) REVERT: O 432 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7882 (tp40) REVERT: O 442 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8777 (mp) REVERT: N 305 MET cc_start: 0.7775 (mmm) cc_final: 0.7271 (mmm) REVERT: N 350 LEU cc_start: 0.8137 (tt) cc_final: 0.7904 (tt) REVERT: N 429 MET cc_start: 0.8116 (mmm) cc_final: 0.7914 (mmt) REVERT: a 271 THR cc_start: 0.7290 (m) cc_final: 0.7076 (p) REVERT: a 295 MET cc_start: 0.7756 (tmm) cc_final: 0.7556 (tmm) REVERT: a 309 ARG cc_start: 0.8174 (ptt180) cc_final: 0.7944 (ptm160) REVERT: a 534 HIS cc_start: 0.7426 (m-70) cc_final: 0.7144 (m-70) REVERT: M 96 LYS cc_start: 0.8049 (ttpt) cc_final: 0.7817 (mtpt) REVERT: L 49 ASP cc_start: 0.7565 (m-30) cc_final: 0.7288 (m-30) REVERT: L 60 SER cc_start: 0.8416 (m) cc_final: 0.8062 (p) REVERT: L 239 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8109 (mp) outliers start: 219 outliers final: 156 residues processed: 1194 average time/residue: 0.5682 time to fit residues: 1180.4687 Evaluate side-chains 1119 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 956 time to evaluate : 5.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 324 LEU Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 479 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 511 GLU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 466 MET Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 90 MET Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 235 ASN Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 108 LEU Chi-restraints excluded: chain z residue 134 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 176 ILE Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 391 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 499 CYS Chi-restraints excluded: chain z residue 506 HIS Chi-restraints excluded: chain z residue 508 CYS Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 117 GLU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 221 MET Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 251 THR Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 380 SER Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain O residue 17 GLN Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 323 MET Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 432 GLN Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain O residue 516 VAL Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 521 ASP Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 170 THR Chi-restraints excluded: chain e residue 179 CYS Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 251 CYS Chi-restraints excluded: chain e residue 264 LEU Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 330 LEU Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain a residue 16 THR Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 149 ILE Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 184 SER Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 336 ILE Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 333 SER Chi-restraints excluded: chain L residue 346 CYS Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 379 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 271 optimal weight: 5.9990 chunk 727 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 474 optimal weight: 0.0980 chunk 199 optimal weight: 1.9990 chunk 808 optimal weight: 0.0980 chunk 671 optimal weight: 0.8980 chunk 374 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 chunk 267 optimal weight: 5.9990 chunk 424 optimal weight: 6.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 154 ASN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN A 135 ASN ** z 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 HIS N 64 ASN ** e 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN ** e 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 65732 Z= 0.152 Angle : 0.590 24.510 88764 Z= 0.284 Chirality : 0.042 0.243 10592 Planarity : 0.003 0.043 11328 Dihedral : 6.814 157.209 9169 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.63 % Allowed : 17.92 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -0.34 (0.09), residues: 8408 helix: 1.01 (0.08), residues: 4144 sheet: -1.00 (0.16), residues: 976 loop : -1.58 (0.10), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 506 HIS 0.006 0.001 HIS E 262 PHE 0.015 0.001 PHE O 216 TYR 0.017 0.001 TYR z 351 ARG 0.007 0.000 ARG G 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1077 time to evaluate : 6.115 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: K 393 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.6697 (t0) REVERT: K 399 LYS cc_start: 0.8709 (tmmt) cc_final: 0.8234 (tttp) REVERT: J 121 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7574 (tp) REVERT: J 302 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8552 (tt) REVERT: