Starting phenix.real_space_refine on Fri Sep 27 20:01:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unf_26623/09_2024/7unf_26623.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unf_26623/09_2024/7unf_26623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unf_26623/09_2024/7unf_26623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unf_26623/09_2024/7unf_26623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unf_26623/09_2024/7unf_26623.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unf_26623/09_2024/7unf_26623.cif" } resolution = 4.08 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= 0.004 sd= 1.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 368 5.16 5 C 42729 2.51 5 N 11339 2.21 5 O 12524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 467 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: 66971 Number of models: 1 Model: "" Number of chains: 40 Chain: "a" Number of atoms: 6127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6127 Classifications: {'peptide': 752} Link IDs: {'PTRANS': 25, 'TRANS': 726} Chain breaks: 3 Chain: "U" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3365 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain breaks: 1 Chain: "L" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "M" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "N" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "O" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "P" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "Q" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "D" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1717 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain: "b" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1809 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain: "c" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1782 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain: "d" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1817 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain: "e" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 938 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "f" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 938 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "g" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 923 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 856 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "C" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 1770 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 323} Link IDs: {'PTRANS': 9, 'TRANS': 346} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1187 Unresolved non-hydrogen angles: 1517 Unresolved non-hydrogen dihedrals: 993 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 14, 'TYR:plan': 15, 'ASN:plan1': 23, 'TRP:plan': 6, 'HIS:plan': 6, 'PHE:plan': 14, 'GLU:plan': 25, 'ASP:plan': 24} Unresolved non-hydrogen planarities: 640 Chain: "H" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 2111 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 383} Link IDs: {'PTRANS': 9, 'TRANS': 415} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1448 Unresolved non-hydrogen angles: 1843 Unresolved non-hydrogen dihedrals: 1223 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 33, 'HIS:plan': 10, 'TYR:plan': 17, 'ASN:plan1': 20, 'TRP:plan': 8, 'ASP:plan': 18, 'PHE:plan': 17, 'GLU:plan': 38, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 851 Chain: "k" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2836 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain: "m" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 621 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain: "n" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 658 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "s" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1662 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "r" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 377 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "8" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "9" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "1" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1498 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 5, 'TRANS': 198} Chain: "2" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "3" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "4" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "5" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "6" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "7" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "0" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "t" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'GLC': 2, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "w" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 173 Unusual residues: {'NAG': 6, 'POV': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 6 Chain: "r" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 142 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "1" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 123 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Time building chain proxies: 28.81, per 1000 atoms: 0.43 Number of scatterers: 66971 At special positions: 0 Unit cell: (251.758, 177.662, 244.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 368 16.00 P 11 15.00 O 12524 8.00 N 11339 7.00 C 42729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS s 371 " - pdb=" SG CYS s 418 " distance=2.05 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=1, symmetry=0 Links applied ALPHA1-2 " MAN t 4 " - " MAN t 5 " " MAN t 5 " - " MAN t 6 " ALPHA1-3 " BMA t 3 " - " MAN t 4 " " MAN t 6 " - " GLC t 7 " " GLC t 7 " - " GLC t 8 " ALPHA1-6 " MAN w 1 " - " MAN w 2 " BETA1-4 " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " NAG-ASN " NAG s 501 " - " ASN s 273 " " NAG s 502 " - " ASN s 296 " " NAG s 503 " - " ASN s 303 " " NAG s 504 " - " ASN s 350 " " NAG s 505 " - " ASN s 357 " " NAG s 506 " - " ASN s 261 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.57 Conformation dependent library (CDL) restraints added in 6.9 seconds 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16326 Finding SS restraints... Secondary structure from input PDB file: 350 helices and 50 sheets defined 55.5% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.29 Creating SS restraints... Processing helix chain 'a' and resid 19 through 23 removed outlier: 3.731A pdb=" N ALA a 22 " --> pdb=" O VAL a 19 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR a 23 " --> pdb=" O GLU a 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 19 through 23' Processing helix chain 'a' and resid 26 through 31 Processing helix chain 'a' and resid 51 through 74 removed outlier: 3.503A pdb=" N ARG a 56 " --> pdb=" O VAL a 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS a 58 " --> pdb=" O GLU a 54 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU a 61 " --> pdb=" O ARG a 57 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP a 70 " --> pdb=" O ARG a 66 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU a 71 " --> pdb=" O PHE a 67 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN a 74 " --> pdb=" O ASP a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 139 removed outlier: 3.710A pdb=" N ILE a 94 " --> pdb=" O PRO a 90 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR a 95 " --> pdb=" O ARG a 91 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU a 96 " --> pdb=" O GLU a 92 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR a 98 " --> pdb=" O ILE a 94 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL a 99 " --> pdb=" O THR a 95 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS a 102 " --> pdb=" O THR a 98 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU a 107 " --> pdb=" O LEU a 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN a 112 " --> pdb=" O GLN a 108 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN a 115 " --> pdb=" O ASN a 111 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU a 126 " --> pdb=" O LEU a 122 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS a 128 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR a 129 " --> pdb=" O THR a 125 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP a 136 " --> pdb=" O LYS a 132 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 183 removed outlier: 3.804A pdb=" N MET a 182 " --> pdb=" O ARG a 179 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 194 removed outlier: 3.601A pdb=" N LEU a 188 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU a 189 " --> pdb=" O PHE a 185 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TRP a 190 " --> pdb=" O GLU a 186 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE a 192 " --> pdb=" O LEU a 188 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS a 193 " --> pdb=" O LEU a 189 " (cutoff:3.500A) Processing helix chain 'a' and resid 234 through 239 removed outlier: 3.832A pdb=" N LYS a 237 " --> pdb=" O LYS a 234 " (cutoff:3.500A) Processing helix chain 'a' and resid 252 through 289 removed outlier: 3.529A pdb=" N ILE a 271 " --> pdb=" O LEU a 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR a 272 " --> pdb=" O GLU a 268 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER a 279 " --> pdb=" O THR a 275 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS a 280 " --> pdb=" O GLN a 276 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU a 284 " --> pdb=" O HIS a 280 " (cutoff:3.500A) Processing helix chain 'a' and resid 292 through 312 removed outlier: 3.776A pdb=" N LEU a 296 " --> pdb=" O TRP a 292 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE a 297 " --> pdb=" O HIS a 293 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS a 298 " --> pdb=" O SER a 294 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN a 310 " --> pdb=" O TYR a 306 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET a 311 " --> pdb=" O HIS a 307 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS a 312 " --> pdb=" O ILE a 308 " (cutoff:3.500A) Processing helix chain 'a' and resid 331 through 345 removed outlier: 3.503A pdb=" N ILE a 335 " --> pdb=" O ASP a 331 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS a 336 " --> pdb=" O ALA a 332 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA a 338 " --> pdb=" O ARG a 334 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET a 343 " --> pdb=" O LEU a 339 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU a 344 " --> pdb=" O GLU a 340 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU a 345 " --> pdb=" O GLN a 341 " (cutoff:3.500A) Processing helix chain 'a' and resid 373 through 382 removed outlier: 3.734A pdb=" N ILE a 379 " --> pdb=" O GLY a 375 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL a 380 " --> pdb=" O PHE a 376 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 409 removed outlier: 3.756A pdb=" N MET a 408 " --> pdb=" O LEU a 404 " (cutoff:3.500A) Processing helix chain 'a' and resid 411 through 428 removed outlier: 3.757A pdb=" N VAL a 417 " --> pdb=" O GLY a 413 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET a 425 " --> pdb=" O ALA a 421 " (cutoff:3.500A) Processing helix chain 'a' and resid 428 through 435 removed outlier: 3.558A pdb=" N LEU a 432 " --> pdb=" O ASN a 428 " (cutoff:3.500A) Processing helix chain 'a' and resid 439 through 448 removed outlier: 3.552A pdb=" N HIS a 447 " --> pdb=" O ASN a 443 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY a 448 " --> pdb=" O THR a 444 " (cutoff:3.500A) Processing helix chain 'a' and resid 448 through 466 removed outlier: 3.689A pdb=" N LEU a 454 " --> pdb=" O TYR a 450 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER a 459 " --> pdb=" O MET a 455 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE a 460 " --> pdb=" O GLY a 456 " (cutoff:3.500A) Processing helix chain 'a' and resid 483 through 489 removed outlier: 3.865A pdb=" N PHE a 487 " --> pdb=" O VAL a 483 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN a 489 " --> pdb=" O PRO a 485 " (cutoff:3.500A) Processing helix chain 'a' and resid 493 through 500 removed outlier: 3.516A pdb=" N MET a 497 " --> pdb=" O ASN a 493 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU a 498 " --> pdb=" O THR a 494 " (cutoff:3.500A) Processing helix chain 'a' and resid 531 through 567 removed outlier: 3.660A pdb=" N PHE a 535 " --> pdb=" O ASN a 531 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN a 537 " --> pdb=" O LEU a 533 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER a 538 " --> pdb=" O THR a 534 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS a 542 " --> pdb=" O SER a 538 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL a 545 " --> pdb=" O MET a 541 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN a 551 " --> pdb=" O LEU a 547 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL a 556 " --> pdb=" O MET a 552 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER a 559 " --> pdb=" O GLY a 555 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS a 563 " --> pdb=" O SER a 559 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR a 565 " --> pdb=" O PHE a 561 " (cutoff:3.500A) Processing helix chain 'a' and resid 568 through 575 removed outlier: 3.761A pdb=" N ILE a 572 " --> pdb=" O ARG a 568 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE a 573 " --> pdb=" O THR a 569 " (cutoff:3.500A) Processing helix chain 'a' and resid 578 through 586 removed outlier: 4.182A pdb=" N LEU a 584 " --> pdb=" O MET a 580 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU a 586 " --> pdb=" O PHE a 582 " (cutoff:3.500A) Processing helix chain 'a' and resid 586 through 600 removed outlier: 3.636A pdb=" N VAL a 591 " --> pdb=" O PHE a 587 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS a 597 " --> pdb=" O MET a 593 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS a 599 " --> pdb=" O ILE a 595 " (cutoff:3.500A) Processing helix chain 'a' and resid 602 through 609 removed outlier: 5.110A pdb=" N GLN a 607 " --> pdb=" O HIS a 604 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA a 609 " --> pdb=" O SER a 606 " (cutoff:3.500A) Processing helix chain 'a' and resid 611 through 622 removed outlier: 3.888A pdb=" N PHE a 620 " --> pdb=" O PHE a 616 " (cutoff:3.500A) Processing helix chain 'a' and resid 635 through 656 removed outlier: 3.863A pdb=" N VAL a 639 " --> pdb=" O HIS a 635 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE a 642 " --> pdb=" O GLU a 638 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE a 643 " --> pdb=" O VAL a 639 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL a 645 " --> pdb=" O SER a 641 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER a 650 " --> pdb=" O MET a 646 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL a 651 " --> pdb=" O ALA a 647 " (cutoff:3.500A) Proline residue: a 652 - end of helix removed outlier: 3.520A pdb=" N LEU a 655 " --> pdb=" O VAL a 651 " (cutoff:3.500A) Processing helix chain 'a' and resid 656 through 668 removed outlier: 3.880A pdb=" N PHE a 660 " --> pdb=" O LEU a 656 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS a 668 " --> pdb=" O ALA a 664 " (cutoff:3.500A) Processing helix chain 'a' and resid 716 through 731 removed outlier: 3.901A pdb=" N HIS a 722 " --> pdb=" O ASP a 718 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN a 723 " --> pdb=" O VAL a 719 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE a 728 " --> pdb=" O ALA a 724 " (cutoff:3.500A) Processing helix chain 'a' and resid 732 through 740 removed outlier: 3.567A pdb=" N SER a 736 " --> pdb=" O LEU a 732 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR a 738 " --> pdb=" O CYS a 734 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA a 739 " --> pdb=" O ILE a 735 " (cutoff:3.500A) Processing helix chain 'a' and resid 742 through 762 removed outlier: 3.971A pdb=" N SER a 748 " --> pdb=" O LEU a 744 " (cutoff:3.500A) Processing helix chain 'a' and resid 762 through 767 Processing helix chain 'a' and resid 773 through 792 removed outlier: 3.695A pdb=" N GLY a 777 " --> pdb=" O GLY a 773 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE a 781 " --> pdb=" O GLY a 777 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA a 783 " --> pdb=" O PHE a 779 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL a 790 " --> pdb=" O ALA a 786 " (cutoff:3.500A) Processing helix chain 'a' and resid 795 through 811 removed outlier: 3.814A pdb=" N LEU a 808 " --> pdb=" O HIS a 804 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS a 809 " --> pdb=" O ALA a 805 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 32 removed outlier: 3.520A pdb=" N ASP U 25 " --> pdb=" O GLN U 21 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN U 26 " --> pdb=" O ALA U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 51 Processing helix chain 'U' and resid 59 through 69 removed outlier: 4.094A pdb=" N VAL U 63 " --> pdb=" O PRO U 59 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR U 64 " --> pdb=" O PRO U 60 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG U 65 " --> pdb=" O GLU U 61 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP U 68 " --> pdb=" O THR U 64 " (cutoff:3.500A) Processing helix chain 'U' and resid 88 through 93 removed outlier: 3.612A pdb=" N ALA U 93 " --> pdb=" O GLU U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 99 Processing helix chain 'U' and resid 102 through 107 removed outlier: 3.583A pdb=" N SER U 107 " --> pdb=" O SER U 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 114 removed outlier: 3.647A pdb=" N ILE U 114 " --> pdb=" O ILE U 110 " (cutoff:3.500A) Processing helix chain 'U' and resid 123 through 135 removed outlier: 3.859A pdb=" N LYS U 128 " --> pdb=" O ARG U 124 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU U 131 " --> pdb=" O GLN U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 135 through 144 removed outlier: 4.162A pdb=" N HIS U 139 " --> pdb=" O GLY U 135 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU U 141 " --> pdb=" O VAL U 137 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 172 removed outlier: 3.930A pdb=" N GLN U 163 " --> pdb=" O ASN U 159 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL U 164 " --> pdb=" O PRO U 160 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU U 165 " --> pdb=" O ARG U 161 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP U 172 " --> pdb=" O GLN U 168 " (cutoff:3.500A) Processing helix chain 'U' and resid 182 through 186 removed outlier: 4.095A pdb=" N GLN U 185 " --> pdb=" O LEU U 182 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TRP U 186 " --> pdb=" O GLY U 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 182 through 186' Processing helix chain 'U' and resid 195 through 203 removed outlier: 3.627A pdb=" N VAL U 200 " --> pdb=" O ILE U 196 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE U 201 " --> pdb=" O GLU U 197 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL U 203 " --> pdb=" O TRP U 199 " (cutoff:3.500A) Processing helix chain 'U' and resid 203 through 213 removed outlier: 4.466A pdb=" N ALA U 207 " --> pdb=" O VAL U 203 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER U 211 " --> pdb=" O ALA U 207 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL U 213 " --> pdb=" O PHE U 209 " (cutoff:3.500A) Processing helix chain 'U' and resid 213 through 218 Processing helix chain 'U' and resid 247 through 255 removed outlier: 3.604A pdb=" N MET U 252 " --> pdb=" O VAL U 248 " (cutoff:3.500A) Processing helix chain 'U' and resid 259 through 263 Processing helix chain 'U' and resid 278 through 287 removed outlier: 3.745A pdb=" N GLY U 284 " --> pdb=" O SER U 280 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE U 286 " --> pdb=" O LEU U 282 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR U 287 " --> pdb=" O CYS U 283 " (cutoff:3.500A) Processing helix chain 'U' and resid 430 through 438 removed outlier: 4.146A pdb=" N GLN U 434 " --> pdb=" O ASP U 430 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA U 435 " --> pdb=" O PRO U 431 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 113 removed outlier: 4.124A pdb=" N SER L 110 " --> pdb=" O LEU L 106 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER L 111 " --> pdb=" O SER L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 261 removed outlier: 3.522A pdb=" N SER L 260 " --> pdb=" O LYS L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 