H 17 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: H 394 MET cc_start: 0.8060 (mmm) cc_final: 0.7855 (mmm) REVERT: G 242 ASP cc_start: 0.7191 (m-30) cc_final: 0.6815 (m-30) REVERT: G 511 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: E 78 MET cc_start: 0.7873 (mtp) cc_final: 0.7636 (mtm) REVERT: E 313 LEU cc_start: 0.7881 (mp) cc_final: 0.7435 (mp) REVERT: E 458 MET cc_start: 0.8031 (mtm) cc_final: 0.7805 (mtm) REVERT: I 70 ILE cc_start: 0.8387 (mp) cc_final: 0.8174 (mp) REVERT: I 323 MET cc_start: 0.8198 (ttm) cc_final: 0.7801 (mtp) REVERT: B 432 GLU cc_start: 0.6359 (mp0) cc_final: 0.6007 (mp0) REVERT: A 30 ASN cc_start: 0.7830 (m-40) cc_final: 0.7583 (m110) REVERT: A 31 ILE cc_start: 0.8537 (mt) cc_final: 0.8230 (mt) REVERT: z 44 MET cc_start: 0.7388 (mmm) cc_final: 0.7131 (mtp) REVERT: z 442 ASP cc_start: 0.7188 (m-30) cc_final: 0.6551 (m-30) REVERT: P 196 HIS cc_start: 0.5980 (m-70) cc_final: 0.5720 (m170) REVERT: O 1 MET cc_start: 0.5793 (ptm) cc_final: 0.5525 (ttp) REVERT: O 78 THR cc_start: 0.9012 (m) cc_final: 0.8763 (m) REVERT: O 87 ASP cc_start: 0.7311 (t0) cc_final: 0.7019 (t0) REVERT: O 382 MET cc_start: 0.7919 (mtm) cc_final: 0.7688 (mtp) REVERT: O 432 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7926 (tp40) REVERT: O 442 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8746 (mp) REVERT: O 518 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6499 (mt-10) REVERT: N 88 ASP cc_start: 0.7419 (t0) cc_final: 0.7116 (t0) REVERT: N 305 MET cc_start: 0.7737 (mmm) cc_final: 0.7243 (mmm) REVERT: N 429 MET cc_start: 0.8122 (mmm) cc_final: 0.7891 (mmt) REVERT: e 78 MET cc_start: 0.7943 (mtp) cc_final: 0.7687 (mtt) REVERT: e 521 MET cc_start: 0.7281 (mmm) cc_final: 0.6757 (tpp) REVERT: a 295 MET cc_start: 0.7753 (tmm) cc_final: 0.7547 (tmm) REVERT: a 534 HIS cc_start: 0.7410 (m-70) cc_final: 0.7131 (m-70) REVERT: L 49 ASP cc_start: 0.7553 (m-30) cc_final: 0.7264 (m-30) REVERT: L 60 SER cc_start: 0.8371 (m) cc_final: 0.8039 (p) outliers start: 185 outliers final: 134 residues processed: 1205 average time/residue: 0.6360 time to fit residues: 1342.2651 Evaluate side-chains 1115 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 974 time to evaluate : 6.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 479 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 452 ILE Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 511 GLU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 261 LYS Chi-restraints excluded: chain E residue 262 HIS Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 466 MET Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 108 LEU Chi-restraints excluded: chain z residue 134 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 176 ILE Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 391 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 506 HIS Chi-restraints excluded: chain z residue 508 CYS Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 221 MET Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain P residue 498 LEU Chi-restraints excluded: chain O residue 16 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 323 MET Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 432 GLN Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 521 ASP Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 179 CYS Chi-restraints excluded: chain e residue 251 CYS Chi-restraints excluded: chain e residue 264 LEU Chi-restraints excluded: chain e residue 330 LEU Chi-restraints excluded: chain e residue 371 VAL Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 399 SER Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 149 ILE Chi-restraints excluded: chain a residue 218 CYS Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 187 SER Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 534 ASP Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 224 ILE Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 333 SER Chi-restraints excluded: chain L residue 346 CYS Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 379 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 779 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 460 optimal weight: 0.6980 chunk 590 optimal weight: 8.9990 chunk 457 optimal weight: 2.9990 chunk 680 optimal weight: 7.9990 chunk 451 optimal weight: 0.9980 chunk 805 optimal weight: 0.9990 chunk 504 optimal weight: 4.9990 chunk 491 optimal weight: 4.9990 chunk 372 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 ASN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 504 GLN E 53 ASN ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 HIS ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN ** e 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 65732 Z= 0.216 Angle : 0.617 21.439 88764 Z= 0.298 Chirality : 0.043 0.221 10592 Planarity : 0.003 0.044 11328 Dihedral : 6.842 159.052 9164 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.04 % Allowed : 17.93 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.17 (0.09), residues: 8408 helix: 1.14 (0.08), residues: 4166 sheet: -0.89 (0.16), residues: 1056 loop : -1.52 (0.11), residues: 3186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 435 HIS 0.006 0.001 HIS z 198 PHE 0.018 0.001 PHE K 362 TYR 0.019 0.001 TYR M 269 ARG 0.011 0.000 ARG M 496 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 986 time to evaluate : 5.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 393 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.6916 (t0) REVERT: K 399 LYS cc_start: 0.8739 (tmmt) cc_final: 0.8317 (tttp) REVERT: J 117 GLU cc_start: 0.7588 (mp0) cc_final: 0.7148 (pm20) REVERT: J 121 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7580 (tp) REVERT: J 302 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8685 (tt) REVERT: H 34 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6537 (mm-30) REVERT: H 359 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7961 (m-40) REVERT: H 394 MET cc_start: 0.8099 (mmm) cc_final: 0.7880 (mmm) REVERT: G 31 LYS cc_start: 0.7776 (mttt) cc_final: 0.7476 (mtpp) REVERT: G 382 GLU cc_start: 0.6827 (mp0) cc_final: 0.6569 (mp0) REVERT: G 511 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: E 458 MET cc_start: 0.8115 (mtm) cc_final: 0.7877 (mtm) REVERT: I 323 MET cc_start: 0.8216 (ttm) cc_final: 0.7805 (mtp) REVERT: B 208 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.7949 (t) REVERT: B 349 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9038 (mm) REVERT: B 432 GLU cc_start: 0.6414 (mp0) cc_final: 0.6086 (mp0) REVERT: A 31 ILE cc_start: 0.8626 (mt) cc_final: 0.8360 (mt) REVERT: A 214 TYR cc_start: 0.8323 (t80) cc_final: 0.8102 (t80) REVERT: A 225 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8226 (mtm) REVERT: z 44 MET cc_start: 0.7444 (mmm) cc_final: 0.7176 (mtp) REVERT: z 442 ASP cc_start: 0.7316 (m-30) cc_final: 0.6708 (m-30) REVERT: P 41 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6841 (mt0) REVERT: P 196 HIS cc_start: 0.6049 (m-70) cc_final: 0.5780 (m170) REVERT: P 521 VAL cc_start: 0.8899 (t) cc_final: 0.8686 (m) REVERT: O 1 MET cc_start: 0.6055 (ptm) cc_final: 0.5799 (ttp) REVERT: O 87 ASP cc_start: 0.7352 (t0) cc_final: 0.7088 (t0) REVERT: O 382 MET cc_start: 0.8002 (mtm) cc_final: 0.7748 (mtp) REVERT: O 432 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7997 (tp40) REVERT: O 442 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8748 (mp) REVERT: N 88 ASP cc_start: 0.7411 (t0) cc_final: 0.7134 (t0) REVERT: N 305 MET cc_start: 0.7869 (mmm) cc_final: 0.7442 (mmm) REVERT: N 429 MET cc_start: 0.8161 (mmm) cc_final: 0.7952 (mmt) REVERT: e 78 MET cc_start: 0.7962 (mtp) cc_final: 0.7710 (mtt) REVERT: a 534 HIS cc_start: 0.7534 (m-70) cc_final: 0.7245 (m-70) REVERT: L 49 ASP cc_start: 0.7568 (m-30) cc_final: 0.7311 (m-30) outliers start: 214 outliers final: 157 residues processed: 1130 average time/residue: 0.5758 time to fit residues: 1132.0923 Evaluate side-chains 1105 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 937 time to evaluate : 5.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 479 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 499 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 452 ILE Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 511 GLU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 HIS Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 466 MET Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 235 ASN Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 108 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 324 LEU Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 391 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 506 HIS Chi-restraints excluded: chain z residue 508 CYS Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 221 MET Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 323 MET Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 432 GLN Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 521 ASP Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 27 MET Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 170 THR Chi-restraints excluded: chain e residue 179 CYS Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 251 CYS Chi-restraints excluded: chain e residue 264 LEU Chi-restraints excluded: chain e residue 312 LEU Chi-restraints excluded: chain e residue 330 LEU Chi-restraints excluded: chain e residue 371 VAL Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 399 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 149 ILE Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 508 ILE Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 