266 Processing helix chain 'L' and resid 280 through 291 removed outlier: 3.559A pdb=" N GLU L 286 " --> pdb=" O ASN L 282 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL L 287 " --> pdb=" O GLU L 283 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU L 288 " --> pdb=" O MET L 284 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG L 289 " --> pdb=" O SER L 285 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP L 290 " --> pdb=" O GLU L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 325 Processing helix chain 'L' and resid 326 through 339 removed outlier: 3.577A pdb=" N PHE L 337 " --> pdb=" O LEU L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 365 removed outlier: 3.627A pdb=" N TRP L 354 " --> pdb=" O SER L 350 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU L 360 " --> pdb=" O GLU L 356 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU L 365 " --> pdb=" O ILE L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 387 Processing helix chain 'L' and resid 419 through 429 removed outlier: 3.605A pdb=" N GLY L 427 " --> pdb=" O SER L 423 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE L 428 " --> pdb=" O ALA L 424 " (cutoff:3.500A) Processing helix chain 'L' and resid 438 through 443 Processing helix chain 'L' and resid 458 through 460 No H-bonds generated for 'chain 'L' and resid 458 through 460' Processing helix chain 'L' and resid 461 through 469 removed outlier: 3.579A pdb=" N ASP L 466 " --> pdb=" O ASP L 462 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS L 467 " --> pdb=" O GLU L 463 " (cutoff:3.500A) Processing helix chain 'L' and resid 471 through 497 removed outlier: 3.826A pdb=" N LEU L 475 " --> pdb=" O GLU L 471 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS L 478 " --> pdb=" O PRO L 474 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA L 479 " --> pdb=" O LEU L 475 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU L 481 " --> pdb=" O THR L 477 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU L 483 " --> pdb=" O ALA L 479 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU L 491 " --> pdb=" O GLU L 487 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE L 492 " --> pdb=" O ASP L 488 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN L 494 " --> pdb=" O ALA L 490 " (cutoff:3.500A) Processing helix chain 'L' and resid 503 through 519 removed outlier: 3.586A pdb=" N ILE L 507 " --> pdb=" O GLU L 503 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR L 508 " --> pdb=" O THR L 504 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU L 510 " --> pdb=" O LYS L 506 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS L 513 " --> pdb=" O LEU L 509 " (cutoff:3.500A) Processing helix chain 'L' and resid 533 through 557 removed outlier: 3.552A pdb=" N ASN L 543 " --> pdb=" O GLY L 539 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE L 547 " --> pdb=" O ASN L 543 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR L 548 " --> pdb=" O MET L 544 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET L 550 " --> pdb=" O ALA L 546 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL L 555 " --> pdb=" O ALA L 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 566 through 574 removed outlier: 3.617A pdb=" N ILE L 570 " --> pdb=" O THR L 566 " (cutoff:3.500A) Processing helix chain 'L' and resid 574 through 582 removed outlier: 3.659A pdb=" N SER L 582 " --> pdb=" O LEU L 578 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 587 removed outlier: 3.596A pdb=" N PHE L 586 " --> pdb=" O SER L 583 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS L 587 " --> pdb=" O MET L 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 583 through 587' Processing helix chain 'L' and resid 593 through 616 removed outlier: 3.601A pdb=" N LYS L 598 " --> pdb=" O GLU L 594 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU L 605 " --> pdb=" O TYR L 601 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU L 606 " --> pdb=" O ALA L 602 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA L 611 " --> pdb=" O ASP L 607 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER L 614 " --> pdb=" O ASN L 610 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 113 removed outlier: 3.625A pdb=" N SER M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 266 removed outlier: 3.773A pdb=" N SER M 262 " --> pdb=" O VAL M 258 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER M 264 " --> pdb=" O SER M 260 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR M 266 " --> pdb=" O SER M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 294 removed outlier: 3.779A pdb=" N MET M 284 " --> pdb=" O ARG M 280 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER M 285 " --> pdb=" O GLY M 281 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU M 286 " --> pdb=" O ASN M 282 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL M 287 " --> pdb=" O GLU M 283 " (cutoff:3.500A) Proline residue: M 292 - end of helix Processing helix chain 'M' and resid 319 through 337 removed outlier: 3.524A pdb=" N ARG M 323 " --> pdb=" O PRO M 319 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU M 324 " --> pdb=" O VAL M 320 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA M 325 " --> pdb=" O ALA M 321 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE M 327 " --> pdb=" O ARG M 323 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR M 328 " --> pdb=" O GLU M 324 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY M 330 " --> pdb=" O SER M 326 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE M 337 " --> pdb=" O LEU M 333 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 365 removed outlier: 3.529A pdb=" N TRP M 354 " --> pdb=" O SER M 350 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG M 359 " --> pdb=" O ALA M 355 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU M 360 " --> pdb=" O GLU M 356 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU M 365 " --> pdb=" O ILE M 361 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 387 removed outlier: 3.539A pdb=" N ARG M 381 " --> pdb=" O TYR M 377 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE M 385 " --> pdb=" O ARG M 381 " (cutoff:3.500A) Processing helix chain 'M' and resid 412 through 416 removed outlier: 4.071A pdb=" N ASP M 416 " --> pdb=" O PRO M 413 " (cutoff:3.500A) Processing helix chain 'M' and resid 437 through 441 removed outlier: 3.725A pdb=" N ALA M 440 " --> pdb=" O LYS M 437 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN M 441 " --> pdb=" O LYS M 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 437 through 441' Processing helix chain 'M' and resid 461 through 469 Processing helix chain 'M' and resid 471 through 494 removed outlier: 3.704A pdb=" N LEU M 475 " --> pdb=" O GLU M 471 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU M 483 " --> pdb=" O ALA M 479 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU M 487 " --> pdb=" O LEU M 483 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP M 488 " --> pdb=" O GLN M 484 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU M 491 " --> pdb=" O GLU M 487 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE M 492 " --> pdb=" O ASP M 488 " (cutoff:3.500A) Processing helix chain 'M' and resid 502 through 519 removed outlier: 3.587A pdb=" N LEU M 509 " --> pdb=" O ASP M 505 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS M 513 " --> pdb=" O LEU M 509 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU M 514 " --> pdb=" O GLU M 510 " (cutoff:3.500A) Processing helix chain 'M' and resid 533 through 552 removed outlier: 3.650A pdb=" N ASN M 543 " --> pdb=" O GLY M 539 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG M 552 " --> pdb=" O TYR M 548 " (cutoff:3.500A) Processing helix chain 'M' and resid 552 through 557 Processing helix chain 'M' and resid 566 through 574 Processing helix chain 'M' and resid 576 through 581 Processing helix chain 'M' and resid 582 through 585 removed outlier: 4.137A pdb=" N LYS M 585 " --> pdb=" O SER M 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 582 through 585' Processing helix chain 'M' and resid 593 through 616 removed outlier: 3.580A pdb=" N LYS M 598 " --> pdb=" O GLU M 594 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA M 602 " --> pdb=" O LYS M 598 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN M 603 " --> pdb=" O SER M 599 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU M 604 " --> pdb=" O ASP M 600 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER M 614 " --> pdb=" O ASN M 610 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU M 615 " --> pdb=" O ALA M 611 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 113 removed outlier: 4.234A pdb=" N SER N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 264 Processing helix chain 'N' and resid 280 through 285 removed outlier: 3.728A pdb=" N MET N 284 " --> pdb=" O ARG N 280 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER N 285 " --> pdb=" O GLY N 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 280 through 285' Processing helix chain 'N' and resid 289 through 294 removed outlier: 4.328A pdb=" N GLU N 293 " --> pdb=" O ARG N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 319 through 325 removed outlier: 3.835A pdb=" N ALA N 325 " --> pdb=" O ALA N 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 325 through 340 removed outlier: 3.628A pdb=" N PHE N 337 " --> pdb=" O LEU N 333 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET N 340 " --> pdb=" O TYR N 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 351 through 365 removed outlier: 3.694A pdb=" N ALA N 357 " --> pdb=" O ARG N 353 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU N 360 " --> pdb=" O GLU N 356 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG N 364 " --> pdb=" O GLU N 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 377 through 387 removed outlier: 3.608A pdb=" N ALA N 383 " --> pdb=" O GLY N 379 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE N 385 " --> pdb=" O ARG N 381 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU N 387 " --> pdb=" O ALA N 383 " (cutoff:3.500A) Processing helix chain 'N' and resid 421 through 426 Processing helix chain 'N' and resid 437 through 441 removed outlier: 3.611A pdb=" N ALA N 440 " --> pdb=" O LYS N 437 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN N 441 " --> pdb=" O LYS N 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 437 through 441' Processing helix chain 'N' and resid 461 through 469 Processing helix chain 'N' and resid 471 through 494 removed outlier: 3.954A pdb=" N LEU N 475 " --> pdb=" O GLU N 471 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU N 483 " --> pdb=" O ALA N 479 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN N 484 " --> pdb=" O LYS N 480 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU N 487 " --> pdb=" O LEU N 483 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP N 488 " --> pdb=" O GLN N 484 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU N 491 " --> pdb=" O GLU N 487 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE N 492 " --> pdb=" O ASP N 488 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL N 493 " --> pdb=" O LEU N 489 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN N 494 " --> pdb=" O ALA N 490 " (cutoff:3.500A) Processing helix chain 'N' and resid 506 through 519 removed outlier: 3.700A pdb=" N ALA N 512 " --> pdb=" O THR N 508 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP N 518 " --> pdb=" O LEU N 514 " (cutoff:3.500A) Processing helix chain 'N' and resid 533 through 558 removed outlier: 3.757A pdb=" N ASN N 543 " --> pdb=" O GLY N 539 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET N 544 " --> pdb=" O MET N 540 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE N 545 " --> pdb=" O LEU N 541 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR N 548 " --> pdb=" O MET N 544 " (cutoff:3.500A) Processing helix chain 'N' and resid 567 through 574 removed outlier: 3.530A pdb=" N GLU N 572 " --> pdb=" O SER N 568 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS N 573 " --> pdb=" O ILE N 569 " (cutoff:3.500A) Processing helix chain 'N' and resid 576 through 581 Processing helix chain 'N' and resid 593 through 614 removed outlier: 3.758A pdb=" N LYS N 598 " --> pdb=" O GLU N 594 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR N 601 " --> pdb=" O ILE N 597 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU N 605 " --> pdb=" O TYR N 601 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU N 606 " --> pdb=" O ALA N 602 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN N 610 " --> pdb=" O GLU N 606 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA N 611 " --> pdb=" O ASP N 607 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE N 612 " --> pdb=" O MET N 608 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG N 613 " --> pdb=" O GLN N 609 " (cutoff:3.500A) Processing helix chain 'O' and resid 159 through 161 No H-bonds generated for 'chain 'O' and resid 159 through 161' Processing helix chain 'O' and resid 174 through 180 removed outlier: 3.955A pdb=" N MET O 180 " --> pdb=" O ALA O 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 198 through 210 Processing helix chain 'O' and resid 218 through 223 removed outlier: 3.938A pdb=" N ASP O 221 " --> pdb=" O ASP O 218 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER O 223 " --> pdb=" O VAL O 220 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 248 removed outlier: 3.793A pdb=" N PHE O 244 " --> pdb=" O THR O 240 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 255 No H-bonds generated for 'chain 'O' and resid 253 through 255' Processing helix chain 'O' and resid 276 through 288 removed outlier: 3.541A pdb=" N THR O 281 " --> pdb=" O LEU O 277 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR O 287 " --> pdb=" O GLU O 283 " (cutoff:3.500A) Processing helix chain 'O' and resid 299 through 305 Processing helix chain 'O' and resid 306 through 314 Processing helix chain 'O' and resid 319 through 323 Processing helix chain 'O' and resid 326 through 336 removed outlier: 3.638A pdb=" N THR O 333 " --> pdb=" O THR O 329 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE O 334 " --> pdb=" O ASP O 330 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 360 Processing helix chain 'O' and resid 363 through 370 Processing helix chain 'O' and resid 381 through 386 removed outlier: 3.781A pdb=" N ARG O 386 " --> pdb=" O GLN O 382 " (cutoff:3.500A) Processing helix chain 'O' and resid 401 through 406 removed outlier: 3.574A pdb=" N ALA O 405 " --> pdb=" O LEU O 401 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 440 removed outlier: 3.680A pdb=" N SER O 419 " --> pdb=" O HIS O 415 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN O 420 " --> pdb=" O ALA O 416 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP O 431 " --> pdb=" O ALA O 427 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA O 437 " --> pdb=" O GLN O 433 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL O 438 " --> pdb=" O ALA O 434 " (cutoff:3.500A) Processing helix chain 'O' and resid 448 through 462 removed outlier: 3.585A pdb=" N LEU O 452 " --> pdb=" O ASP O 448 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN O 456 " --> pdb=" O LEU O 452 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG O 460 " --> pdb=" O GLN O 456 " (cutoff:3.500A) Processing helix chain 'O' and resid 472 through 482 removed outlier: 3.625A pdb=" N THR O 476 " --> pdb=" O THR O 472 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU O 477 " --> pdb=" O VAL O 473 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN O 482 " --> pdb=" O ASP O 478 " (cutoff:3.500A) Processing helix chain 'O' and resid 496 through 504 removed outlier: 3.563A pdb=" N SER O 501 " --> pdb=" O GLN O 497 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU O 502 " --> pdb=" O SER O 498 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR O 504 " --> pdb=" O LEU O 500 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 161 No H-bonds generated for 'chain 'P' and resid 159 through 161' Processing helix chain 'P' and resid 175 through 180 removed outlier: 3.857A pdb=" N MET P 180 " --> pdb=" O ALA P 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 210 removed outlier: 3.518A pdb=" N ILE P 202 " --> pdb=" O PRO P 198 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS P 207 " --> pdb=" O ALA P 203 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG P 208 " --> pdb=" O ALA P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 224 Processing helix chain 'P' and resid 237 through 251 removed outlier: 3.586A pdb=" N PHE P 248 " --> pdb=" O PHE P 244 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN P 251 " --> pdb=" O ASP P 247 " (cutoff:3.500A) Processing helix chain 'P' and resid 253 through 255 No H-bonds generated for 'chain 'P' and resid 253 through 255' Processing helix chain 'P' and resid 267 through 272 Processing helix chain 'P' and resid 273 through 288 removed outlier: 3.519A pdb=" N LEU P 279 " --> pdb=" O PRO P 275 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA P 286 " --> pdb=" O ALA P 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN P 288 " --> pdb=" O PHE P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 315 removed outlier: 3.647A pdb=" N ALA P 304 " --> pdb=" O MET P 300 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA P 306 " --> pdb=" O SER P 302 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL P 310 " --> pdb=" O ALA P 306 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER P 311 " --> pdb=" O LEU P 307 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA P 313 " --> pdb=" O GLU P 309 " (cutoff:3.500A) Processing helix chain 'P' and resid 324 through 326 No H-bonds generated for 'chain 'P' and resid 324 through 326' Processing helix chain 'P' and resid 327 through 336 removed outlier: 4.042A pdb=" N THR P 333 " --> pdb=" O THR P 329 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE P 334 " --> pdb=" O ASP P 330 " (cutoff:3.500A) Processing helix chain 'P' and resid 357 through 360 removed outlier: 3.646A pdb=" N ASP P 360 " --> pdb=" O PRO P 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 357 through 360' Processing helix chain 'P' and resid 363 through 371 removed outlier: 3.599A pdb=" N LEU P 368 " --> pdb=" O PRO P 364 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY P 370 " --> pdb=" O PRO P 366 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR P 371 " --> pdb=" O ASP P 367 " (cutoff:3.500A) Processing helix chain 'P' and resid 381 through 386 removed outlier: 3.629A pdb=" N ARG P 386 " --> pdb=" O GLN P 382 " (cutoff:3.500A) Processing helix chain 'P' and resid 401 through 406 removed outlier: 3.796A pdb=" N ALA P 405 " --> pdb=" O LEU P 401 " (cutoff:3.500A) Processing helix chain 'P' and resid 414 through 440 removed outlier: 3.586A pdb=" N TYR P 423 " --> pdb=" O SER P 419 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA P 424 " --> pdb=" O ASN P 420 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA P 434 " --> pdb=" O LYS P 430 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA P 437 " --> pdb=" O GLN P 433 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL P 438 " --> pdb=" O ALA P 434 " (cutoff:3.500A) Processing helix chain 'P' and resid 441 through 444 removed outlier: 3.749A pdb=" N LEU P 444 " --> pdb=" O GLU P 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 441 through 444' Processing helix chain 'P' and resid 448 through 462 removed outlier: 3.637A pdb=" N GLN P 456 " --> pdb=" O LEU P 452 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG P 460 " --> pdb=" O GLN P 456 " (cutoff:3.500A) Processing helix chain 'P' and resid 472 through 485 removed outlier: 3.920A pdb=" N ASP P 478 " --> pdb=" O PHE P 474 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY P 480 " --> pdb=" O THR P 476 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN P 482 " --> pdb=" O ASP P 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 496 through 504 removed outlier: 3.866A pdb=" N GLU P 502 " --> pdb=" O SER P 498 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 161 No H-bonds generated for 'chain 'Q' and resid 159 through 161' Processing helix chain 'Q' and resid 174 through 178 Processing helix chain 'Q' and resid 198 through 210 Processing helix chain 'Q' and resid 216 through 221 removed outlier: 4.116A pdb=" N VAL Q 220 " --> pdb=" O SER Q 216 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP Q 221 " --> pdb=" O LYS Q 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 216 through 221' Processing helix chain 'Q' and resid 237 through 246 removed outlier: 3.684A pdb=" N ARG Q 242 " --> pdb=" O MET Q 238 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE Q 243 " --> pdb=" O GLU Q 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 269 through 286 removed outlier: 4.094A pdb=" N ILE Q 273 " --> pdb=" O ILE Q 269 " (cutoff:3.500A) Proline residue: Q 275 - end of helix removed outlier: 3.529A pdb=" N LEU Q 279 " --> pdb=" O PRO Q 275 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR Q 281 " --> pdb=" O LEU Q 277 " (cutoff:3.500A) Processing helix chain 'Q' and resid 300 through 314 removed outlier: 3.618A pdb=" N ALA Q 304 " --> pdb=" O MET Q 300 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA Q 306 " --> pdb=" O SER Q 302 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU Q 309 " --> pdb=" O GLU Q 305 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA Q 313 " --> pdb=" O GLU Q 309 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG Q 314 " --> pdb=" O VAL Q 310 " (cutoff:3.500A) Processing helix chain 'Q' and resid 319 through 323 removed outlier: 4.075A pdb=" N GLY Q 322 " --> pdb=" O GLY Q 319 " (cutoff:3.500A) Processing helix chain 'Q' and resid 324 through 325 No H-bonds generated for 'chain 'Q' and resid 324 through 325' Processing helix chain 'Q' and resid 326 through 336 removed outlier: 3.562A pdb=" N ILE Q 334 " --> pdb=" O ASP Q 330 " (cutoff:3.500A) Processing helix chain 'Q' and resid 356 through 360 Processing helix chain 'Q' and resid 363 through 371 removed outlier: 3.592A pdb=" N TYR Q 371 " --> pdb=" O ASP Q 367 " (cutoff:3.500A) Processing helix chain 'Q' and resid 414 through 436 removed outlier: 4.246A pdb=" N ASN Q 420 " --> pdb=" O ALA Q 416 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN Q 421 " --> pdb=" O ASP Q 417 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA Q 424 " --> pdb=" O ASN Q 420 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP Q 431 " --> pdb=" O ALA Q 427 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN Q 433 " --> pdb=" O GLY Q 429 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA Q 434 " --> pdb=" O LYS Q 430 " (cutoff:3.500A) Processing helix chain 'Q' and resid 449 through 462 removed outlier: 3.640A pdb=" N GLN Q 456 " --> pdb=" O LEU Q 452 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU Q 459 " --> pdb=" O LEU Q 455 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG Q 460 " --> pdb=" O GLN Q 456 " (cutoff:3.500A) Processing helix chain 'Q' and resid 472 through 482 removed outlier: 3.680A pdb=" N LEU Q 477 " --> pdb=" O VAL Q 473 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP Q 478 " --> pdb=" O PHE Q 474 " (cutoff:3.500A) Processing helix chain 'Q' and resid 488 through 492 removed outlier: 3.817A pdb=" N LEU Q 492 " --> pdb=" O LYS Q 489 " (cutoff:3.500A) Processing helix chain 'Q' and resid 496 through 504 removed outlier: 3.569A pdb=" N GLU Q 502 " --> pdb=" O SER Q 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 65 removed outlier: 3.502A pdb=" N ILE D 18 " --> pdb=" O MET D 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY D 29 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN D 31 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 33 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET D 56 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU D 60 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG D 63 " --> pdb=" O GLY D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 77 removed outlier: 3.834A pdb=" N THR D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 85 Processing helix chain 'D' and resid 128 through 166 removed outlier: 3.566A pdb=" N ARG D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER D 154 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 175 removed outlier: 3.546A pdb=" N VAL D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 216 removed outlier: 3.575A pdb=" N THR D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE D 205 " --> pdb=" O ARG D 201 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS D 208 " --> pdb=" O LYS D 204 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS D 210 " --> pdb=" O GLN D 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 108 removed outlier: 3.782A pdb=" N LYS b 10 " --> pdb=" O ALA b 6 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS b 26 " --> pdb=" O GLU b 22 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA b 27 " --> pdb=" O ALA b 23 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU b 29 " --> pdb=" O GLU b 25 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA b 34 " --> pdb=" O ILE b 30 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU b 36 " --> pdb=" O ALA b 32 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU b 37 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE b 40 " --> pdb=" O GLU b 36 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU b 41 " --> pdb=" O GLU b 37 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU b 45 " --> pdb=" O GLU b 41 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN b 47 " --> pdb=" O GLY b 43 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR b 48 " --> pdb=" O ARG b 44 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU b 51 " --> pdb=" O GLN b 47 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE b 64 " --> pdb=" O LYS b 60 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN b 67 " --> pdb=" O GLN b 63 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS b 69 " --> pdb=" O GLU b 65 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN b 71 " --> pdb=" O GLN b 67 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU b 81 " --> pdb=" O ASN b 77 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS b 82 " --> pdb=" O GLN b 78 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL b 83 " --> pdb=" O ALA b 79 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN b 100 " --> pdb=" O ASN b 96 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL b 105 " --> pdb=" O ARG b 101 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL b 106 " --> pdb=" O LEU b 102 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS b 107 " --> pdb=" O SER b 103 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 109 through 128 removed outlier: 4.343A pdb=" N VAL b 114 " --> pdb=" O THR b 110 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU b 115 " --> pdb=" O ARG b 111 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY b 118 " --> pdb=" O VAL b 114 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU b 121 " --> pdb=" O ASP b 117 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY b 123 " --> pdb=" O LEU b 119 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU b 127 " --> pdb=" O GLY b 123 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU b 128 " --> pdb=" O LEU b 124 " (cutoff:3.500A) Processing helix chain 'b' and resid 140 through 159 removed outlier: 3.682A pdb=" N LYS b 150 " --> pdb=" O ALA b 146 " (cutoff:3.500A) Proline residue: b 153 - end of helix removed outlier: 3.568A pdb=" N ILE b 157 " --> pdb=" O PRO b 153 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA b 158 " --> pdb=" O MET b 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 207 removed outlier: 3.811A pdb=" N LEU b 200 " --> pdb=" O LEU b 196 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP b 201 " --> pdb=" O GLU b 197 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN b 205 " --> pdb=" O ASP b 201 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN b 206 " --> pdb=" O LEU b 202 " (cutoff:3.500A) Processing helix chain 'b' and resid 207 through 216 removed outlier: 3.611A pdb=" N GLY b 213 " --> pdb=" O PRO b 209 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 16 removed outlier: 3.690A pdb=" N MET c 15 " --> pdb=" O GLN c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 17 through 21 removed outlier: 3.918A pdb=" N GLU c 20 " --> pdb=" O ALA c 17 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 101 removed outlier: 3.725A pdb=" N GLU c 29 " --> pdb=" O GLU c 25 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP c 31 " --> pdb=" O ALA c 27 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU c 41 " --> pdb=" O GLU c 37 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL c 46 " --> pdb=" O LYS c 42 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN c 47 " --> pdb=" O GLY c 43 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG c 50 " --> pdb=" O VAL c 46 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU c 51 " --> pdb=" O GLN c 47 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU c 55 " --> pdb=" O LEU c 51 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU c 58 " --> pdb=" O MET c 54 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU c 61 " --> pdb=" O TYR c 57 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN c 63 " --> pdb=" O LYS c 59 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS c 69 " --> pdb=" O GLU c 65 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG c 80 " --> pdb=" O MET c 76 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL c 83 " --> pdb=" O ALA c 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE c 91 " --> pdb=" O ARG c 87 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU c 97 " --> pdb=" O ASP c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 110 through 127 removed outlier: 4.075A pdb=" N VAL c 114 " --> pdb=" O THR c 110 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU c 127 " --> pdb=" O GLY c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 140 through 158 removed outlier: 3.723A pdb=" N ALA c 146 " --> pdb=" O PRO c 142 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN c 149 " --> pdb=" O LYS c 145 " (cutoff:3.500A) Proline residue: c 153 - end of helix removed outlier: 3.875A pdb=" N ALA c 158 " --> pdb=" O MET c 154 " (cutoff:3.500A) Processing helix chain 'c' and resid 197 through 216 removed outlier: 3.605A pdb=" N ILE c 203 " --> pdb=" O ARG c 199 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN c 205 " --> pdb=" O ASP c 201 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN c 206 " --> pdb=" O LEU c 202 " (cutoff:3.500A) Proline residue: c 209 - end of helix Processing helix chain 'd' and resid 5 through 16 removed outlier: 3.569A pdb=" N LYS d 10 " --> pdb=" O ALA d 6 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN d 11 " --> pdb=" O ASP d 7 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS d 14 " --> pdb=" O LYS d 10 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET d 15 " --> pdb=" O GLN d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 19 through 29 removed outlier: 3.504A pdb=" N GLU d 29 " --> pdb=" O GLU d 25 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 51 removed outlier: 3.900A pdb=" N GLU d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE d 38 " --> pdb=" O ALA d 34 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN d 49 " --> pdb=" O LEU d 45 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU d 51 " --> pdb=" O GLN d 47 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 62 removed outlier: 3.674A pdb=" N GLU d 55 " --> pdb=" O LEU d 51 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR d 57 " --> pdb=" O ILE d 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 72 Processing helix chain 'd' and resid 75 through 106 removed outlier: 3.699A pdb=" N LEU d 81 " --> pdb=" O ASN d 77 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG d 85 " --> pdb=" O LEU d 81 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA d 86 " --> pdb=" O LYS d 82 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP d 88 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP d 89 " --> pdb=" O ARG d 85 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER d 103 " --> pdb=" O LYS d 99 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL d 105 " --> pdb=" O ARG d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 128 removed outlier: 3.511A pdb=" N GLY d 118 " --> pdb=" O VAL d 114 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 160 removed outlier: 3.828A pdb=" N GLN d 149 " --> pdb=" O LYS d 145 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS d 150 " --> pdb=" O ALA d 146 " (cutoff:3.500A) Proline residue: d 153 - end of helix removed outlier: 3.986A pdb=" N ALA d 158 " --> pdb=" O MET d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 204 Processing helix chain 'd' and resid 207 through 216 removed outlier: 3.727A pdb=" N PHE d 216 " --> pdb=" O ARG d 212 " (cutoff:3.500A) Processing helix chain 'e' and resid 4 through 22 removed outlier: 3.793A pdb=" N GLN e 9 " --> pdb=" O SER e 5 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN e 10 " --> pdb=" O GLN e 6 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU e 11 " --> pdb=" O GLY e 7 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN e 13 " --> pdb=" O GLN e 9 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA e 14 " --> pdb=" O GLN e 10 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL e 22 " --> pdb=" O ALA e 18 " (cutoff:3.500A) Processing helix chain 'e' and resid 26 through 51 removed outlier: 3.593A pdb=" N ARG e 31 " --> pdb=" O LYS e 27 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG e 32 " --> pdb=" O ARG e 28 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU e 33 " --> pdb=" O LYS e 29 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS e 34 " --> pdb=" O ASN e 30 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS e 37 " --> pdb=" O LEU e 33 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU e 38 " --> pdb=" O LYS e 34 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU e 45 " --> pdb=" O GLN e 41 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN e 46 " --> pdb=" O ALA e 42 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR e 47 " --> pdb=" O GLU e 43 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU e 49 " --> pdb=" O GLU e 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 52 through 61 Processing helix chain 'e' and resid 67 through 104 removed outlier: 3.646A pdb=" N THR e 71 " --> pdb=" O GLY e 67 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU e 72 " --> pdb=" O SER e 68 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL e 73 " --> pdb=" O CYS e 69 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS e 75 " --> pdb=" O THR e 71 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU e 76 " --> pdb=" O GLU e 72 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU e 79 " --> pdb=" O LYS e 75 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR e 82 " --> pdb=" O GLN e 78 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE e 83 " --> pdb=" O GLU e 79 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR e 86 " --> pdb=" O THR e 82 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR e 87 " --> pdb=" O ILE e 83 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG e 89 " --> pdb=" O GLN e 85 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN e 91 " --> pdb=" O TYR e 87 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASP e 93 " --> pdb=" O ARG e 89 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLU e 94 " --> pdb=" O GLN e 90 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL e 95 " --> pdb=" O ASN e 91 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA e 101 " --> pdb=" O ASP e 97 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE e 102 " --> pdb=" O ASN e 98 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL e 103 " --> pdb=" O LEU e 99 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS e 104 " --> pdb=" O LEU e 100 " (cutoff:3.500A) Processing helix chain 'f' and resid 4 through 35 removed outlier: 4.392A pdb=" N ILE f 8 " --> pdb=" O GLN f 4 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN f 9 " --> pdb=" O SER f 5 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN f 10 " --> pdb=" O GLN f 6 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU f 11 " --> pdb=" O GLY f 7 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER f 23 " --> pdb=" O ALA f 19 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 46 removed outlier: 3.610A pdb=" N GLN f 46 " --> pdb=" O ALA f 42 " (cutoff:3.500A) Processing helix chain 'f' and resid 47 through 82 removed outlier: 3.708A pdb=" N ALA f 57 " --> pdb=" O LYS f 53 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA f 61 " --> pdb=" O ALA f 57 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER f 65 " --> pdb=" O ALA f 61 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY f 67 " --> pdb=" O LEU f 63 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR f 71 " --> pdb=" O GLY f 67 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS f 75 " --> pdb=" O THR f 71 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN f 78 " --> pdb=" O GLU f 74 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS f 80 " --> pdb=" O GLU f 76 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 103 removed outlier: 3.598A pdb=" N GLN f 90 " --> pdb=" O THR f 86 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASP f 93 " --> pdb=" O ARG f 89 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU f 94 " --> pdb=" O GLN f 90 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL f 95 " --> pdb=" O ASN f 91 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU f 96 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP f 97 " --> pdb=" O ASP f 93 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE f 102 " --> pdb=" O ASN f 98 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL f 103 " --> pdb=" O LEU f 99 " (cutoff:3.500A) Processing helix chain 'g' and resid 6 through 20 removed outlier: 4.113A pdb=" N LEU g 12 " --> pdb=" O ILE g 8 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN g 13 " --> pdb=" O GLN g 9 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG g 17 " --> pdb=" O GLN g 13 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA g 18 " --> pdb=" O ALA g 14 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU g 20 " --> pdb=" O LYS g 16 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 27 removed outlier: 3.853A pdb=" N LYS g 27 " --> pdb=" O SER g 23 " (cutoff:3.500A) Processing helix chain 'g' and resid 28 through 36 removed outlier: 3.623A pdb=" N ARG g 32 " --> pdb=" O ARG g 28 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA g 36 " --> pdb=" O ARG g 32 " (cutoff:3.500A) Processing helix chain 'g' and resid 41 through 48 Processing helix chain 'g' and resid 50 through 61 removed outlier: 3.928A pdb=" N ALA g 60 " --> pdb=" O LYS g 56 " (cutoff:3.500A) Processing helix chain 'g' and resid 61 through 70 removed outlier: 4.187A pdb=" N SER g 65 " --> pdb=" O ALA g 61 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG g 66 " --> pdb=" O ALA g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 72 through 81 Processing helix chain 'g' and resid 83 through 91 removed outlier: 3.814A pdb=" N TYR g 87 " --> pdb=" O ILE g 83 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG g 89 " --> pdb=" O GLN g 85 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN g 90 " --> pdb=" O THR g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 104 removed outlier: 3.537A pdb=" N LEU g 96 " --> pdb=" O ARG g 92 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP g 97 " --> pdb=" O ASP g 93 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN g 98 " --> pdb=" O GLU g 94 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE g 102 " --> pdb=" O ASN g 98 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL g 103 " --> pdb=" O LEU g 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 24 removed outlier: 4.076A pdb=" N GLY F 19 " --> pdb=" O ASP F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 58 removed outlier: 3.643A pdb=" N ILE F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU F 49 " --> pdb=" O ILE F 45 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR F 51 " --> pdb=" O GLU F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 74 removed outlier: 3.697A pdb=" N MET F 73 " --> pdb=" O TYR F 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 79 Processing helix chain 'F' and resid 99 through 103 removed outlier: 3.715A pdb=" N LYS F 102 " --> pdb=" O ASP F 99 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP F 103 " --> pdb=" O ALA F 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 