184 SER Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 394 ASN Chi-restraints excluded: chain M residue 429 GLU Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 333 SER Chi-restraints excluded: chain L residue 346 CYS Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 379 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 498 optimal weight: 0.7980 chunk 321 optimal weight: 0.8980 chunk 481 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 chunk 512 optimal weight: 0.3980 chunk 548 optimal weight: 7.9990 chunk 398 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 633 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 GLN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN A 30 ASN z 214 HIS P 34 GLN ** P 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 HIS ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN ** e 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 65732 Z= 0.180 Angle : 0.608 18.875 88764 Z= 0.293 Chirality : 0.043 0.225 10592 Planarity : 0.003 0.040 11328 Dihedral : 6.619 157.834 9162 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.73 % Allowed : 18.67 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -0.00 (0.09), residues: 8408 helix: 1.29 (0.08), residues: 4156 sheet: -0.88 (0.16), residues: 1040 loop : -1.42 (0.11), residues: 3212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 506 HIS 0.005 0.001 HIS e 262 PHE 0.015 0.001 PHE O 216 TYR 0.022 0.001 TYR z 353 ARG 0.009 0.000 ARG M 496 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 989 time to evaluate : 5.956 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: K 393 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.6928 (t0) REVERT: K 399 LYS cc_start: 0.8731 (tmmt) cc_final: 0.8320 (tttp) REVERT: J 121 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7647 (tp) REVERT: H 34 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6622 (mm-30) REVERT: H 394 MET cc_start: 0.8068 (mmm) cc_final: 0.7851 (mmm) REVERT: G 31 LYS cc_start: 0.7777 (mttt) cc_final: 0.7528 (mtpp) REVERT: G 382 GLU cc_start: 0.6901 (mp0) cc_final: 0.6666 (mp0) REVERT: G 511 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: I 323 MET cc_start: 0.8216 (ttm) cc_final: 0.7799 (mtp) REVERT: B 432 GLU cc_start: 0.6475 (mp0) cc_final: 0.6093 (mp0) REVERT: A 31 ILE cc_start: 0.8668 (mt) cc_final: 0.8410 (mt) REVERT: A 225 MET cc_start: 0.8535 (ptp) cc_final: 0.8208 (mtm) REVERT: A 344 MET cc_start: 0.7100 (ppp) cc_final: 0.6182 (ppp) REVERT: z 44 MET cc_start: 0.7490 (mmm) cc_final: 0.7238 (mtp) REVERT: z 442 ASP cc_start: 0.7314 (m-30) cc_final: 0.6789 (m-30) REVERT: P 41 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6828 (mt0) REVERT: P 196 HIS cc_start: 0.6147 (m-70) cc_final: 0.5898 (m170) REVERT: P 521 VAL cc_start: 0.8943 (t) cc_final: 0.8683 (m) REVERT: O 87 ASP cc_start: 0.7350 (t0) cc_final: 0.7108 (t0) REVERT: O 382 MET cc_start: 0.7986 (mtm) cc_final: 0.7740 (mtp) REVERT: O 432 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7996 (tp40) REVERT: O 442 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8708 (mp) REVERT: N 88 ASP cc_start: 0.7406 (t0) cc_final: 0.7111 (t0) REVERT: N 305 MET cc_start: 0.7867 (mmm) cc_final: 0.7439 (mmm) REVERT: N 429 MET cc_start: 0.8153 (mmm) cc_final: 0.7952 (mmt) REVERT: a 534 HIS cc_start: 0.7535 (m-70) cc_final: 0.7250 (m-70) REVERT: L 49 ASP cc_start: 0.7551 (m-30) cc_final: 0.7318 (m-30) outliers start: 192 outliers final: 156 residues processed: 1120 average time/residue: 0.5619 time to fit residues: 1097.3911 Evaluate side-chains 1098 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 936 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 479 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 452 ILE Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 511 GLU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 HIS Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 466 MET Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 235 ASN Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 373 LEU Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 108 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 324 LEU Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 391 VAL Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 506 HIS Chi-restraints excluded: chain z residue 508 CYS Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 221 MET Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 323 MET Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 432 GLN Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 521 ASP Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 27 MET Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 179 CYS Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 251 CYS Chi-restraints excluded: chain e residue 264 LEU Chi-restraints