99 through 103' Processing helix chain 'C' and resid 15 through 20 removed outlier: 3.655A pdb=" N GLU C 20 " --> pdb=" O GLN C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 78 removed outlier: 3.621A pdb=" N LEU C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA C 73 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 117 through 157 removed outlier: 3.854A pdb=" N ILE C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE C 124 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER C 141 " --> pdb=" O LYS C 137 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR C 143 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN C 149 " --> pdb=" O ASN C 145 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 removed outlier: 4.304A pdb=" N GLU C 168 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 removed outlier: 3.934A pdb=" N ASP C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 244 removed outlier: 3.769A pdb=" N PHE C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS C 240 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 309 removed outlier: 3.997A pdb=" N ASP C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS C 262 " --> pdb=" O MET C 258 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER C 269 " --> pdb=" O MET C 265 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 4.103A pdb=" N ARG C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 285 " --> pdb=" O ARG C 281 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN C 286 " --> pdb=" O TRP C 282 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 287 " --> pdb=" O LEU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 339 removed outlier: 3.753A pdb=" N VAL C 334 " --> pdb=" O LYS C 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 26 Processing helix chain 'H' and resid 62 through 66 removed outlier: 4.061A pdb=" N MET H 65 " --> pdb=" O LYS H 62 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU H 66 " --> pdb=" O GLN H 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 66' Processing helix chain 'H' and resid 74 through 84 removed outlier: 4.352A pdb=" N THR H 82 " --> pdb=" O ILE H 78 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 96 removed outlier: 3.898A pdb=" N LEU H 94 " --> pdb=" O VAL H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 104 removed outlier: 4.101A pdb=" N GLU H 103 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASN H 104 " --> pdb=" O MET H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 Processing helix chain 'H' and resid 135 through 145 removed outlier: 4.197A pdb=" N HIS H 139 " --> pdb=" O PRO H 135 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA H 142 " --> pdb=" O VAL H 138 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG H 143 " --> pdb=" O HIS H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 172 removed outlier: 3.652A pdb=" N THR H 170 " --> pdb=" O TRP H 167 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN H 171 " --> pdb=" O ILE H 168 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU H 172 " --> pdb=" O LYS H 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 167 through 172' Processing helix chain 'H' and resid 195 through 209 removed outlier: 3.659A pdb=" N GLN H 199 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N CYS H 200 " --> pdb=" O GLN H 196 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA H 202 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU H 207 " --> pdb=" O GLY H 203 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET H 208 " --> pdb=" O CYS H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 215 No H-bonds generated for 'chain 'H' and resid 213 through 215' Processing helix chain 'H' and resid 216 through 221 Processing helix chain 'H' and resid 223 through 233 removed outlier: 3.754A pdb=" N ASN H 233 " --> pdb=" O GLY H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 251 removed outlier: 3.563A pdb=" N LEU H 250 " --> pdb=" O SER H 246 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA H 251 " --> pdb=" O ILE H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 260 removed outlier: 4.077A pdb=" N HIS H 259 " --> pdb=" O GLN H 255 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU H 260 " --> pdb=" O MET H 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 255 through 260' Processing helix chain 'H' and resid 261 through 263 No H-bonds generated for 'chain 'H' and resid 261 through 263' Processing helix chain 'H' and resid 265 through 274 removed outlier: 3.708A pdb=" N ILE H 272 " --> pdb=" O VAL H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 290 Processing helix chain 'H' and resid 290 through 295 Processing helix chain 'H' and resid 302 through 307 removed outlier: 3.901A pdb=" N ALA H 306 " --> pdb=" O ARG H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 315 through 322 removed outlier: 3.643A pdb=" N GLU H 319 " --> pdb=" O LEU H 315 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN H 320 " --> pdb=" O LYS H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 350 removed outlier: 4.002A pdb=" N LYS H 336 " --> pdb=" O SER H 332 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS H 341 " --> pdb=" O PHE H 337 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU H 342 " --> pdb=" O LEU H 338 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER H 350 " --> pdb=" O VAL H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 362 Processing helix chain 'H' and resid 385 through 387 No H-bonds generated for 'chain 'H' and resid 385 through 387' Processing helix chain 'H' and resid 388 through 400 removed outlier: 3.561A pdb=" N LEU H 394 " --> pdb=" O LEU H 390 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR H 395 " --> pdb=" O LEU H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 415 removed outlier: 3.885A pdb=" N VAL H 409 " --> pdb=" O GLN H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 423 through 431 Processing helix chain 'H' and resid 432 through 441 removed outlier: 3.823A pdb=" N LEU H 436 " --> pdb=" O GLY H 432 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET H 438 " --> pdb=" O LYS H 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 445 through 456 removed outlier: 3.682A pdb=" N ASN H 451 " --> pdb=" O GLN H 447 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU H 453 " --> pdb=" O ARG H 449 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU H 454 " --> pdb=" O TYR H 450 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 13 removed outlier: 4.761A pdb=" N ASP k 12 " --> pdb=" O TYR k 8 " (cutoff:3.500A) Processing helix chain 'k' and resid 14 through 25 removed outlier: 3.708A pdb=" N ALA k 25 " --> pdb=" O ARG k 21 " (cutoff:3.500A) Processing helix chain 'k' and resid 29 through 37 Processing helix chain 'k' and resid 41 through 49 Processing helix chain 'k' and resid 66 through 87 removed outlier: 3.509A pdb=" N ILE k 70 " --> pdb=" O THR k 66 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS k 75 " --> pdb=" O ASP k 71 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL k 79 " --> pdb=" O LYS k 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU k 81 " --> pdb=" O LYS k 77 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS k 84 " --> pdb=" O VAL k 80 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN k 87 " --> pdb=" O ARG k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 90 through 99 removed outlier: 4.044A pdb=" N PHE k 96 " --> pdb=" O PRO k 92 " (cutoff:3.500A) Processing helix chain 'k' and resid 101 through 113 removed outlier: 3.986A pdb=" N ASP k 107 " --> pdb=" O SER k 103 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU k 111 " --> pdb=" O ASP k 107 " (cutoff:3.500A) Processing helix chain 'k' and resid 121 through 129 removed outlier: 3.797A pdb=" N VAL k 126 " --> pdb=" O ALA k 123 " (cutoff:3.500A) Proline residue: k 127 - end of helix Processing helix chain 'k' and resid 146 through 158 removed outlier: 3.514A pdb=" N ALA k 153 " --> pdb=" O GLU k 149 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR k 158 " --> pdb=" O ILE k 154 " (cutoff:3.500A) Processing helix chain 'k' and resid 159 through 164 removed outlier: 4.273A pdb=" N ALA k 162 " --> pdb=" O PRO k 159 " (cutoff:3.500A) Processing helix chain 'k' and resid 171 through 176 removed outlier: 3.538A pdb=" N GLU k 175 " --> pdb=" O GLN k 171 " (cutoff:3.500A) Processing helix chain 'k' and resid 177 through 200 removed outlier: 3.597A pdb=" N ILE k 181 " --> pdb=" O ASN k 177 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN k 183 " --> pdb=" O GLU k 179 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS k 187 " --> pdb=" O ASN k 183 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS k 195 " --> pdb=" O GLU k 191 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU k 200 " --> pdb=" O PHE k 196 " (cutoff:3.500A) Processing helix chain 'k' and resid 203 through 208 Processing helix chain 'k' and resid 208 through 226 removed outlier: 3.606A pdb=" N LEU k 212 " --> pdb=" O MET k 208 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE k 214 " --> pdb=" O PRO k 210 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG k 219 " --> pdb=" O GLU k 215 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA k 220 " --> pdb=" O ALA k 216 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE k 223 " --> pdb=" O ARG k 219 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR k 224 " --> pdb=" O ALA k 220 " (cutoff:3.500A) Processing helix chain 'k' and resid 237 through 241 removed outlier: 3.585A pdb=" N LEU k 240 " --> pdb=" O ARG k 237 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE k 241 " --> pdb=" O ALA k 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 237 through 241' Processing helix chain 'k' and resid 260 through 266 Processing helix chain 'k' and resid 267 through 270 Processing helix chain 'k' and resid 271 through 279 removed outlier: 3.790A pdb=" N LEU k 276 " --> pdb=" O PRO k 272 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU k 277 " --> pdb=" O GLU k 273 " (cutoff:3.500A) Processing helix chain 'k' and resid 289 through 304 removed outlier: 3.706A pdb=" N PHE k 295 " --> pdb=" O GLU k 291 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS k 297 " --> pdb=" O ARG k 293 " (cutoff:3.500A) Processing helix chain 'k' and resid 305 through 307 No H-bonds generated for 'chain 'k' and resid 305 through 307' Processing helix chain 'k' and resid 312 through 338 removed outlier: 3.972A pdb=" N TYR k 316 " --> pdb=" O PHE k 312 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL k 319 " --> pdb=" O PHE k 315 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN k 324 " --> pdb=" O LYS k 320 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL k 330 " --> pdb=" O CYS k 326 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA k 337 " --> pdb=" O ALA k 333 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 23 removed outlier: 3.620A pdb=" N VAL m 12 " --> pdb=" O VAL m 8 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL m 20 " --> pdb=" O PHE m 16 " (cutoff:3.500A) Processing helix chain 'm' and resid 33 through 41 removed outlier: 3.649A pdb=" N ILE m 37 " --> pdb=" O ASN m 33 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR m 39 " --> pdb=" O GLY m 35 " (cutoff:3.500A) Processing helix chain 'm' and resid 41 through 59 removed outlier: 3.523A pdb=" N CYS m 47 " --> pdb=" O THR m 43 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU m 50 " --> pdb=" O VAL m 46 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA m 55 " --> pdb=" O PHE m 51 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN m 59 " --> pdb=" O ALA m 55 " (cutoff:3.500A) Processing helix chain 'm' and resid 70 through 78 removed outlier: 4.169A pdb=" N TYR m 75 " --> pdb=" O GLU m 71 " (cutoff:3.500A) Processing helix chain 'n' and resid 47 through 74 removed outlier: 3.655A pdb=" N ALA n 51 " --> pdb=" O GLY n 47 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS n 53 " --> pdb=" O LYS n 49 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE n 55 " --> pdb=" O ALA n 51 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN n 73 " --> pdb=" O GLY n 69 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL n 74 " --> pdb=" O ILE n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 97 through 128 removed outlier: 3.557A pdb=" N GLU n 102 " --> pdb=" O TYR n 98 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN n 103 " --> pdb=" O ASN n 99 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE n 110 " --> pdb=" O TYR n 106 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA n 112 " --> pdb=" O CYS n 108 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR n 115 " --> pdb=" O ALA n 111 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU n 116 " --> pdb=" O ALA n 112 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU n 117 " --> pdb=" O GLY n 113 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL n 126 " --> pdb=" O SER n 122 " (cutoff:3.500A) Processing helix chain 's' and resid 423 through 448 removed outlier: 3.631A pdb=" N MET s 428 " --> pdb=" O PRO s 424 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER s 433 " --> pdb=" O GLY s 429 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE s 435 " --> pdb=" O LEU s 431 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE s 438 " --> pdb=" O LEU s 434 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE s 439 " --> pdb=" O PHE s 435 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET s 446 " --> pdb=" O TYR s 442 " (cutoff:3.500A) Processing helix chain 'r' and resid 297 through 325 removed outlier: 3.834A pdb=" N ASN r 303 " --> pdb=" O SER r 299 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL r 305 " --> pdb=" O VAL r 301 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE r 308 " --> pdb=" O MET r 304 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA r 311 " --> pdb=" O TRP r 307 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL r 316 " --> pdb=" O LEU r 312 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN r 322 " --> pdb=" O ILE r 318 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE r 323 " --> pdb=" O THR r 319 " (cutoff:3.500A) Processing helix chain '8' and resid 12 through 45 removed outlier: 3.787A pdb=" N GLY 8 18 " --> pdb=" O PHE 8 14 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA 8 21 " --> pdb=" O MET 8 17 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET 8 23 " --> pdb=" O ALA 8 19 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER 8 26 " --> pdb=" O ALA 8 22 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR 8 32 " --> pdb=" O LEU 8 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY 8 33 " --> pdb=" O GLY 8 29 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER 8 37 " --> pdb=" O GLY 8 33 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR 8 39 " --> pdb=" O ALA 8 35 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE 8 41 " --> pdb=" O SER 8 37 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA 8 42 " --> pdb=" O GLY 8 38 " (cutoff:3.500A) Processing helix chain '8' and resid 48 through 52 removed outlier: 3.954A pdb=" N ILE 8 52 " --> pdb=" O PRO 8 49 " (cutoff:3.500A) Processing helix chain '8' and resid 56 through 61 Processing helix chain '8' and resid 64 through 77 removed outlier: 3.507A pdb=" N TYR 8 68 " --> pdb=" O ILE 8 64 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL 8 72 " --> pdb=" O TYR 8 68 " (cutoff:3.500A) Processing helix chain '8' and resid 89 through 120 removed outlier: 3.552A pdb=" N LEU 8 93 " --> pdb=" O SER 8 89 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER 8 98 " --> pdb=" O GLY 8 94 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER 8 102 " --> pdb=" O SER 8 98 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE 8 110 " --> pdb=" O ALA 8 106 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY 8 111 " --> pdb=" O GLY 8 107 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL 8 113 " --> pdb=" O ALA 8 109 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL 8 118 " --> pdb=" O GLY 8 114 " (cutoff:3.500A) Processing helix chain '8' and resid 124 through 126 No H-bonds generated for 'chain '8' and resid 124 through 126' Processing helix chain '8' and resid 127 through 154 removed outlier: 3.696A pdb=" N LEU 8 133 " --> pdb=" O VAL 8 129 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 8 134 " --> pdb=" O GLY 8 130 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE 8 137 " --> pdb=" O LEU 8 133 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU 8 141 " --> pdb=" O PHE 8 137 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY 8 142 " --> pdb=" O ALA 8 138 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY 8 145 " --> pdb=" O LEU 8 141 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU 8 146 " --> pdb=" O GLY 8 142 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL 8 148 " --> pdb=" O TYR 8 144 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR 8 154 " --> pdb=" O LEU 8 150 " (cutoff:3.500A) Processing helix chain '9' and resid 11 through 36 removed outlier: 3.715A pdb=" N ALA 9 15 " --> pdb=" O ALA 9 11 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY 9 18 " --> pdb=" O PHE 9 14 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA 9 21 " --> pdb=" O MET 9 17 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA 9 22 " --> pdb=" O GLY 9 18 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET 9 23 " --> pdb=" O ALA 9 19 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE 9 25 " --> pdb=" O ALA 9 21 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER 9 26 " --> pdb=" O ALA 9 22 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU 9 28 " --> pdb=" O VAL 9 24 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY 9 29 " --> pdb=" O PHE 9 25 " (cutoff:3.500A) Processing helix chain '9' and resid 37 through 45 removed outlier: 3.793A pdb=" N ILE 9 41 " --> pdb=" O SER 9 37 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER 9 45 " --> pdb=" O ILE 9 41 " (cutoff:3.500A) Processing helix chain '9' and resid 48 through 52 removed outlier: 3.824A pdb=" N GLN 9 51 " --> pdb=" O ARG 9 48 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE 9 52 " --> pdb=" O PRO 9 49 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 48 through 52' Processing helix chain '9' and resid 53 through 55 No H-bonds generated for 'chain '9' and resid 53 through 55' Processing helix chain '9' and resid 56 through 79 removed outlier: 3.936A pdb=" N ILE 9 65 " --> pdb=" O MET 9 61 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA 9 66 " --> pdb=" O ALA 9 62 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE 9 67 " --> pdb=" O GLY 9 63 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER 9 79 " --> pdb=" O LEU 9 75 " (cutoff:3.500A) Processing helix chain '9' and resid 87 through 122 removed outlier: 3.580A pdb=" N VAL 9 99 " --> pdb=" O ALA 9 95 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER 9 102 " --> pdb=" O SER 9 98 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA 9 105 " --> pdb=" O LEU 9 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE 9 110 " --> pdb=" O ALA 9 106 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP 9 115 " --> pdb=" O GLY 9 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA 9 116 " --> pdb=" O ILE 9 112 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL 9 118 " --> pdb=" O GLY 9 114 " (cutoff:3.500A) Processing helix chain '9' and resid 127 through 154 removed outlier: 3.871A pdb=" N LEU 9 133 " --> pdb=" O VAL 9 129 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE 9 134 " --> pdb=" O GLY 9 130 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU 9 141 " --> pdb=" O PHE 9 137 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY 9 142 " --> pdb=" O ALA 9 138 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY 9 145 " --> pdb=" O LEU 9 141 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR 9 154 " --> pdb=" O LEU 9 150 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 9 removed outlier: 3.518A pdb=" N LEU 1 6 " --> pdb=" O THR 1 2 " (cutoff:3.500A) Processing helix chain '1' and resid 9 through 17 removed outlier: 3.805A pdb=" N VAL 1 13 " --> pdb=" O SER 1 9 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE 1 15 " --> pdb=" O VAL 1 11 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 29 removed outlier: 4.018A pdb=" N THR 1 27 " --> pdb=" O GLY 1 23 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE 1 29 " --> pdb=" O CYS 1 25 " (cutoff:3.500A) Processing helix chain '1' and resid 36 through 44 removed outlier: 3.520A pdb=" N THR 1 42 " --> pdb=" O ALA 1 38 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR 1 44 " --> pdb=" O PHE 1 40 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 78 removed outlier: 3.999A pdb=" N TRP 1 49 " --> pdb=" O SER 1 45 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY 1 53 " --> pdb=" O TRP 1 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE 1 54 " --> pdb=" O SER 1 50 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY 1 55 " --> pdb=" O ASN 1 51 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU 1 56 " --> pdb=" O LEU 1 52 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE 1 58 " --> pdb=" O ILE 1 54 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU 1 60 " --> pdb=" O LEU 1 56 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER 1 61 " --> pdb=" O ALA 1 57 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY 1 64 " --> pdb=" O LEU 1 60 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY 1 68 " --> pdb=" O GLY 1 64 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR 1 70 " --> pdb=" O ALA 1 66 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE 1 71 " --> pdb=" O TRP 1 67 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR 1 72 " --> pdb=" O GLY 1 68 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER 1 75 " --> pdb=" O ILE 1 71 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE 1 77 " --> pdb=" O GLY 1 73 " (cutoff:3.500A) Processing helix chain '1' and resid 85 through 90 removed outlier: 4.577A pdb=" N LYS 1 89 " --> pdb=" O ARG 1 85 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN 1 90 " --> pdb=" O ILE 1 86 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 85 through 90' Processing helix chain '1' and resid 91 through 113 removed outlier: 3.543A pdb=" N CYS 1 97 " --> pdb=" O SER 1 93 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL 1 100 " --> pdb=" O PHE 1 96 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA 1 101 " --> pdb=" O CYS 1 97 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR 1 103 " --> pdb=" O ALA 1 99 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY 1 104 " --> pdb=" O VAL 1 100 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE 1 111 " --> pdb=" O MET 1 107 " (cutoff:3.500A) Processing helix chain '1' and resid 129 through 169 removed outlier: 3.504A pdb=" N ALA 1 133 " --> pdb=" O ARG 1 129 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET 1 137 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE 1 138 " --> pdb=" O GLY 1 134 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN 1 148 " --> pdb=" O VAL 1 144 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL 1 153 " --> pdb=" O LEU 1 149 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY 1 159 " --> pdb=" O VAL 1 155 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA 1 167 " --> pdb=" O ALA 1 163 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN 1 168 " --> pdb=" O LEU 1 164 " (cutoff:3.500A) Processing helix chain '1' and resid 177 through 184 removed outlier: 3.659A pdb=" N ILE 1 181 " --> pdb=" O LEU 1 177 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY 1 183 " --> pdb=" O VAL 1 179 " (cutoff:3.500A) Processing helix chain '1' and resid 187 through 198 removed outlier: 3.951A pdb=" N VAL 1 193 " --> pdb=" O PHE 1 189 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR 1 198 " --> pdb=" O ALA 1 194 " (cutoff:3.500A) Processing helix chain '2' and resid 12 through 20 removed outlier: 3.788A pdb=" N GLY 2 18 " --> pdb=" O PHE 2 14 " (cutoff:3.500A) Processing helix chain '2' and resid 20 through 45 removed outlier: 3.565A pdb=" N PHE 2 25 " --> pdb=" O ALA 2 21 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER 2 26 " --> pdb=" O ALA 2 22 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU 2 28 " --> pdb=" O VAL 2 24 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR 2 32 " --> pdb=" O LEU 2 28 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER 2 37 " --> pdb=" O GLY 2 33 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR 2 39 " --> pdb=" O ALA 2 35 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY 2 40 " --> pdb=" O LYS 2 36 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 79 removed outlier: 3.969A pdb=" N ILE 2 65 " --> pdb=" O MET 2 61 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA 2 66 " --> pdb=" O ALA 2 62 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE 2 67 " --> pdb=" O GLY 2 63 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY 2 69 " --> pdb=" O ILE 2 65 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU 2 70 " --> pdb=" O ALA 2 66 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL 2 72 " --> pdb=" O TYR 2 68 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER 2 79 " --> pdb=" O LEU 2 75 " (cutoff:3.500A) Processing helix chain '2' and resid 87 through 122 removed outlier: 3.578A pdb=" N GLN 2 92 " --> pdb=" O LYS 2 88 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU 2 93 " --> pdb=" O SER 2 89 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER 2 98 " --> pdb=" O GLY 2 94 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL 2 99 " --> pdb=" O ALA 2 95 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER 2 102 " --> pdb=" O SER 2 98 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY 2 107 " --> pdb=" O GLY 2 103 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE 2 108 " --> pdb=" O LEU 2 104 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA 2 109 " --> pdb=" O ALA 2 105 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG 2 119 " --> pdb=" O ASP 2 115 " (cutoff:3.500A) Processing helix chain '2' and resid 124 through 127 Processing helix chain '2' and resid 128 through 140 removed outlier: 4.235A pdb=" N ILE 2 134 " --> pdb=" O GLY 2 130 " (cutoff:3.500A) Processing helix chain '2' and resid 140 through 154 removed outlier: 3.577A pdb=" N TYR 2 144 " --> pdb=" O VAL 2 140 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY 2 145 " --> pdb=" O LEU 2 141 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU 2 146 " --> pdb=" O GLY 2 142 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR 2 154 " --> pdb=" O LEU 2 150 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 20 removed outlier: 3.730A pdb=" N GLY 3 18 " --> pdb=" O PHE 3 14 " (cutoff:3.500A) Processing helix chain '3' and resid 20 through 25 Processing helix chain '3' and resid 28 through 45 removed outlier: 3.655A pdb=" N TYR 3 32 " --> pdb=" O LEU 3 28 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR 3 34 " --> pdb=" O ALA 3 30 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR 3 39 " --> pdb=" O ALA 3 35 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE 3 41 " --> pdb=" O SER 3 37 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA 3 42 " --> pdb=" O GLY 3 38 " (cutoff:3.500A) Processing helix chain '3' and resid 56 through 62 Processing helix chain '3' and resid 64 through 79 removed outlier: 3.513A pdb=" N LEU 3 70 " --> pdb=" O ALA 3 66 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER 3 79 " --> pdb=" O LEU 3 75 " (cutoff:3.500A) Processing helix chain '3' and resid 87 through 122 removed outlier: 3.912A pdb=" N LEU 3 93 " --> pdb=" O SER 3 89 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL 3 99 " --> pdb=" O ALA 3 95 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER 3 102 " --> pdb=" O SER 3 98 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA 3 105 " --> pdb=" O LEU 3 101 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE 3 112 " --> pdb=" O PHE 3 108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL 3 118 " --> pdb=" O GLY 3 114 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG 3 119 " --> pdb=" O ASP 3 115 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY 3 120 " --> pdb=" O ALA 3 116 " (cutoff:3.500A) Processing helix chain '3' and resid 124 through 126 No H-bonds generated for 'chain '3' and resid 124 through 126' Processing helix chain '3' and resid 127 through 140 removed outlier: 3.513A pdb=" N LEU 3 133 " --> pdb=" O VAL 3 129 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE 3 134 " --> pdb=" O GLY 3 130 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE 3 137 " --> pdb=" O LEU 3 133 " (cutoff:3.500A) Processing helix chain '3' and resid 140 through 155 removed outlier: 3.694A pdb=" N GLY 3 145 " --> pdb=" O LEU 3 141 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU 3 146 " --> pdb=" O GLY 3 142 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL 3 148 " --> pdb=" O TYR 3 144 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR 3 154 " --> pdb=" O LEU 3 150 " (cutoff:3.500A) Processing helix chain '4' and resid 11 through 28 removed outlier: 3.889A pdb=" N ALA 4 15 " --> pdb=" O ALA 4 11 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET 4 23 " --> pdb=" O ALA 4 19 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER 4 26 " --> pdb=" O ALA 4 22 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA 4 27 " --> pdb=" O MET 4 23 " (cutoff:3.500A) Processing helix chain '4' and resid 28 through 45 removed outlier: 3.973A pdb=" N TYR 4 32 " --> pdb=" O LEU 4 28 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR 4 34 " --> pdb=" O ALA 4 30 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER 4 37 " --> pdb=" O GLY 4 33 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY 4 40 " --> pdb=" O LYS 4 36 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA 4 42 " --> pdb=" O GLY 4 38 " (cutoff:3.500A) Processing helix chain '4' and resid 56 through 64 removed outlier: 3.792A pdb=" N ALA 4 62 " --> pdb=" O PRO 4 58 " (cutoff:3.500A) Processing helix chain '4' and resid 64 through 79 removed outlier: 3.650A pdb=" N VAL 4 72 " --> pdb=" O TYR 4 68 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA 4 77 " --> pdb=" O ALA 4 73 " (cutoff:3.500A) Processing helix chain '4' and resid 87 through 122 removed outlier: 3.510A pdb=" N LEU 4 101 " --> pdb=" O LEU 4 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER 4 102 " --> pdb=" O SER 4 98 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA 4 105 " --> pdb=" O LEU 4 101 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA 4 122 " --> pdb=" O VAL 4 118 " (cutoff:3.500A) Processing helix chain '4' and resid 124 through 126 No H-bonds generated for 'chain '4' and resid 124 through 126' Processing helix chain '4' and resid 127 through 138 removed outlier: 4.100A pdb=" N LEU 4 133 " --> pdb=" O VAL 4 129 " (cutoff:3.500A) Processing helix chain '4' and resid 139 through 154 removed outlier: 3.820A pdb=" N VAL 4 148 " --> pdb=" O TYR 4 144 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER 4 153 " --> pdb=" O ALA 4 149 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR 4 154 " --> pdb=" O LEU 4 150 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 25 removed outlier: 4.143A pdb=" N MET 5 23 " --> pdb=" O ALA 5 19 " (cutoff:3.500A) Processing helix chain '5' and resid 25 through 45 removed outlier: 3.544A pdb=" N ALA 5 31 " --> pdb=" O ALA 5 27 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA 5 35 " --> pdb=" O ALA 5 31 " (cutoff:3.500A) Processing helix chain '5' and resid 46 through 47 No H-bonds generated for 'chain '5' and resid 46 through 47' Processing helix chain '5' and resid 48 through 52 removed outlier: 4.036A pdb=" N GLN 5 51 " --> pdb=" O ARG 5 48 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE 5 52 " --> pdb=" O PRO 5 49 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 48 through 52' Processing helix chain '5' and resid 56 through 64 Processing helix chain '5' and resid 64 through 78 removed outlier: 3.540A pdb=" N ALA 5 77 " --> pdb=" O ALA 5 73 " (cutoff:3.500A) Processing helix chain '5' and resid 89 through 122 removed outlier: 3.618A pdb=" N SER 5 98 " --> pdb=" O GLY 5 94 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL 5 99 " --> pdb=" O ALA 5 95 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER 5 102 " --> pdb=" O SER 5 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY 5 103 " --> pdb=" O VAL 5 99 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE 5 110 " --> pdb=" O ALA 5 106 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE 5 112 " --> pdb=" O PHE 5 108 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL 5 118 " --> pdb=" O GLY 5 114 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG 5 119 " --> pdb=" O ASP 5 115 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY 5 120 " --> pdb=" O ALA 5 116 " (cutoff:3.500A) Processing helix chain '5' and resid 124 through 126 No H-bonds generated for 'chain '5' and resid 124 through 126' Processing helix chain '5' and resid 127 through 155 removed outlier: 3.727A pdb=" N PHE 5 137 " --> pdb=" O LEU 5 133 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU 5 141 " --> pdb=" O PHE 5 137 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY 5 142 " --> pdb=" O ALA 5 138 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL 5 148 " --> pdb=" O TYR 5 144 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR 5 154 " --> pdb=" O LEU 5 150 " (cutoff:3.500A) Processing helix chain '6' and resid 11 through 44 removed outlier: 4.086A pdb=" N ALA 6 15 " --> pdb=" O ALA 6 11 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET 6 23 " --> pdb=" O ALA 6 19 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER 6 26 " --> pdb=" O ALA 6 22 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR 6 32 " --> pdb=" O LEU 6 28 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER 6 37 " --> pdb=" O GLY 6 33 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR 6 39 " --> pdb=" O ALA 6 35 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA 6 42 " --> pdb=" O GLY 6 38 " (cutoff:3.500A) Processing helix chain '6' and resid 48 through 52 removed outlier: 3.555A pdb=" N GLN 6 51 " --> pdb=" O ARG 6 48 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE 6 52 " --> pdb=" O PRO 6 49 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 48 through 52' Processing helix chain '6' and resid 56 through 79 removed outlier: 4.286A pdb=" N ILE 6 65 " --> pdb=" O MET 6 61 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA 6 66 " --> pdb=" O ALA 6 62 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE 6 67 " --> pdb=" O GLY 6 63 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL 6 72 " --> pdb=" O TYR 6 68 " (cutoff:3.500A) Processing helix chain '6' and resid 87 through 122 removed outlier: 3.796A pdb=" N GLN 6 92 " --> pdb=" O LYS 6 88 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER 6 98 " --> pdb=" O GLY 6 94 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY 6 103 " --> pdb=" O VAL 6 99 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE 6 110 " --> pdb=" O ALA 6 106 " (cutoff:3.500A) Processing helix chain '6' and resid 127 through 154 removed outlier: 4.050A pdb=" N PHE 6 137 " --> pdb=" O LEU 6 133 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU 6 141 " --> pdb=" O PHE 6 137 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY 6 142 " --> pdb=" O ALA 6 138 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL 6 148 " --> pdb=" O TYR 6 144 " (cutoff:3.500A) Processing helix chain '7' and resid 12 through 20 Processing helix chain '7' and resid 20 through 30 removed outlier: 3.979A pdb=" N SER 7 26 " --> pdb=" O ALA 7 22 " (cutoff:3.500A) Processing helix chain '7' and resid 31 through 45 removed outlier: 3.547A pdb=" N ALA 7 35 " --> pdb=" O ALA 7 31 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER 7 37 " --> pdb=" O GLY 7 33 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY 7 40 " --> pdb=" O LYS 7 36 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET 7 44 " --> pdb=" O GLY 7 40 " (cutoff:3.500A) Processing helix chain '7' and resid 56 through 62 Processing helix chain '7' and resid 63 through 79 removed outlier: 3.605A pdb=" N GLY 7 69 " --> pdb=" O ILE 7 65 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER 7 79 " --> pdb=" O LEU 7 75 " (cutoff:3.500A) Processing helix chain '7' and resid 87 through 121 removed outlier: 3.532A pdb=" N SER 7 98 " --> pdb=" O GLY 7 94 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL 7 99 " --> pdb=" O ALA 7 95 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER 7 102 " --> pdb=" O SER 7 98 " (cutoff:3.500A) Processing helix chain '7' and resid 124 through 126 No H-bonds generated for 'chain '7' and resid 124 through 126' Processing helix chain '7' and resid 127 through 154 removed outlier: 3.761A pdb=" N LEU 7 133 " --> pdb=" O VAL 7 129 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE 7 137 " --> pdb=" O LEU 7 133 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU 7 141 " --> pdb=" O PHE 7 137 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLY 7 142 " --> pdb=" O ALA 7 138 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU 7 143 " --> pdb=" O GLU 7 139 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU 7 152 " --> pdb=" O VAL 7 148 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR 7 154 " --> pdb=" O LEU 7 150 " (cutoff:3.500A) Processing helix chain '0' and resid 11 through 45 removed outlier: 4.339A pdb=" N ALA 0 15 " --> pdb=" O ALA 0 11 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET 0 23 " --> pdb=" O ALA 0 19 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE 0 25 " --> pdb=" O ALA 0 21 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER 0 26 " --> pdb=" O ALA 0 22 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY 0 29 " --> pdb=" O PHE 0 25 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR 0 34 " --> pdb=" O ALA 0 30 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER 0 37 " --> pdb=" O GLY 0 33 " (cutoff:3.500A) Processing helix chain '0' and resid 56 through 62 Processing helix chain '0' and resid 64 through 79 removed outlier: 3.833A pdb=" N VAL 0 72 " --> pdb=" O TYR 0 68 " (cutoff:3.500A) Processing helix chain '0' and resid 87 through 124 removed outlier: 3.595A pdb=" N VAL 0 99 " --> pdb=" O ALA 0 95 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY 0 103 " --> pdb=" O VAL 0 99 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA 0 105 " --> pdb=" O LEU 0 101 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE 0 110 " --> pdb=" O ALA 0 106 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY 0 111 " --> pdb=" O GLY 0 107 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA 0 122 " --> pdb=" O VAL 0 118 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN 0 123 " --> pdb=" O ARG 0 119 " (cutoff:3.500A) Processing helix chain '0' and resid 127 through 154 removed outlier: 3.666A pdb=" N LEU 0 133 " --> pdb=" O VAL 0 129 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE 0 134 " --> pdb=" O GLY 0 130 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU 0 141 " --> pdb=" O PHE 0 137 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY 0 142 " --> pdb=" O ALA 0 138 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU 0 143 " --> pdb=" O GLU 0 139 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY 0 145 " --> pdb=" O LEU 0 141 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL 0 148 " --> pdb=" O TYR 0 144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 10 through 17 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 10 through 17 current: chain 'a' and resid 320 through 328 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'a' and resid 174 through 177 Processing sheet with id=AA3, first strand: chain 'a' and resid 502 through 504 Processing sheet with id=AA4, first strand: chain 'U' and resid 44 through 45 Processing sheet with id=AA5, first strand: chain 'U' and resid 121 through 122 Processing sheet with id=AA6, first strand: chain 'U' and resid 233 through 235 removed outlier: 5.571A pdb=" N GLU U 233 " --> pdb=" O TRP U 266 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU U 268 " --> pdb=" O GLU U 233 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLN U 235 " --> pdb=" O LEU U 268 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N PHE U 270 " --> pdb=" O GLN U 235 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL U 408 " --> pdb=" O LEU U 269 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER U 271 " --> pdb=" O MET U 406 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N MET U 406 " --> pdb=" O SER U 271 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS U 405 " --> pdb=" O GLU U 297 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE U 325 " --> pdb=" O PHE U 307 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'U' and