excluded: chain e residue 312 LEU Chi-restraints excluded: chain e residue 330 LEU Chi-restraints excluded: chain e residue 371 VAL Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 399 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 149 ILE Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 508 ILE Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 184 SER Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 265 VAL Chi-restraints excluded: chain M residue 336 ILE Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 534 ASP Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 333 SER Chi-restraints excluded: chain L residue 346 CYS Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 379 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 732 optimal weight: 4.9990 chunk 771 optimal weight: 1.9990 chunk 704 optimal weight: 4.9990 chunk 750 optimal weight: 4.9990 chunk 451 optimal weight: 3.9990 chunk 327 optimal weight: 0.9980 chunk 589 optimal weight: 0.7980 chunk 230 optimal weight: 7.9990 chunk 678 optimal weight: 5.9990 chunk 710 optimal weight: 0.9990 chunk 748 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 HIS ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN ** e 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 65732 Z= 0.188 Angle : 0.613 18.614 88764 Z= 0.296 Chirality : 0.043 0.225 10592 Planarity : 0.003 0.040 11328 Dihedral : 6.566 157.634 9162 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.64 % Allowed : 18.84 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.10 (0.09), residues: 8408 helix: 1.39 (0.08), residues: 4144 sheet: -0.80 (0.16), residues: 1100 loop : -1.39 (0.11), residues: 3164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 506 HIS 0.011 0.001 HIS e 262 PHE 0.014 0.001 PHE O 216 TYR 0.028 0.001 TYR K 353 ARG 0.009 0.000 ARG M 496 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 971 time to evaluate : 5.924 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: K 393 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.6950 (t0) REVERT: K 399 LYS cc_start: 0.8743 (tmmt) cc_final: 0.8337 (tttp) REVERT: J 121 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7526 (tp) REVERT: J 443 GLU cc_start: 0.6967 (tp30) cc_final: 0.6426 (tp30) REVERT: H 394 MET cc_start: 0.8077 (mmm) cc_final: 0.7848 (mmm) REVERT: G 31 LYS cc_start: 0.7866 (mttt) cc_final: 0.7567 (mtpp) REVERT: G 382 GLU cc_start: 0.6885 (mp0) cc_final: 0.6650 (mp0) REVERT: G 511 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: I 323 MET cc_start: 0.8203 (ttm) cc_final: 0.7773 (mtp) REVERT: B 432 GLU cc_start: 0.6397 (mp0) cc_final: 0.6081 (mp0) REVERT: A 31 ILE cc_start: 0.8697 (mt) cc_final: 0.8447 (mt) REVERT: A 225 MET cc_start: 0.8530 (ptp) cc_final: 0.8208 (mtm) REVERT: A 344 MET cc_start: 0.7191 (ppp) cc_final: 0.6827 (ppp) REVERT: z 44 MET cc_start: 0.7533 (mmm) cc_final: 0.7250 (mtp) REVERT: z 442 ASP cc_start: 0.7303 (m-30) cc_final: 0.6782 (m-30) REVERT: P 41 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6846 (mt0) REVERT: P 196 HIS cc_start: 0.6152 (m-70) cc_final: 0.5906 (m170) REVERT: O 382 MET cc_start: 0.7995 (mtm) cc_final: 0.7749 (mtp) REVERT: O 432 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7992 (tp40) REVERT: O 442 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8719 (mp) REVERT: N 88 ASP cc_start: 0.7503 (t0) cc_final: 0.7140 (t0) REVERT: N 305 MET cc_start: 0.7871 (mmm) cc_final: 0.7431 (mmm) REVERT: a 534 HIS cc_start: 0.7567 (m-70) cc_final: 0.7297 (m-70) REVERT: L 49 ASP cc_start: 0.7577 (m-30) cc_final: 0.7345 (m-30) outliers start: 186 outliers final: 157 residues processed: 1098 average time/residue: 0.5878 time to fit residues: 1128.7660 Evaluate side-chains 1099 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 936 time to evaluate : 5.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 479 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 433 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 360 PHE Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 452 ILE Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 511 GLU Chi-restraints excluded: chain E residue 27 MET Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 HIS Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 472 MET Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 235 ASN Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 373 LEU Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 108 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 324 LEU Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 391 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 506 HIS Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 221 MET Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 308 MET Chi-restraints excluded: chain O residue 323 