resid 315 through 319 removed outlier: 6.292A pdb=" N GLN U 317 " --> pdb=" O LEU U 348 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU U 348 " --> pdb=" O GLN U 317 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY U 379 " --> pdb=" O PHE U 401 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 25 removed outlier: 5.471A pdb=" N VAL L 21 " --> pdb=" O CYS L 32 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N CYS L 32 " --> pdb=" O VAL L 21 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 28 through 32 current: chain 'L' and resid 50 through 58 removed outlier: 7.064A pdb=" N THR L 63 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU L 57 " --> pdb=" O MET L 61 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N MET L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 61 through 66 current: chain 'N' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 28 through 32 current: chain 'N' and resid 50 through 58 removed outlier: 6.714A pdb=" N THR N 63 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU N 57 " --> pdb=" O MET N 61 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 61 through 66 current: chain 'O' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 60 current: chain 'O' and resid 81 through 90 removed outlier: 6.627A pdb=" N VAL O 95 " --> pdb=" O LEU O 87 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL O 89 " --> pdb=" O LYS O 93 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS O 93 " --> pdb=" O VAL O 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 93 through 98 current: chain 'P' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 60 current: chain 'P' and resid 81 through 90 removed outlier: 6.698A pdb=" N VAL P 95 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL P 89 " --> pdb=" O LYS P 93 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LYS P 93 " --> pdb=" O VAL P 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 93 through 98 current: chain 'b' and resid 166 through 167 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 166 through 167 current: chain 'b' and resid 191 through 195 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 191 through 195 current: chain 'c' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 164 through 167 current: chain 'c' and resid 190 through 195 Processing sheet with id=AA9, first strand: chain 'L' and resid 87 through 90 Processing sheet with id=AB1, first strand: chain 'L' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 98 through 99 current: chain 'L' and resid 309 through 315 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 309 through 315 current: chain 'L' and resid 401 through 410 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'L' and resid 164 through 167 removed outlier: 3.815A pdb=" N GLY L 154 " --> pdb=" O ILE L 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 146 through 147 removed outlier: 6.798A pdb=" N GLU L 193 " --> pdb=" O THR L 177 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL L 199 " --> pdb=" O PHE L 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 295 through 298 Processing sheet with id=AB5, first strand: chain 'L' and resid 431 through 432 Processing sheet with id=AB6, first strand: chain 'M' and resid 20 through 25 removed outlier: 5.426A pdb=" N VAL M 21 " --> pdb=" O CYS M 32 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N CYS M 32 " --> pdb=" O VAL M 21 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL M 28 " --> pdb=" O SER M 25 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 28 through 32 current: chain 'M' and resid 50 through 58 removed outlier: 6.656A pdb=" N THR M 63 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU M 57 " --> pdb=" O MET M 61 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 61 through 66 current: chain 'Q' and resid 57 through 61 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 57 through 61 current: chain 'Q' and resid 93 through 98 Processing sheet with id=AB7, first strand: chain 'M' and resid 87 through 90 Processing sheet with id=AB8, first strand: chain 'M' and resid 98 through 99 removed outlier: 6.291A pdb=" N PHE M 99 " --> pdb=" O ALA M 313 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N THR M 315 " --> pdb=" O PHE M 99 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N VAL M 407 " --> pdb=" O VAL M 344 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N MET M 346 " --> pdb=" O VAL M 407 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 133 through 134 Processing sheet with id=AC1, first strand: chain 'M' and resid 146 through 147 removed outlier: 6.282A pdb=" N GLU M 193 " --> pdb=" O THR M 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 152 through 156 removed outlier: 3.694A pdb=" N GLY M 154 " --> pdb=" O ILE M 166 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 219 through 221 removed outlier: 3.588A pdb=" N GLU M 219 " --> pdb=" O LYS M 393 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG M 391 " --> pdb=" O LEU M 221 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 295 through 297 Processing sheet with id=AC5, first strand: chain 'M' and resid 431 through 432 Processing sheet with id=AC6, first strand: chain 'N' and resid 87 through 90 Processing sheet with id=AC7, first strand: chain 'N' and resid 98 through 99 removed outlier: 6.608A pdb=" N ILE N 272 " --> pdb=" O ALA N 310 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL N 312 " --> pdb=" O ILE N 272 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR N 274 " --> pdb=" O VAL N 312 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASN N 314 " --> pdb=" O TYR N 274 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY N 276 " --> pdb=" O ASN N 314 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL N 271 " --> pdb=" O SER N 345 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N MET N 347 " --> pdb=" O VAL N 271 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE N 273 " --> pdb=" O MET N 347 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ASP N 349 " --> pdb=" O ILE N 273 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL N 275 " --> pdb=" O ASP N 349 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 146 through 147 removed outlier: 6.609A pdb=" N GLU N 193 " --> pdb=" O THR N 177 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 152 through 157 removed outlier: 3.698A pdb=" N GLY N 154 " --> pdb=" O ILE N 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 219 through 220 removed outlier: 3.671A pdb=" N GLU N 219 " --> pdb=" O LYS N 393 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 295 through 297 Processing sheet with id=AD3, first strand: chain 'N' and resid 431 through 432 Processing sheet with id=AD4, first strand: chain 'O' and resid 120 through 123 removed outlier: 3.574A pdb=" N ASP O 149 " --> pdb=" O VAL O 123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 131 through 133 removed outlier: 6.811A pdb=" N ALA O 228 " --> pdb=" O LEU O 294 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE O 296 " --> pdb=" O ALA O 228 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL O 230 " --> pdb=" O ILE O 296 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR O 298 " --> pdb=" O VAL O 230 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA O 232 " --> pdb=" O THR O 298 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL O 293 " --> pdb=" O THR O 349 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE O 351 " --> pdb=" O VAL O 293 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL O 295 " --> pdb=" O ILE O 351 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 163 through 164 removed outlier: 4.333A pdb=" N ARG O 340 " --> pdb=" O ILE O 164 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 120 through 123 removed outlier: 3.618A pdb=" N ASP P 149 " --> pdb=" O VAL P 123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 131 through 132 removed outlier: 6.583A pdb=" N PHE P 132 " --> pdb=" O LEU P 261 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N LEU P 263 " --> pdb=" O PHE P 132 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET P 234 " --> pdb=" O THR P 298 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU P 297 " --> pdb=" O ILE P 351 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE P 191 " --> pdb=" O LEU P 354 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 163 through 164 removed outlier: 4.533A pdb=" N ARG P 340 " --> pdb=" O ILE P 164 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 169 through 170 removed outlier: 4.858A pdb=" N ILE P 183 " --> pdb=" O ILE P 170 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 72 through 75 removed outlier: 4.304A pdb=" N LEU Q 45 " --> pdb=" O PHE Q 114 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL d 181 " --> pdb=" O ASN d 194 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU d 182 " --> pdb=" O ARG d 135 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE d 133 " --> pdb=" O TYR d 184 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N MET d 132 " --> pdb=" O GLN d 166 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASP d 168 " --> pdb=" O MET d 132 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL d 134 " --> pdb=" O ASP d 168 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 120 through 123 Processing sheet with id=AE4, first strand: chain 'Q' and resid 131 through 133 removed outlier: 6.960A pdb=" N ALA Q 228 " --> pdb=" O LEU Q 294 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE Q 296 " --> pdb=" O ALA Q 228 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL Q 230 " --> pdb=" O ILE Q 296 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR Q 298 " --> pdb=" O VAL Q 230 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA Q 232 " --> pdb=" O THR Q 298 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU Q 297 " --> pdb=" O ILE Q 351 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 163 through 164 removed outlier: 4.257A pdb=" N ARG Q 340 " --> pdb=" O ILE Q 164 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 375 through 376 removed outlier: 3.975A pdb=" N LEU Q 398 " --> pdb=" O GLN Q 376 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 92 through 101 Processing sheet with id=AE8, first strand: chain 'F' and resid 36 through 38 removed outlier: 6.276A pdb=" N ALA F 9 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N ASN F 67 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ILE F 11 " --> pdb=" O ASN F 67 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE F 64 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE F 91 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE F 66 " --> pdb=" O ILE F 91 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 34 through 37 Processing sheet with id=AF1, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AF2, first strand: chain 'C' and resid 214 through 218 removed outlier: 4.565A pdb=" N ASN C 214 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN C 226 " --> pdb=" O ASN C 214 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU C 224 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU C 218 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N SER C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 189 " --> pdb=" O TYR C 223 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N CYS C 225 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 187 " --> pdb=" O CYS C 225 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU C 186 " --> pdb=" O ARG C 249 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 's' and resid 258 through 260 WARNING: can't find start of bonding for strands! previous: chain 's' and resid 267 through 270 current: chain 's' and resid 282 through 284 WARNING: can't find start of bonding for strands! previous: chain 's' and resid 282 through 284 current: chain 's' and resid 394 through 403 Processing sheet with id=AF4, first strand: chain 's' and resid 301 through 302 WARNING: can't find start of bonding for strands! previous: chain 's' and resid 321 through 328 current: chain 's' and resid 337 through 348 Processing sheet with id=AF5, first strand: chain 's' and resid 356 through 357 2854 hydrogen bonds defined for protein. 8334 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: 28.06 Time building geometry restraints manager: 15.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 11211 1.28 - 1.42: 16526 1.42 - 1.56: 39738 1.56 - 1.70: 29 1.70 - 1.84: 640 Bond restraints: 68144 Sorted by residual: bond pdb=" C29 POV 1 301 " pdb="C210 POV 1 301 " ideal model delta sigma weight residual 1.333 1.532 -0.199 2.00e-02 2.50e+03 9.88e+01 bond pdb=" C29 POV 1 303 " pdb="C210 POV 1 303 " ideal model delta sigma weight residual 1.333 1.530 -0.197 2.00e-02 2.50e+03 9.68e+01 bond pdb=" C29 POV r 401 " pdb="C210 POV r 401 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.49e+01 bond pdb=" C29 POV 1 302 " pdb="C210 POV 1 302 " ideal model delta sigma weight residual 1.333 1.527 -0.194 2.00e-02 2.50e+03 9.42e+01 bond pdb=" C29 POV r 402 " pdb="C210 POV r 402 " ideal model delta sigma weight residual 1.333 1.526 -0.193 2.00e-02 2.50e+03 9.36e+01 ... (remaining 68139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 91614 4.08 - 8.17: 540 8.17 - 12.25: 61 12.25 - 16.33: 25 16.33 - 20.41: 8 Bond angle restraints: 92248 Sorted by residual: angle pdb=" N ASN a 178 " pdb=" CA ASN a 178 " pdb=" C ASN a 178 " ideal model delta sigma weight residual 111.03 122.98 -11.95 1.11e+00 8.12e-01 1.16e+02 angle pdb=" N ASP s 417 " pdb=" CA ASP s 417 " pdb=" C ASP s 417 " ideal model delta sigma weight residual 110.41 120.03 -9.62 1.23e+00 6.61e-01 6.12e+01 angle pdb=" N SER Q 501 " pdb=" CA SER Q 501 " pdb=" C SER Q 501 " ideal model delta sigma weight residual 112.93 121.64 -8.71 1.12e+00 7.97e-01 6.04e+01 angle pdb=" N GLN Q 497 " pdb=" CA GLN Q 497 " pdb=" C GLN Q 497 " ideal model delta sigma weight residual 111.28 119.52 -8.24 1.09e+00 8.42e-01 5.71e+01 angle pdb=" O13 POV r 401 " pdb=" P POV r 401 " pdb=" O14 POV r 401 " ideal model delta sigma weight residual 121.11 100.70 20.41 3.00e+00 1.11e-01 4.63e+01 ... (remaining 92243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.62: 40162 33.62 - 67.24: 999 67.24 - 100.86: 161 100.86 - 134.48: 8 134.48 - 168.10: 3 Dihedral angle restraints: 41333 sinusoidal: 15951 harmonic: 25382 Sorted by residual: dihedral pdb=" O2A ADP M 701 " pdb=" O3A ADP M 701 " pdb=" PA ADP M 701 " pdb=" PB ADP M 701 " ideal model delta sinusoidal sigma weight residual -60.00 91.27 -151.26 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O1B ADP M 701 " pdb=" O3A ADP M 701 " pdb=" PB ADP M 701 " pdb=" PA ADP M 701 " ideal model delta sinusoidal sigma weight residual -60.00 80.25 -140.25 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" CA ILE 2 84 " pdb=" C ILE 2 84 " pdb=" N SER 2 85 " pdb=" CA SER 2 85 " ideal model delta harmonic sigma weight residual 180.00 -152.02 -27.98 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 41330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 10346 0.126 - 0.252: 253 0.252 - 0.378: 14 0.378 - 0.504: 1 0.504 - 0.630: 2 Chirality restraints: 10616 Sorted by residual: chirality pdb=" C1 NAG s 505 " pdb=" ND2 ASN s 357 " pdb=" C2 NAG s 505 " pdb=" O5 NAG s 505 " both_signs ideal model delta sigma weight residual False -2.40 -3.03 0.63 2.00e-01 2.50e+01 9.93e+00 chirality pdb=" CA SER Q 501 " pdb=" N SER Q 501 " pdb=" C SER Q 501 " pdb=" CB SER Q 501 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" CA GLN Q 497 " pdb=" N GLN Q 497 " pdb=" C GLN Q 497 " pdb=" CB GLN Q 497 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.86e+00 ... (remaining 10613 not shown) Planarity restraints: 11865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV s 507 " 0.302 2.00e-02 2.50e+03 3.35e-01 1.12e+03 pdb=" C29 POV s 507 " -0.558 2.00e-02 2.50e+03 pdb="C210 POV s 507 " 0.207 2.00e-02 2.50e+03 pdb="C211 POV s 507 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV 1 302 " -0.145 2.00e-02 2.50e+03 2.63e-01 6.93e+02 pdb=" C29 POV 1 302 " 0.341 2.00e-02 2.50e+03 pdb="C210 POV 1 302 " -0.344 2.00e-02 2.50e+03 pdb="C211 POV 1 302 " 0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN s 261 " -0.171 2.00e-02 2.50e+03 2.08e-01 5.40e+02 pdb=" CG ASN s 261 " 0.072 2.00e-02 2.50e+03 pdb=" OD1 ASN s 261 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN s 261 " 0.354 2.00e-02 2.50e+03 pdb=" C1 NAG s 506 " -0.237 2.00e-02 2.50e+03 ... (remaining 11862 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 437 2.59 - 3.17: 50964 3.17 - 3.74: 98173 3.74 - 4.32: 139403 4.32 - 4.90: 229611 Nonbonded interactions: 518588 Sorted by model distance: nonbonded pdb=" NH2 ARG P 400 " pdb=" O1B ADP M 701 " model vdw 2.011 2.496 nonbonded pdb=" O ILE O 71 " pdb=" OG1 THR O 115 " model vdw 2.262 3.040 nonbonded pdb=" O ALA 9 11 " pdb=" OG SER 9 89 " model vdw 2.264 3.040 nonbonded pdb=" CE1 TYR U 367 " pdb=" O ARG U 382 " model vdw 2.264 3.340 nonbonded pdb=" OG SER U 103 " pdb=" O GLU U 197 " model vdw 2.267 3.040 ... (remaining 518583 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 '0' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = (chain '8' and resid 6 through 155) selection = chain '9' } ncs_group { reference = chain 'L' selection = (chain 'M' and resid 17 through 616) selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = (chain 'b' and resid 8 through 226) selection = chain 'c' selection = (chain 'd' and resid 8 through 226) } ncs_group { reference = (chain 'e' and resid 5 through 116) selection = (chain 'f' and resid 5 through 116) selection = chain 'g' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 2.260 Check model and map are aligned: 0.390 Set scattering table: 0.480 Process input model: 120.170 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.007 0.199 68144 Z= 0.466 Angle : 0.981 20.414 92248 Z= 0.530 Chirality : 0.054 0.630 10616 Planarity : 0.008 0.335 11859 Dihedral : 15.889 168.098 25004 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.27 % Allowed : 8.21 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.90 (0.06), residues: 8727 helix: -4.67 (0.03), residues: 4540 sheet: -2.37 (0.16), residues: 799 loop : -2.86 (0.09), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP 1 67 HIS 0.012 0.001 HIS M 47 PHE 0.030 0.002 PHE s 274 TYR 0.031 0.002 TYR a 741 ARG 0.011 0.001 ARG P 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1285 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1267 time to evaluate : 5.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 71 GLU cc_start: 0.7561 (tp30) cc_final: 0.7094 (tm-30) REVERT: a 199 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5374 (mm) REVERT: a 236 LYS cc_start: 0.6566 (tptt) cc_final: 0.5957 (mmtp) REVERT: a 247 TYR cc_start: 0.3692 (m-80) cc_final: 0.3490 (m-80) REVERT: a 266 ARG cc_start: 0.5393 (mtt180) cc_final: 0.5090 (ttt180) REVERT: a 350 MET cc_start: 0.4876 (mtp) cc_final: 0.4047 (mtp) REVERT: a 451 LEU cc_start: 0.8372 (tt) cc_final: 0.7964 (tt) REVERT: a 486 MET cc_start: 0.7659 (mmt) cc_final: 0.7378 (mmt) REVERT: a 646 MET cc_start: 0.7772 (mmm) cc_final: 0.7545 (tpt) REVERT: a 728 ILE cc_start: 0.9235 (pt) cc_final: 0.8431 (mt) REVERT: U 333 MET cc_start: 0.7629 (mtt) cc_final: 0.7317 (mtt) REVERT: L 95 MET cc_start: 0.8994 (mmt) cc_final: 0.8684 (mmt) REVERT: L 301 LYS cc_start: 0.7698 (pttt) cc_final: 0.7121 (ptmt) REVERT: L 303 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7340 (mp0) REVERT: L 442 ARG cc_start: 0.7350 (mtt180) cc_final: 0.7055 (mtm-85) REVERT: L 544 MET cc_start: 0.7912 (mtt) cc_final: 0.7619 (mtm) REVERT: L 574 MET cc_start: 0.5737 (mtt) cc_final: 0.5245 (mtp) REVERT: L 577 ILE cc_start: 0.7658 (mm) cc_final: 0.7434 (tp) REVERT: L 597 ILE cc_start: 0.8995 (mt) cc_final: 0.8706 (tt) REVERT: L 607 ASP cc_start: 0.8203 (m-30) cc_final: 0.7946 (m-30) REVERT: M 613 ARG cc_start: 0.7024 (mtm180) cc_final: 0.6485 (tpm170) REVERT: N 114 GLN cc_start: 0.8262 (mm-40) cc_final: 0.8011 (tp-100) REVERT: N 139 LYS cc_start: 0.7661 (pptt) cc_final: 0.7440 (ptmt) REVERT: N 279 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6408 (mt-10) REVERT: N 506 LYS cc_start: 0.5660 (mttt) cc_final: 0.5346 (mttt) REVERT: N 541 LEU cc_start: 0.8491 (tp) cc_final: 0.8151 (tt) REVERT: N 574 MET cc_start: 0.4686 (mtm) cc_final: 0.4233 (mmm) REVERT: O 54 ASN cc_start: 0.8833 (t0) cc_final: 0.8585 (t0) REVERT: P 39 TYR cc_start: 0.5826 (m-10) cc_final: 0.5353 (m-10) REVERT: P 265 ASN cc_start: 0.8064 (p0) cc_final: 0.7858 (m-40) REVERT: P 433 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8158 (tm-30) REVERT: P 435 MET cc_start: 0.7748 (mmm) cc_final: 0.7345 (mmt) REVERT: Q 54 ASN cc_start: 0.8601 (t0) cc_final: 0.8203 (t0) REVERT: Q 249 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7871 (mt-10) REVERT: D 85 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7813 (mm-40) REVERT: D 86 ASN cc_start: 0.7396 (t0) cc_final: 0.7048 (t0) REVERT: b 68 LYS cc_start: 0.8778 (mttt) cc_final: 0.8299 (mtpp) REVERT: c 72 MET cc_start: 0.8183 (tpp) cc_final: 0.7804 (tpp) REVERT: c 112 TYR cc_start: 0.9045 (t80) cc_final: 0.8718 (t80) REVERT: d 26 LYS cc_start: 0.7306 (mmtt) cc_final: 0.6919 (mtmt) REVERT: d 39 ASN cc_start: 0.8641 (m-40) cc_final: 0.8349 (m-40) REVERT: d 72 MET cc_start: 0.7460 (mmm) cc_final: 0.6912 (ptt) REVERT: d 77 ASN cc_start: 0.8382 (t0) cc_final: 0.8109 (t0) REVERT: d 125 TYR cc_start: 0.8808 (m-10) cc_final: 0.8526 (m-80) REVERT: e 53 LYS cc_start: 0.6397 (mtpt) cc_final: 0.5981 (ptpp) REVERT: e 80 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7591 (mtpt) REVERT: F 53 ARG cc_start: 0.8131 (ttp-110) cc_final: 0.7888 (mtm110) REVERT: F 82 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8324 (mm110) REVERT: k 78 MET cc_start: 0.7944 (ttp) cc_final: 0.7680 (ttp) REVERT: k 150 LEU cc_start: 0.8615 (tp) cc_final: 0.8256 (tp) REVERT: k 154 ILE cc_start: 0.8337 (mm) cc_final: 0.8106 (mt) REVERT: k 209 CYS cc_start: 0.7812 (m) cc_final: 0.7479 (m) REVERT: m 13 MET cc_start: 0.8164 (mmm) cc_final: 0.7860 (mmt) REVERT: m 27 PHE cc_start: 0.7963 (m-80) cc_final: 0.7671 (m-10) REVERT: m 56 ILE cc_start: 0.9237 (tt) cc_final: 0.9012 (tt) REVERT: n 67 MET cc_start: 0.7489 (ttp) cc_final: 0.7269 (ttp) REVERT: s 398 GLN cc_start: 0.8141 (tt0) cc_final: 0.7866 (tt0) REVERT: s 453 MET cc_start: 0.8219 (pmm) cc_final: 0.7992 (pmm) REVERT: 8 139 GLU cc_start: 0.7820 (tt0) cc_final: 0.7541 (tt0) REVERT: 9 54 LYS cc_start: 0.8184 (pttt) cc_final: 0.7935 (ptpt) REVERT: 9 64 ILE cc_start: 0.8590 (mt) cc_final: 0.8066 (mm) REVERT: 9 68 TYR cc_start: 0.8499 (m-10) cc_final: 0.8245 (m-10) REVERT: 9 134 ILE cc_start: 0.9335 (mm) cc_final: 0.9034 (mm) REVERT: 1 82 LYS cc_start: 0.8597 (mmmm) cc_final: 0.7916 (tppt) REVERT: 1 107 MET cc_start: 0.8357 (mmm) cc_final: 0.8134 (tpt) REVERT: 1 113 ASN cc_start: 0.8047 (m-40) cc_final: 0.7672 (t0) REVERT: 1 114 MET cc_start: 0.8139 (mtt) cc_final: 0.7893 (mpp) REVERT: 1 116 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7906 (mt-10) REVERT: 4 127 LEU cc_start: 0.8877 (tp) cc_final: 0.8656 (tp) REVERT: 4 139 GLU cc_start: 0.8912 (tp30) cc_final: 0.8711 (tp30) REVERT: 5 92 GLN cc_start: 0.9248 (mm-40) cc_final: 0.8983 (mm-40) REVERT: 6 83 ASP cc_start: 0.8062 (p0) cc_final: 0.7263 (p0) REVERT: 6 124 GLN cc_start: 0.8602 (tp-100) cc_final: 0.8342 (tm-30) REVERT: 7 23 MET cc_start: 0.8211 (tpt) cc_final: 0.7883 (tpp) REVERT: 0 54 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7693 (mttt) REVERT: 0 68 TYR cc_start: 0.8452 (m-10) cc_final: 0.8243 (m-10) REVERT: 0 132 ILE cc_start: 0.8989 (mm) cc_final: 0.8761 (mm) outliers start: 18 outliers final: 6 residues processed: 1283 average time/residue: 0.6979 time to fit residues: 1490.9227 Evaluate side-chains 889 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 882 time to evaluate : 5.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 734 optimal weight: 4.9990 chunk 659 optimal weight: 0.6980 chunk 365 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 444 optimal weight: 4.9990 chunk 352 optimal weight: 0.7980 chunk 681 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 chunk 414 optimal weight: 1.9990 chunk 507 optimal weight: 0.9980 chunk 790 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 300 GLN a 318 GLN a 435 GLN a 495 HIS a 516 ASN a 640 GLN a 814 GLN ** U 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 GLN U 97 HIS U 143 HIS U 159 ASN U 380 HIS L 314 ASN L 449 ASN L 468 HIS L 573 HIS M 172 ASN M 261 GLN M 397 ASN M 430 GLN M 449 ASN M 484 GLN ** N 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 573 HIS N 603 GLN O 199 HIS O 205 GLN O 292 HIS O 382 GLN ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 421 GLN P 497 GLN Q 199 HIS Q 209 GLN Q 256 ASN Q 262 ASN Q 292 HIS ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 421 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS b 21 GLN b 39 ASN b 77 ASN c 66 GLN c 77 ASN c 161 ASN d 14 HIS d 24 ASN d 126 GLN d 139 GLN d 206 GLN d 221 ASN f 35 GLN f 111 HIS f 113 ASN g 85 GLN g 91 ASN k 50 GLN ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 183 ASN m 67 GLN n 103 GLN s 255 HIS s 329 ASN s 398 GLN s 403 GLN 9 51 GLN 9 123 GLN 1 128 HIS 1 148 ASN 2 51 GLN 2 123 GLN 6 51 GLN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 68144 Z= 0.180 Angle : 0.610 11.400 92248 Z= 0.322 Chirality : 0.043 0.423 10616 Planarity : 0.005 0.085 11859 Dihedral : 9.216 177.695 10104 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.36 % Favored : 96.63 % Rotamer: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.07), residues: 8727 helix: -2.65 (0.06), residues: 4643 sheet: -2.02 (0.16), residues: 812 loop : -2.42 (0.09), residues: 3272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP m 74 HIS 0.006 0.001 HIS U 53 PHE 0.025 0.001 PHE N 547 TYR 0.022 0.001 TYR 1 70 ARG 0.009 0.000 ARG a 807 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1147 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1145 time to evaluate : 5.867 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: a 10 MET cc_start: 0.7398 (mmm) cc_final: 0.6902 (mmm) REVERT: a 236 LYS cc_start: 0.6689 (tptt) cc_final: 0.6212 (tppt) REVERT: a 247 TYR cc_start: 0.3640 (m-80) cc_final: 0.3414 (m-80) REVERT: a 261 GLU cc_start: 0.5790 (pp20) cc_final: 0.5410 (pm20) REVERT: a 266 ARG cc_start: 0.5277 (mtt180) cc_final: 0.5046 (ttt180) REVERT: a 486 MET cc_start: 0.7631 (mmt) cc_final: 0.7384 (mmt) REVERT: a 728 ILE cc_start: 0.9161 (pt) cc_final: 0.8383 (mt) REVERT: U 253 TYR cc_start: 0.8339 (t80) cc_final: 0.8051 (t80) REVERT: U 424 LYS cc_start: 0.5652 (tttt) cc_final: 0.5198 (mtpt) REVERT: L 178 TYR cc_start: 0.8191 (t80) cc_final: 0.7888 (t80) REVERT: L 303 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7354 (mm-30) REVERT: L 574 MET cc_start: 0.5542 (mtt) cc_final: 0.5226 (mtp) REVERT: L 577 ILE cc_start: 0.7477 (mm) cc_final: 0.7245 (tp) REVERT: M 347 MET cc_start: 0.8071 (mmm) cc_final: 0.7817 (mmm) REVERT: M 613 ARG cc_start: 0.7131 (mtm180) cc_final: 0.5826 (tpm170) REVERT: N 114 GLN cc_start: 0.8243 (mm-40) cc_final: 0.8008 (tp-100) REVERT: N 139 LYS cc_start: 0.7576 (pptt) cc_final: 0.7362 (ptmt) REVERT: N 405 SER cc_start: 0.9512 (m) cc_final: 0.9076 (t) REVERT: N 506 LYS cc_start: 0.4991 (mttt) cc_final: 0.4591 (mttt) REVERT: N 574 MET cc_start: 0.5387 (mtm) cc_final: 0.4990 (mmt) REVERT: O 54 ASN cc_start: 0.8701 (t0) cc_final: 0.8363 (t0) REVERT: O 249 GLU cc_start: 0.7506 (pt0) cc_final: 0.7261 (pt0) REVERT: P 433 GLN cc_start: 0.8332 (tm-30) cc_final: 0.8028 (tm-30) REVERT: Q 54 ASN cc_start: 0.8460 (t0) cc_final: 0.8078 (t0) REVERT: Q 249 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7886 (mt-10) REVERT: D 86 ASN cc_start: 0.7236 (t0) cc_final: 0.7019 (t0) REVERT: b 68 LYS cc_start: 0.8852 (mttt) cc_final: 0.8352 (mtpp) REVERT: c 72 MET cc_start: 0.8255 (tpp) cc_final: 0.7805 (tpp) REVERT: d 26 LYS cc_start: 0.7390 (mmtt) cc_final: 0.6980 (mttp) REVERT: d 44 ARG cc_start: 0.7148 (ttp-170) cc_final: 0.6887 (tmm160) REVERT: d 55 GLU cc_start: 0.6859 (tp30) cc_final: 0.6292 (mm-30) REVERT: d 72 MET cc_start: 0.7594 (mmm) cc_final: 0.7065 (ptt) REVERT: d 77 ASN cc_start: 0.8045 (t0) cc_final: 0.7673 (t0) REVERT: e 80 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7725 (mtpt) REVERT: f 46 GLN cc_start: 0.6866 (pt0) cc_final: 0.6213 (tm-30) REVERT: F 75 ARG cc_start: 0.8115 (tpp-160) cc_final: 0.7758 (tpt-90) REVERT: k 120 ARG cc_start: 0.7758 (tpp80) cc_final: 0.7539 (ttm110) REVERT: k 150 LEU cc_start: 0.8531 (tp) cc_final: 0.8153 (tp) REVERT: k 154 ILE cc_start: 0.8262 (mm) cc_final: 0.7988 (mt) REVERT: k 209 CYS cc_start: 0.7801 (m) cc_final: 0.7486 (m) REVERT: m 23 LEU cc_start: 0.8012 (mp) cc_final: 0.7550 (tp) REVERT: m 46 VAL cc_start: 0.9352 (p) cc_final: 0.9151 (t) REVERT: m 56 ILE cc_start: 0.9151 (tt) cc_final: 0.8857 (tt) REVERT: s 453 MET cc_start: 0.8174 (pmm) cc_final: 0.7488 (ptp) REVERT: 8 121 THR cc_start: 0.8978 (m) cc_final: 0.8729 (t) REVERT: 9 68 TYR cc_start: 0.8328 (m-10) cc_final: 0.8028 (m-10) REVERT: 1 82 LYS cc_start: 0.8524 (mmmm) cc_final: 0.7820 (tppt) REVERT: 1 116 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7980 (mt-10) REVERT: 1 197 GLN cc_start: 0.8520 (mt0) cc_final: 0.8212 (mt0) REVERT: 2 124 GLN cc_start: 0.8529 (tp-100) cc_final: 0.8305 (tp40) REVERT: 2 134 ILE cc_start: 0.9217 (mm) cc_final: 0.8910 (mm) REVERT: 3 144 TYR cc_start: 0.8599 (m-10) cc_final: 0.8335 (m-10) REVERT: 4 23 MET cc_start: 0.8621 (tpt) cc_final: 0.8319 (tpp) REVERT: 5 61 MET cc_start: 0.7761 (ttm) cc_final: 0.6681 (ttm) REVERT: 5 84 ILE cc_start: 0.9002 (mm) cc_final: 0.8662 (mt) REVERT: 6 83 ASP cc_start: 0.7881 (p0) cc_final: 0.7099 (p0) REVERT: 7 84 ILE cc_start: 0.8509 (mt) cc_final: 0.8201 (mt) REVERT: 0 54 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7758 (tttt) REVERT: 0 57 ILE cc_start: 0.9037 (mp) cc_final: 0.8520 (mp) outliers start: 2 outliers final: 0 residues processed: 1147 average time/residue: 0.6443 time to fit residues: 1259.8640 Evaluate side-chains 872 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 872 time to evaluate : 5.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 439 optimal weight: 7.9990 chunk 245 optimal weight: 7.9990 chunk 657 optimal weight: 1.9990 chunk 537 optimal weight: 20.0000 chunk 217 optimal weight: 5.9990 chunk 791 optimal weight: 6.9990 chunk 855 optimal weight: 5.9990 chunk 704 optimal weight: 4.9990 chunk 784 optimal weight: 6.9990 chunk 269 optimal weight: 5.9990 chunk 634 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 443 ASN U 264 HIS L 207 GLN L 449 ASN L 573 HIS M 65 GLN M 172 ASN M 468 HIS N 231 GLN ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 HIS P 205 GLN P 265 ASN ** Q 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 206 GLN b 9 GLN d 49 GLN d 139 GLN e 9 GLN f 10 GLN f 35 GLN k 84 HIS ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 67 GLN n 129 ASN 1 90 ASN 6 124 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 68144 Z= 0.407 Angle : 0.690 10.967 92248 Z= 0.358 Chirality : 0.048 0.631 10616 Planarity : 0.005 0.081 11859 Dihedral : 9.036 168.882 10104 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.08), residues: 8727 helix: -1.64 (0.07), residues: 4664 sheet: -1.88 (0.17), residues: 777 loop : -2.29 (0.10), residues: 3286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 450 HIS 0.014 0.001 HIS b 14 PHE 0.026 0.002 PHE L 291 TYR 0.031 0.002 TYR O 371 ARG 0.012 0.001 ARG 5 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1030 time to evaluate : 5.960 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: a 177 ILE cc_start: 0.3611 (tp) cc_final: 0.3287 (tp) REVERT: a 236 LYS cc_start: 0.6702 (tptt) cc_final: 0.6099 (tppt) REVERT: a 247 TYR cc_start: 0.3813 (m-80) cc_final: 0.3547 (m-80) REVERT: a 266 ARG cc_start: 0.5352 (mtt180) cc_final: 0.4965 (ttt180) REVERT: a 350 MET cc_start: 0.4540 (mmm) cc_final: 0.4214 (mmt) REVERT: a 486 MET cc_start: 0.7678 (mmt) cc_final: 0.7274 (mmt) REVERT: a 552 MET cc_start: 0.9013 (mtp) cc_final: 0.8796 (mtt) REVERT: a 728 ILE cc_start: 0.9216 (pt) cc_final: 0.8414 (mt) REVERT: a 796 MET cc_start: 0.7438 (ttm) cc_final: 0.6947 (mtt) REVERT: a 821 ASP cc_start: 0.7578 (m-30) cc_final: 0.7304 (m-30) REVERT: U 424 LYS cc_start: 0.5686 (tttt) cc_final: 0.5235 (mtpt) REVERT: L 95 MET cc_start: 0.8973 (mmt) cc_final: 0.8536 (mmt) REVERT: L 131 ILE cc_start: 0.9050 (mm) cc_final: 0.8769 (mm) REVERT: L 574 MET cc_start: 0.5726 (mtt) cc_final: 0.5337 (mtp) REVERT: M 488 ASP cc_start: 0.7602 (m-30) cc_final: 0.7269 (m-30) REVERT: M 613 ARG cc_start: 0.7142 (mtm180) cc_final: 0.6083 (tpm170) REVERT: N 139 LYS cc_start: 0.7803 (pptt) cc_final: 0.7524 (ptmt) REVERT: N 481 GLU cc_start: 0.7728 (tp30) cc_final: 0.7386 (tp30) REVERT: N 506 LYS cc_start: 0.5091 (mttt) cc_final: 0.4728 (mttt) REVERT: N 507 ILE cc_start: 0.5129 (mt) cc_final: 0.4902 (mt) REVERT: N 535 TYR cc_start: 0.7450 (p90) cc_final: 0.7235 (p90) REVERT: N 574 MET cc_start: 0.5194 (mtm) cc_final: 0.4735 (mmp) REVERT: O 54 ASN cc_start: 0.8829 (t0) cc_final: 0.8587 (t0) REVERT: O 428 ILE cc_start: 0.8549 (mt) cc_final: 0.8325 (mm) REVERT: Q 54 ASN cc_start: 0.8583 (t0) cc_final: 0.8181 (t0) REVERT: Q 360 ASP cc_start: 0.7782 (t0) cc_final: 0.7551 (t0) REVERT: D 86 ASN cc_start: 0.7464 (t0) cc_final: 0.7185 (t0) REVERT: b 68 LYS cc_start: 0.8836 (mttt) cc_final: 0.8351 (mtpp) REVERT: c 66 GLN cc_start: 0.7809 (tt0) cc_final: 0.7421 (tt0) REVERT: c 72 MET cc_start: 0.8361 (tpp) cc_final: 0.8079 (tpp) REVERT: d 26 LYS cc_start: 0.7678 (mmtt) cc_final: 0.7079 (mtmt) REVERT: d 55 GLU cc_start: 0.6844 (tp30) cc_final: 0.6575 (mm-30) REVERT: d 72 MET cc_start: 0.7914 (mmm) cc_final: 0.7372 (ptt) REVERT: e 10 GLN cc_start: 0.8047 (mm110) cc_final: 0.7455 (mm-40) REVERT: e 80 LYS cc_start: 0.8057 (mtmt) cc_final: 0.7712 (mtpt) REVERT: f 46 GLN cc_start: 0.6982 (pt0) cc_final: 0.6507 (tm-30) REVERT: g 75 LYS cc_start: 0.7698 (mtmt) cc_final: 0.7248 (mtpp) REVERT: F 46 ASN cc_start: 0.8075 (p0) cc_final: 0.7525 (p0) REVERT: F 75 ARG cc_start: 0.8146 (tpp-160) cc_final: 0.7807 (tpt-90) REVERT: k 120 ARG cc_start: 0.7735 (tpp80) cc_final: 0.7410 (ttm110) REVERT: k 150 LEU cc_start: 0.8589 (tp) cc_final: 0.8217 (tp) REVERT: k 209 CYS cc_start: 0.8026 (m) cc_final: 0.7508 (m) REVERT: m 23 LEU cc_start: 0.8120 (mp) cc_final: 0.7715 (tp) REVERT: m 56 ILE cc_start: 0.9212 (tt) cc_final: 0.8928 (tt) REVERT: s 360 GLN cc_start: 0.8059 (mp10) cc_final: 0.7652 (mp10) REVERT: s 453 MET cc_start: 0.8228 (pmm) cc_final: 0.7769 (ptp) REVERT: 1 82 LYS cc_start: 0.8518 (mmmm) cc_final: 0.7911 (tppt) REVERT: 1 116 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7959 (mt-10) REVERT: 2 139 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8253 (tm-30) REVERT: 3 134 ILE cc_start: 0.8830 (mm) cc_final: 0.8520 (mt) REVERT: 4 23 MET cc_start: 0.8562 (tpt) cc_final: 0.8130 (tpp) REVERT: 6 83 ASP cc_start: 0.7929 (p0) cc_final: 0.7166 (p0) outliers start: 6 outliers final: 2 residues processed: 1034 average time/residue: 0.6569 time to fit residues: 1157.0233 Evaluate side-chains 832 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 830 time to evaluate : 5.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 781 optimal weight: 5.9990 chunk 595 optimal weight: 4.9990 chunk 410 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 377 optimal weight: 2.9990 chunk 531 optimal weight: 10.0000 chunk 794 optimal weight: 0.9980 chunk 840 optimal weight: 4.9990 chunk 414 optimal weight: 3.9990 chunk 752 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 135 GLN ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 443 ASN U 277 HIS L 314 ASN M 172 ASN M 573 HIS ** N 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 497 GLN D 46 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** b 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 HIS d 39 ASN d 139 GLN ** e 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 35 GLN g 41 GLN ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 297 HIS m 67 GLN n 129 ASN 2 124 GLN 6 124 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 68144 Z= 0.260 Angle : 0.588 9.699 92248 Z= 0.304 Chirality : 0.044 0.414 10616 Planarity : 0.004 0.081 11859 Dihedral : 8.499 149.753 10104 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.08), residues: 8727 helix: -1.00 (0.07), residues: 4614 sheet: -1.68 (0.18), residues: 768 loop : -2.08 (0.10), residues: 3345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP m 74 HIS 0.007 0.001 HIS U 285 PHE 0.017 0.001 PHE L 291 TYR 0.025 0.001 TYR a 741 ARG 0.013 0.000 ARG M 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1045 time to evaluate : 5.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 236 LYS cc_start: 0.6456 (tptt) cc_final: 0.5964 (tppt) REVERT: a 247 TYR cc_start: 0.3899 (m-80) cc_final: 0.3618 (m-80) REVERT: a 266 ARG cc_start: 0.5435 (mtt180) cc_final: 0.5072 (ttt180) REVERT: a 350 MET cc_start: 0.4840 (mmm) cc_final: 0.4391 (mmt) REVERT: a 666 HIS cc_start: 0.7560 (t70) cc_final: 0.6794 (t-170) REVERT: a 728 ILE cc_start: 0.9214 (pt) cc_final: 0.8452 (mt) REVERT: a 796 MET cc_start: 0.7368 (ttm) cc_final: 0.6800 (mtt) REVERT: U 424 LYS cc_start: 0.5744 (tttt) cc_final: 0.5259 (mtpt) REVERT: L 131 ILE cc_start: 0.9086 (mm) cc_final: 0.8823 (mm) REVERT: L 187 THR cc_start: 0.8113 (p) cc_final: 0.7899 (p) REVERT: L 462 ASP cc_start: 0.8295 (m-30) cc_final: 0.7710 (m-30) REVERT: M 205 MET cc_start: 0.8173 (mtm) cc_final: 0.7873 (mtm) REVERT: M 488 ASP cc_start: 0.7573 (m-30) cc_final: 0.7255 (m-30) REVERT: M 565 ILE cc_start: 0.8430 (mt) cc_final: 0.8230 (tp) REVERT: M 574 MET cc_start: 0.8022 (mmt) cc_final: 0.7277 (mmt) REVERT: M 613 ARG cc_start: 0.7126 (mtm180) cc_final: 0.6049 (tpm170) REVERT: N 114 GLN cc_start: 0.8321 (mm-40) cc_final: 0.8097 (tp-100) REVERT: N 139 LYS cc_start: 0.7822 (pptt) cc_final: 0.7428 (ptmt) REVERT: N 506 LYS cc_start: 0.5179 (mttt) cc_final: 0.4806 (mttt) REVERT: N 573 HIS cc_start: 0.5729 (t-170) cc_final: 0.5326 (t-170) REVERT: N 574 MET cc_start: 0.5271 (mtm) cc_final: 0.4859 (mmt) REVERT: O 135 SER cc_start: 0.8420 (p) cc_final: 0.7629 (t) REVERT: P 316 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6878 (mt-10) REVERT: P 433 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8031 (tm-30) REVERT: Q 54 ASN cc_start: 0.8498 (t0) cc_final: 0.8202 (t0) REVERT: D 86 ASN cc_start: 0.7333 (t0) cc_final: 0.7111 (t0) REVERT: b 68 LYS cc_start: 0.8813 (mttt) cc_final: 0.8316 (mtpp) REVERT: b 159 THR cc_start: 0.8908 (p) cc_final: 0.8359 (p) REVERT: b 161 ASN cc_start: 0.7352 (m110) cc_final: 0.6962 (m110) REVERT: d 15 MET cc_start: 0.2862 (mmp) cc_final: 0.2055 (tpt) REVERT: d 26 LYS cc_start: 0.7775 (mmtt) cc_final: 0.7038 (mttp) REVERT: d 55 GLU cc_start: 0.6862 (tp30) cc_final: 0.6640 (mm-30) REVERT: e 10 GLN cc_start: 0.8187 (mm110) cc_final: 0.7209 (mm-40) REVERT: f 46 GLN cc_start: 0.6903 (pt0) cc_final: 0.6356 (tm-30) REVERT: F 46 ASN cc_start: 0.7994 (p0) cc_final: 0.7420 (p0) REVERT: F 75 ARG cc_start: 0.8181 (tpp-160) cc_final: 0.7555 (tpt-90) REVERT: k 38 GLN cc_start: 0.7719 (mp10) cc_final: 0.7484 (pm20) REVERT: k 150 LEU cc_start: 0.8546 (tp) cc_final: 0.7907 (tp) REVERT: k 154 ILE cc_start: 0.8163 (mm) cc_final: 0.7789 (mt) REVERT: m 23 LEU cc_start: 0.8067 (mp) cc_final: 0.7630 (tp) REVERT: m 46 VAL cc_start: 0.9339 (p) cc_final: 0.9117 (t) REVERT: s 360 GLN cc_start: 0.7983 (mp10) cc_final: 0.7618 (mp10) REVERT: s 453 MET cc_start: 0.8058 (pmm) cc_final: 0.7781 (ptp) REVERT: 9 139 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7671 (tm-30) REVERT: 1 82 LYS cc_start: 0.8511 (mmmm) cc_final: 0.7892 (tppt) REVERT: 1 116 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7938 (mt-10) REVERT: 1 197 GLN cc_start: 0.8398 (mt0) cc_final: 0.8051 (mt0) REVERT: 2 139 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8231 (tm-30) REVERT: 4 23 MET cc_start: 0.8537 (tpt) cc_final: 0.8112 (tpp) REVERT: 5 83 ASP cc_start: 0.6918 (m-30) cc_final: 0.6646 (p0) REVERT: 6 48 ARG cc_start: 0.7829 (mtp-110) cc_final: 0.7489 (mtp-110) REVERT: 6 83 ASP cc_start: 0.7889 (p0) cc_final: 0.7100 (p0) REVERT: 0 132 ILE cc_start: 0.8824 (mm) cc_final: 0.8508 (mm) outliers start: 2 outliers final: 0 residues processed: 1047 average time/residue: 0.6336 time to fit residues: 1135.1227 Evaluate side-chains 836 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 836 time to evaluate : 5.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 700 optimal weight: 5.9990 chunk 477 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 626 optimal weight: 0.0670 chunk 346 optimal weight: 2.9990 chunk 717 optimal weight: 10.0000 chunk 581 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 429 optimal weight: 5.9990 chunk 754 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 overall best weight: 3.