MET Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 432 GLN Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 375 LEU Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 521 ASP Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 27 MET Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 179 CYS Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 251 CYS Chi-restraints excluded: chain e residue 264 LEU Chi-restraints excluded: chain e residue 312 LEU Chi-restraints excluded: chain e residue 330 LEU Chi-restraints excluded: chain e residue 371 VAL Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 399 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 149 ILE Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 508 ILE Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 184 SER Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 265 VAL Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 534 ASP Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 333 SER Chi-restraints excluded: chain L residue 346 CYS Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 379 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 493 optimal weight: 1.9990 chunk 794 optimal weight: 0.8980 chunk 484 optimal weight: 9.9990 chunk 376 optimal weight: 2.9990 chunk 551 optimal weight: 1.9990 chunk 832 optimal weight: 1.9990 chunk 766 optimal weight: 8.9990 chunk 663 optimal weight: 0.3980 chunk 68 optimal weight: 7.9990 chunk 512 optimal weight: 3.9990 chunk 406 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 ASN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 301 GLN ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 HIS ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN ** e 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 139 ASN L 73 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 65732 Z= 0.199 Angle : 0.624 15.889 88764 Z= 0.302 Chirality : 0.043 0.275 10592 Planarity : 0.003 0.040 11328 Dihedral : 6.576 157.908 9162 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.47 % Allowed : 19.27 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.14 (0.09), residues: 8408 helix: 1.40 (0.08), residues: 4168 sheet: -0.75 (0.16), residues: 1088 loop : -1.37 (0.11), residues: 3152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 474 HIS 0.013 0.001 HIS e 262 PHE 0.014 0.001 PHE O 216 TYR 0.027 0.001 TYR K 353 ARG 0.009 0.000 ARG M 496 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16816 Ramachandran restraints generated. 8408 Oldfield, 0 Emsley, 8408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 971 time to evaluate : 5.928 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: K 393 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.6865 (t0) REVERT: K 399 LYS cc_start: 0.8754 (tmmt) cc_final: 0.8347 (tttp) REVERT: J 121 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7525 (tp) REVERT: H 292 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7653 (ptpt) REVERT: H 394 MET cc_start: 0.8084 (mmm) cc_final: 0.7844 (mmm) REVERT: G 31 LYS cc_start: 0.7878 (mttt) cc_final: 0.7561 (mtpp) REVERT: G 382 GLU cc_start: 0.6880 (mp0) cc_final: 0.6659 (mp0) REVERT: G 511 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: I 260 MET cc_start: 0.8287 (ptm) cc_final: 0.7849 (ptp) REVERT: I 323 MET cc_start: 0.8204 (ttm) cc_final: 0.7780 (mtp) REVERT: B 208 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.7925 (t) REVERT: B 432 GLU cc_start: 0.6484 (mp0) cc_final: 0.6115 (mp0) REVERT: A 31 ILE cc_start: 0.8732 (mt) cc_final: 0.8483 (mt) REVERT: A 225 MET cc_start: 0.8572 (ptp) cc_final: 0.8237 (mtm) REVERT: z 44 MET cc_start: 0.7547 (mmm) cc_final: 0.7227 (mtp) REVERT: z 442 ASP cc_start: 0.7332 (m-30) cc_final: 0.6801 (m-30) REVERT: P 41 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6883 (mt0) REVERT: P 196 HIS cc_start: 0.6357 (m-70) cc_final: 0.6108 (m170) REVERT: O 382 MET cc_start: 0.7998 (mtm) cc_final: 0.7760 (mtp) REVERT: O 432 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7958 (tp40) REVERT: O 442 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8715 (mp) REVERT: N 88 ASP cc_start: 0.7501 (t0) cc_final: 0.7125 (t0) REVERT: N 305 MET cc_start: 0.7865 (mmm) cc_final: 0.7449 (mmm) REVERT: e 176 VAL cc_start: 0.8870 (m) cc_final: 0.8523 (t) REVERT: a 534 HIS cc_start: 0.7556 (m-70) cc_final: 0.7310 (m-70) REVERT: L 49 ASP cc_start: 0.7584 (m-30) cc_final: 0.7354 (m-30) outliers start: 174 outliers final: 150 residues processed: 1091 average time/residue: 0.5686 time to fit residues: 1079.2641 Evaluate side-chains 1094 residues out of total 7042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 936 time to evaluate : 5.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 352 GLU Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 479 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 11 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 297 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 433 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 292 LYS Chi-restraints excluded: chain H residue 359 ASN Chi-restraints excluded: chain H residue 360 PHE Chi-restraints excluded: chain H residue 395 ILE Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 452 ILE Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 511 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 262 HIS Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 235 ASN Chi-restraints excluded: chain I residue 304 ILE Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 373 LEU Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 503 ILE Chi-restraints excluded: chain I residue 535 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain z residue 63 LEU Chi-restraints excluded: chain z residue 108 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 324 LEU Chi-restraints excluded: chain z residue 333 LEU Chi-restraints excluded: chain z residue 391 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain z residue 463 LEU Chi-restraints excluded: chain z residue 506 HIS Chi-restraints excluded: chain P residue 11 PHE Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 113 GLU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain P residue 221 MET Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 297 VAL Chi-restraints excluded: chain P residue 302 LEU Chi-restraints excluded: chain P residue 415 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 323 MET Chi-restraints excluded: chain O residue 364 CYS Chi-restraints excluded: chain O residue 395 ILE Chi-restraints excluded: chain O residue 432 GLN Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain N residue 144 VAL Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 285 LEU Chi-restraints excluded: chain N residue 383 ILE Chi-restraints excluded: chain N residue 459 THR Chi-restraints excluded: chain N residue 521 ASP Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain e residue 27 MET Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 154 LEU Chi-restraints excluded: chain e residue 179 CYS Chi-restraints excluded: chain e residue 226 VAL Chi-restraints excluded: chain e residue 251 CYS Chi-restraints excluded: chain e residue 264 LEU Chi-restraints excluded: chain e residue 312 LEU Chi-restraints excluded: chain e residue 330 LEU Chi-restraints excluded: chain e residue 371 VAL Chi-restraints excluded: chain e residue 375 CYS Chi-restraints excluded: chain e residue 393 ILE Chi-restraints excluded: chain e residue 399 SER Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 149 ILE Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 237 LEU Chi-restraints excluded: chain a residue 352 VAL Chi-restraints excluded: chain a residue 508 ILE Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 162 THR Chi-restraints excluded: chain M residue 184 SER Chi-restraints excluded: chain M residue 203 VAL Chi-restraints excluded: chain M residue 265 VAL Chi-restraints excluded: chain M residue 503 ILE Chi-restraints excluded: chain M residue 534 ASP Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain L residue 261 THR Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 333 SER Chi-restraints excluded: chain L residue 346 CYS Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 379 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 836 random chunks: chunk 526 optimal weight: 7.9990 chunk 706 optimal weight: 0.5980 chunk 203 optimal weight: 0.0030 chunk 611 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 664 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 682 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** P 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 HIS ** e 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 377 ASN L 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.093163 restraints weight = 123715.035| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.71 r_work: 0.3107 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 65732 Z= 0.205 Angle : 0.632 17.070 88764 Z= 0.306 Chirality : 0.044 0.299 10592 Planarity : 0.003 0.039 11328 Dihedral : 6.584 158.002 9162 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.42 % Allowed : 19.51 % Favored : 78.08 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.19 (0.09), residues: 8408 helix: 1.43 (0.08), residues: 4170 sheet: -0.76 (0.16), residues: 1084 loop : -1.32 (0.11), residues: 3154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 302 HIS 0.013 0.001 HIS G 226 PHE 0.015 0.001 PHE E 232 TYR 0.026 0.001 TYR K 353 ARG 0.012 0.000 ARG E 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20301.96 seconds wall clock time: 351 minutes 21.68 seconds (21081.68 seconds total)