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 GLN L 573 HIS M 65 GLN M 172 ASN N 231 GLN ** N 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 209 GLN O 363 HIS ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 11 GLN d 39 ASN d 139 GLN ** e 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 35 GLN ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 124 GLN 0 123 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 68144 Z= 0.266 Angle : 0.585 9.681 92248 Z= 0.302 Chirality : 0.044 0.560 10616 Planarity : 0.004 0.084 11859 Dihedral : 8.257 151.836 10104 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.09), residues: 8727 helix: -0.64 (0.08), residues: 4645 sheet: -1.64 (0.18), residues: 792 loop : -1.99 (0.10), residues: 3290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 450 HIS 0.011 0.001 HIS a 293 PHE 0.033 0.001 PHE L 291 TYR 0.022 0.001 TYR O 371 ARG 0.008 0.000 ARG P 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1029 time to evaluate : 5.679 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: a 182 MET cc_start: 0.5274 (tmm) cc_final: 0.4358 (ppp) REVERT: a 247 TYR cc_start: 0.3967 (m-80) cc_final: 0.3710 (m-80) REVERT: a 266 ARG cc_start: 0.5499 (mtt180) cc_final: 0.5063 (ttt180) REVERT: a 666 HIS cc_start: 0.7647 (t70) cc_final: 0.6866 (t-170) REVERT: a 728 ILE cc_start: 0.9214 (pt) cc_final: 0.8468 (mt) REVERT: a 796 MET cc_start: 0.7360 (ttm) cc_final: 0.6950 (mtt) REVERT: U 424 LYS cc_start: 0.5767 (tttt) cc_final: 0.5286 (mtpt) REVERT: L 95 MET cc_start: 0.8923 (mmt) cc_final: 0.8544 (mmt) REVERT: L 131 ILE cc_start: 0.9104 (mm) cc_final: 0.8826 (mm) REVERT: L 544 MET cc_start: 0.7801 (mmm) cc_final: 0.7100 (mmm) REVERT: M 205 MET cc_start: 0.8170 (mtm) cc_final: 0.7865 (mtm) REVERT: M 349 ASP cc_start: 0.8771 (t70) cc_final: 0.8546 (t0) REVERT: M 488 ASP cc_start: 0.7395 (m-30) cc_final: 0.7158 (m-30) REVERT: M 574 MET cc_start: 0.8078 (mmt) cc_final: 0.7291 (mmt) REVERT: M 613 ARG cc_start: 0.7162 (mtm180) cc_final: 0.6165 (tpm170) REVERT: N 114 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8075 (tp-100) REVERT: N 139 LYS cc_start: 0.7762 (pptt) cc_final: 0.7399 (ptmt) REVERT: N 232 ARG cc_start: 0.6419 (mtm180) cc_final: 0.6145 (mtm180) REVERT: N 405 SER cc_start: 0.9557 (m) cc_final: 0.9079 (t) REVERT: N 506 LYS cc_start: 0.5127 (mttt) cc_final: 0.4808 (mttt) REVERT: N 552 ARG cc_start: 0.7726 (tpp-160) cc_final: 0.7411 (tpp-160) REVERT: N 573 HIS cc_start: 0.5770 (t-170) cc_final: 0.5486 (t-170) REVERT: N 574 MET cc_start: 0.5373 (mtm) cc_final: 0.4909 (mmt) REVERT: O 135 SER cc_start: 0.8340 (p) cc_final: 0.7576 (t) REVERT: O 433 GLN cc_start: 0.8274 (tp-100) cc_final: 0.7793 (tt0) REVERT: Q 54 ASN cc_start: 0.8503 (t0) cc_final: 0.8177 (t0) REVERT: D 86 ASN cc_start: 0.7467 (t0) cc_final: 0.7209 (t0) REVERT: b 68 LYS cc_start: 0.8747 (mttt) cc_final: 0.8299 (mtpp) REVERT: b 159 THR cc_start: 0.8887 (p) cc_final: 0.8347 (p) REVERT: b 161 ASN cc_start: 0.7335 (m110) cc_final: 0.6927 (m110) REVERT: d 26 LYS cc_start: 0.7797 (mmtt) cc_final: 0.7056 (mttp) REVERT: d 39 ASN cc_start: 0.8486 (m110) cc_final: 0.8201 (m-40) REVERT: e 9 GLN cc_start: 0.7795 (mp10) cc_final: 0.7280 (mt0) REVERT: e 13 GLN cc_start: 0.6583 (pt0) cc_final: 0.6255 (pt0) REVERT: e 24 GLU cc_start: 0.4035 (pp20) cc_final: 0.3612 (pp20) REVERT: e 80 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7628 (mtpt) REVERT: f 41 GLN cc_start: 0.7323 (pp30) cc_final: 0.6509 (mt0) REVERT: f 46 GLN cc_start: 0.6811 (pt0) cc_final: 0.6056 (tm-30) REVERT: F 46 ASN cc_start: 0.7964 (p0) cc_final: 0.7468 (p0) REVERT: F 47 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7301 (mm-30) REVERT: F 69 TYR cc_start: 0.7655 (p90) cc_final: 0.7240 (p90) REVERT: F 75 ARG cc_start: 0.8193 (tpp-160) cc_final: 0.7562 (mmm-85) REVERT: k 60 ASN cc_start: 0.6777 (t0) cc_final: 0.6564 (t0) REVERT: k 150 LEU cc_start: 0.8476 (tp) cc_final: 0.7967 (tp) REVERT: k 154 ILE cc_start: 0.8185 (mm) cc_final: 0.7816 (mt) REVERT: m 23 LEU cc_start: 0.8075 (mp) cc_final: 0.7682 (tp) REVERT: m 46 VAL cc_start: 0.9353 (p) cc_final: 0.9091 (t) REVERT: n 103 GLN cc_start: 0.7205 (tp40) cc_final: 0.6817 (tp40) REVERT: s 360 GLN cc_start: 0.7966 (mp10) cc_final: 0.7624 (mp10) REVERT: 1 30 ASP cc_start: 0.7616 (t0) cc_final: 0.7297 (t0) REVERT: 1 82 LYS cc_start: 0.8487 (mmmm) cc_final: 0.7837 (tppt) REVERT: 1 116 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7899 (mt-10) REVERT: 1 197 GLN cc_start: 0.8460 (mt0) cc_final: 0.8098 (mt0) REVERT: 4 23 MET cc_start: 0.8486 (tpt) cc_final: 0.8077 (tpp) REVERT: 6 83 ASP cc_start: 0.7849 (p0) cc_final: 0.7114 (p0) outliers start: 0 outliers final: 0 residues processed: 1029 average time/residue: 0.6418 time to fit residues: 1130.2382 Evaluate side-chains 824 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 824 time to evaluate : 5.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 282 optimal weight: 0.5980 chunk 757 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 493 optimal weight: 9.9990 chunk 207 optimal weight: 0.1980 chunk 841 optimal weight: 5.9990 chunk 698 optimal weight: 8.9990 chunk 389 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 chunk 441 optimal weight: 0.8980 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 443 ASN L 449 ASN L 573 HIS M 172 ASN ** N 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN d 139 GLN e 6 GLN ** e 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 35 GLN ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 145 GLN ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 124 GLN 6 51 GLN 6 124 GLN 0 123 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 68144 Z= 0.243 Angle : 0.573 9.717 92248 Z= 0.296 Chirality : 0.044 0.436 10616 Planarity : 0.004 0.081 11859 Dihedral : 8.073 150.929 10104 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.09), residues: 8727 helix: -0.36 (0.08), residues: 4651 sheet: -1.54 (0.18), residues: 799 loop : -1.89 (0.10), residues: 3277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 450 HIS 0.008 0.001 HIS a 293 PHE 0.026 0.001 PHE N 547 TYR 0.025 0.001 TYR a 741 ARG 0.011 0.000 ARG P 400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1005 time to evaluate : 5.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 266 ARG cc_start: 0.5441 (mtt180) cc_final: 0.5098 (ttt180) REVERT: a 666 HIS cc_start: 0.7651 (t70) cc_final: 0.6855 (t-170) REVERT: a 728 ILE cc_start: 0.9206 (pt) cc_final: 0.8458 (mt) REVERT: a 796 MET cc_start: 0.7265 (ttm) cc_final: 0.6844 (mtt) REVERT: U 341 TYR cc_start: 0.7811 (m-10) cc_final: 0.7508 (m-80) REVERT: U 424 LYS cc_start: 0.5778 (tttt) cc_final: 0.5282 (mtpt) REVERT: L 95 MET cc_start: 0.8882 (mmt) cc_final: 0.8565 (mmt) REVERT: L 131 ILE cc_start: 0.9098 (mm) cc_final: 0.8826 (mm) REVERT: L 462 ASP cc_start: 0.8512 (m-30) cc_final: 0.7778 (m-30) REVERT: L 574 MET cc_start: 0.6033 (mtt) cc_final: 0.5799 (mtp) REVERT: L 608 MET cc_start: 0.7383 (tmm) cc_final: 0.7052 (tmm) REVERT: M 39 MET cc_start: 0.8043 (mmm) cc_final: 0.7762 (mtp) REVERT: M 205 MET cc_start: 0.8134 (mtm) cc_final: 0.7839 (mtm) REVERT: M 488 ASP cc_start: 0.7575 (m-30) cc_final: 0.7130 (m-30) REVERT: M 574 MET cc_start: 0.7895 (mmt) cc_final: 0.7166 (mmt) REVERT: M 613 ARG cc_start: 0.7128 (mtm180) cc_final: 0.6126 (tpm170) REVERT: N 114 GLN cc_start: 0.8286 (mm-40) cc_final: 0.8039 (tp-100) REVERT: N 139 LYS cc_start: 0.7726 (pptt) cc_final: 0.7355 (ptmt) REVERT: N 405 SER cc_start: 0.9574 (m) cc_final: 0.9057 (t) REVERT: N 506 LYS cc_start: 0.5158 (mttt) cc_final: 0.4884 (mtmt) REVERT: N 565 ILE cc_start: 0.5575 (pt) cc_final: 0.5091 (pt) REVERT: N 573 HIS cc_start: 0.5752 (t-170) cc_final: 0.5486 (t-170) REVERT: N 574 MET cc_start: 0.5445 (mtm) cc_final: 0.4965 (mmt) REVERT: O 135 SER cc_start: 0.8350 (p) cc_final: 0.7592 (t) REVERT: O 433 GLN cc_start: 0.8248 (tp-100) cc_final: 0.7742 (tt0) REVERT: Q 54 ASN cc_start: 0.8406 (t0) cc_final: 0.8165 (t0) REVERT: D 35 LYS cc_start: 0.8233 (pttt) cc_final: 0.7803 (mttt) REVERT: D 86 ASN cc_start: 0.7508 (t0) cc_final: 0.7239 (t0) REVERT: b 68 LYS cc_start: 0.8731 (mttt) cc_final: 0.8286 (mtpp) REVERT: b 159 THR cc_start: 0.9004 (p) cc_final: 0.8369 (p) REVERT: b 161 ASN cc_start: 0.7407 (m110) cc_final: 0.7002 (m110) REVERT: d 21 GLN cc_start: 0.7400 (mm-40) cc_final: 0.6654 (mp10) REVERT: d 26 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7138 (mttp) REVERT: e 9 GLN cc_start: 0.7763 (mp10) cc_final: 0.7038 (mt0) REVERT: e 10 GLN cc_start: 0.7942 (mm110) cc_final: 0.7470 (mm-40) REVERT: e 13 GLN cc_start: 0.6414 (pt0) cc_final: 0.5920 (pt0) REVERT: e 93 ASP cc_start: 0.6888 (m-30) cc_final: 0.6391 (p0) REVERT: f 46 GLN cc_start: 0.6808 (pt0) cc_final: 0.6024 (tm-30) REVERT: F 46 ASN cc_start: 0.7997 (p0) cc_final: 0.7510 (p0) REVERT: k 150 LEU cc_start: 0.8500 (tp) cc_final: 0.7960 (tp) REVERT: k 154 ILE cc_start: 0.8165 (mm) cc_final: 0.7769 (mt) REVERT: m 23 LEU cc_start: 0.8034 (mp) cc_final: 0.7793 (tp) REVERT: m 46 VAL cc_start: 0.9315 (p) cc_final: 0.9058 (t) REVERT: n 103 GLN cc_start: 0.7233 (tp40) cc_final: 0.6803 (tp40) REVERT: 1 30 ASP cc_start: 0.7626 (t0) cc_final: 0.7274 (t0) REVERT: 1 82 LYS cc_start: 0.8448 (mmmm) cc_final: 0.7783 (tppt) REVERT: 1 116 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7886 (mt-10) REVERT: 1 197 GLN cc_start: 0.8429 (mt0) cc_final: 0.8119 (mt0) REVERT: 3 134 ILE cc_start: 0.8714 (mm) cc_final: 0.8381 (mm) REVERT: 3 144 TYR cc_start: 0.8499 (m-10) cc_final: 0.8206 (m-10) REVERT: 4 23 MET cc_start: 0.8445 (tpt) cc_final: 0.8066 (tpp) REVERT: 4 44 MET cc_start: 0.8297 (tmm) cc_final: 0.8091 (tmm) REVERT: 6 83 ASP cc_start: 0.7778 (p0) cc_final: 0.7036 (p0) REVERT: 0 41 ILE cc_start: 0.8949 (mt) cc_final: 0.8692 (mm) outliers start: 2 outliers final: 0 residues processed: 1005 average time/residue: 0.6462 time to fit residues: 1110.0421 Evaluate side-chains 822 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 822 time to evaluate : 5.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 811 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 479 optimal weight: 8.9990 chunk 614 optimal weight: 50.0000 chunk 476 optimal weight: 5.9990 chunk 708 optimal weight: 3.9990 chunk 470 optimal weight: 7.9990 chunk 838 optimal weight: 0.9990 chunk 524 optimal weight: 3.9990 chunk 511 optimal weight: 5.9990 chunk 387 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 310 ASN U 434 GLN L 449 ASN L 573 HIS M 65 GLN M 172 ASN ** N 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 497 GLN ** Q 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 HIS d 39 ASN d 139 GLN e 6 GLN ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 35 GLN ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 HIS k 145 GLN ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 348 HIS 2 124 GLN ** 6 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 68144 Z= 0.275 Angle : 0.592 10.044 92248 Z= 0.306 Chirality : 0.045 0.400 10616 Planarity : 0.004 0.081 11859 Dihedral : 7.993 156.518 10104 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.04 % Allowed : 1.56 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.09), residues: 8727 helix: -0.23 (0.08), residues: 4646 sheet: -1.50 (0.18), residues: 786 loop : -1.84 (0.10), residues: 3295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 450 HIS 0.007 0.001 HIS a 293 PHE 0.032 0.001 PHE k 193 TYR 0.022 0.001 TYR L 535 ARG 0.010 0.000 ARG Q 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 978 time to evaluate : 7.415 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: a 266 ARG cc_start: 0.5579 (mtt180) cc_final: 0.5183 (ttt180) REVERT: a 728 ILE cc_start: 0.9197 (pt) cc_final: 0.8497 (mt) REVERT: a 796 MET cc_start: 0.7344 (ttm) cc_final: 0.6893 (mtt) REVERT: U 341 TYR cc_start: 0.7854 (m-10) cc_final: 0.7576 (m-80) REVERT: U 424 LYS cc_start: 0.5716 (tttt) cc_final: 0.5127 (mtpt) REVERT: L 95 MET cc_start: 0.8963 (mmt) cc_final: 0.8642 (mmt) REVERT: L 131 ILE cc_start: 0.9095 (mm) cc_final: 0.8884 (mm) REVERT: L 544 MET cc_start: 0.7653 (mmm) cc_final: 0.7075 (mmm) REVERT: M 205 MET cc_start: 0.8174 (mtm) cc_final: 0.7866 (mtm) REVERT: M 488 ASP cc_start: 0.7587 (m-30) cc_final: 0.7090 (m-30) REVERT: M 574 MET cc_start: 0.7930 (mmt) cc_final: 0.7133 (mmt) REVERT: M 613 ARG cc_start: 0.7187 (mtm180) cc_final: 0.6254 (tpm170) REVERT: N 139 LYS cc_start: 0.7674 (pptt) cc_final: 0.7337 (ptmt) REVERT: N 405 SER cc_start: 0.9586 (m) cc_final: 0.9068 (t) REVERT: N 481 GLU cc_start: 0.7629 (tp30) cc_final: 0.7273 (tp30) REVERT: N 565 ILE cc_start: 0.5855 (pt) cc_final: 0.5450 (pt) REVERT: N 573 HIS cc_start: 0.5748 (t-170) cc_final: 0.5526 (t-170) REVERT: N 574 MET cc_start: 0.5524 (mtm) cc_final: 0.4882 (mmt) REVERT: O 135 SER cc_start: 0.8282 (p) cc_final: 0.7519 (t) REVERT: O 433 GLN cc_start: 0.8118 (tp-100) cc_final: 0.7666 (tt0) REVERT: P 433 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8041 (tm-30) REVERT: Q 54 ASN cc_start: 0.8439 (t0) cc_final: 0.8170 (t0) REVERT: D 86 ASN cc_start: 0.7547 (t0) cc_final: 0.7208 (t0) REVERT: b 68 LYS cc_start: 0.8710 (mttt) cc_final: 0.8280 (mtpp) REVERT: b 159 THR cc_start: 0.8936 (p) cc_final: 0.8266 (p) REVERT: b 161 ASN cc_start: 0.7419 (m110) cc_final: 0.7015 (m110) REVERT: d 21 GLN cc_start: 0.7469 (mm-40) cc_final: 0.6774 (mp10) REVERT: d 39 ASN cc_start: 0.8432 (m110) cc_final: 0.8059 (m-40) REVERT: e 9 GLN cc_start: 0.7791 (mp10) cc_final: 0.7023 (mt0) REVERT: e 13 GLN cc_start: 0.6407 (pt0) cc_final: 0.6038 (pt0) REVERT: e 79 GLU cc_start: 0.8179 (pp20) cc_final: 0.7946 (pp20) REVERT: e 80 LYS cc_start: 0.7979 (mtmt) cc_final: 0.7721 (mtpt) REVERT: e 93 ASP cc_start: 0.6844 (m-30) cc_final: 0.6399 (p0) REVERT: f 46 GLN cc_start: 0.6759 (pt0) cc_final: 0.5964 (tm-30) REVERT: F 46 ASN cc_start: 0.7917 (p0) cc_final: 0.7460 (p0) REVERT: k 150 LEU cc_start: 0.8510 (tp) cc_final: 0.7978 (tp) REVERT: k 154 ILE cc_start: 0.8140 (mm) cc_final: 0.7769 (mt) REVERT: m 23 LEU cc_start: 0.8112 (mp) cc_final: 0.7831 (tp) REVERT: m 46 VAL cc_start: 0.9285 (p) cc_final: 0.9019 (t) REVERT: m 56 ILE cc_start: 0.9133 (tt) cc_final: 0.8927 (tt) REVERT: n 103 GLN cc_start: 0.7249 (tp40) cc_final: 0.6811 (tp40) REVERT: 1 30 ASP cc_start: 0.7655 (t0) cc_final: 0.7315 (t0) REVERT: 1 82 LYS cc_start: 0.8387 (mmmm) cc_final: 0.7795 (tppt) REVERT: 1 116 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7859 (mt-10) REVERT: 1 197 GLN cc_start: 0.8416 (mt0) cc_final: 0.8092 (mt0) REVERT: 2 50 GLU cc_start: 0.7396 (pm20) cc_final: 0.7101 (pm20) REVERT: 3 134 ILE cc_start: 0.8672 (mm) cc_final: 0.8296 (mm) REVERT: 3 144 TYR cc_start: 0.8557 (m-10) cc_final: 0.8240 (m-10) REVERT: 4 23 MET cc_start: 0.8415 (tpt) cc_final: 0.8043 (tpp) REVERT: 4 81 ASN cc_start: 0.7724 (t0) cc_final: 0.7514 (t0) REVERT: 6 83 ASP cc_start: 0.7811 (p0) cc_final: 0.7032 (p0) REVERT: 0 41 ILE cc_start: 0.8953 (mt) cc_final: 0.8674 (mm) outliers start: 3 outliers final: 0 residues processed: 978 average time/residue: 0.6385 time to fit residues: 1076.9241 Evaluate side-chains 825 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 825 time to evaluate : 5.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 518 optimal weight: 3.9990 chunk 334 optimal weight: 9.9990 chunk 500 optimal weight: 20.0000 chunk 252 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 533 optimal weight: 7.9990 chunk 571 optimal weight: 50.0000 chunk 414 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 659 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 108 GLN ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 443 ASN U 302 HIS L 172 ASN L 207 GLN L 449 ASN L 573 HIS M 172 ASN ** N 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 GLN e 6 GLN ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 41 GLN ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 145 GLN ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 113 ASN 6 51 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 68144 Z= 0.332 Angle : 0.627 9.449 92248 Z= 0.323 Chirality : 0.046 0.557 10616 Planarity : 0.004 0.079 11859 Dihedral : 8.043 167.150 10104 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.06 % Allowed : 1.56 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.09), residues: 8727 helix: -0.21 (0.08), residues: 4646 sheet: -1.49 (0.18), residues: 792 loop : -1.87 (0.10), residues: 3289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 567 HIS 0.007 0.001 HIS D 111 PHE 0.031 0.002 PHE L 291 TYR 0.026 0.002 TYR O 371 ARG 0.011 0.001 ARG P 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 964 time to evaluate : 5.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 182 MET cc_start: 0.5307 (tmm) cc_final: 0.4353 (ppp) REVERT: a 266 ARG cc_start: 0.5624 (mtt180) cc_final: 0.5170 (ttt180) REVERT: a 728 ILE cc_start: 0.9217 (pt) cc_final: 0.8471 (mt) REVERT: a 796 MET cc_start: 0.7389 (ttm) cc_final: 0.6945 (mtt) REVERT: U 28 PHE cc_start: 0.4754 (t80) cc_final: 0.4503 (t80) REVERT: U 341 TYR cc_start: 0.7908 (m-10) cc_final: 0.7639 (m-80) REVERT: U 424 LYS cc_start: 0.5789 (tttt) cc_final: 0.5202 (mtpt) REVERT: L 95 MET cc_start: 0.8983 (mmt) cc_final: 0.8676 (mmt) REVERT: L 131 ILE cc_start: 0.9099 (mm) cc_final: 0.8866 (mm) REVERT: L 544 MET cc_start: 0.7611 (mmm) cc_final: 0.7261 (mmm) REVERT: M 205 MET cc_start: 0.8205 (mtm) cc_final: 0.7869 (mtm) REVERT: M 488 ASP cc_start: 0.7596 (m-30) cc_final: 0.7109 (m-30) REVERT: M 574 MET cc_start: 0.7945 (mmt) cc_final: 0.7122 (mmt) REVERT: M 613 ARG cc_start: 0.7228 (mtm180) cc_final: 0.6349 (tpm170) REVERT: N 139 LYS cc_start: 0.7690 (pptt) cc_final: 0.7333 (ptmt) REVERT: N 405 SER cc_start: 0.9572 (m) cc_final: 0.9057 (t) REVERT: N 507 ILE cc_start: 0.5137 (mt) cc_final: 0.4904 (mt) REVERT: N 574 MET cc_start: 0.5301 (mtm) cc_final: 0.4888 (mmt) REVERT: O 164 ILE cc_start: 0.8822 (mt) cc_final: 0.8463 (mm) REVERT: O 433 GLN cc_start: 0.8157 (tp-100) cc_final: 0.7750 (tt0) REVERT: P 433 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8074 (tm-30) REVERT: Q 54 ASN cc_start: 0.8424 (t0) cc_final: 0.8198 (t0) REVERT: Q 448 ASP cc_start: 0.7120 (t70) cc_final: 0.6819 (t70) REVERT: D 86 ASN cc_start: 0.7585 (t0) cc_final: 0.7320 (t0) REVERT: b 68 LYS cc_start: 0.8712 (mttt) cc_final: 0.8272 (mtpp) REVERT: b 161 ASN cc_start: 0.7458 (m110) cc_final: 0.7023 (m110) REVERT: d 21 GLN cc_start: 0.7423 (mm-40) cc_final: 0.6817 (mp10) REVERT: e 9 GLN cc_start: 0.7812 (mp10) cc_final: 0.7067 (mt0) REVERT: e 10 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7462 (mm-40) REVERT: e 53 LYS cc_start: 0.6749 (ptpp) cc_final: 0.6055 (mtmt) REVERT: e 55 PHE cc_start: 0.5085 (t80) cc_final: 0.4791 (t80) REVERT: F 46 ASN cc_start: 0.7960 (p0) cc_final: 0.7476 (p0) REVERT: F 47 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7376 (mm-30) REVERT: k 150 LEU cc_start: 0.8543 (tp) cc_final: 0.8017 (tp) REVERT: k 154 ILE cc_start: 0.8156 (mm) cc_final: 0.7746 (mt) REVERT: m 23 LEU cc_start: 0.8133 (mp) cc_final: 0.7847 (tp) REVERT: m 46 VAL cc_start: 0.9297 (p) cc_final: 0.8992 (t) REVERT: m 56 ILE cc_start: 0.9153 (tt) cc_final: 0.8946 (tt) REVERT: 8 44 MET cc_start: 0.8100 (tmm) cc_final: 0.7869 (ttp) REVERT: 1 30 ASP cc_start: 0.7685 (t0) cc_final: 0.7343 (t0) REVERT: 1 82 LYS cc_start: 0.8478 (mmmm) cc_final: 0.7844 (tppt) REVERT: 1 116 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7867 (mt-10) REVERT: 3 134 ILE cc_start: 0.8600 (mm) cc_final: 0.8203 (mm) REVERT: 3 144 TYR cc_start: 0.8615 (m-10) cc_final: 0.8358 (m-10) REVERT: 4 23 MET cc_start: 0.8376 (tpt) cc_final: 0.8019 (tpp) REVERT: 6 83 ASP cc_start: 0.7811 (p0) cc_final: 0.7032 (p0) REVERT: 0 41 ILE cc_start: 0.8920 (mt) cc_final: 0.8628 (mm) REVERT: 0 132 ILE cc_start: 0.8728 (mm) cc_final: 0.8496 (mm) outliers start: 4 outliers final: 0 residues processed: 966 average time/residue: 0.6492 time to fit residues: 1075.5578 Evaluate side-chains 815 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 815 time to evaluate : 5.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 762 optimal weight: 1.9990 chunk 803 optimal weight: 2.9990 chunk 732 optimal weight: 8.9990 chunk 781 optimal weight: 4.9990 chunk 470 optimal weight: 3.9990 chunk 340 optimal weight: 4.9990 chunk 613 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 706 optimal weight: 6.9990 chunk 739 optimal weight: 1.9990 chunk 778 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 288 HIS L 444 HIS L 449 ASN L 573 HIS M 172 ASN ** N 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN d 139 GLN e 10 GLN ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 HIS ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 124 GLN 6 123 GLN ** 6 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 68144 Z= 0.254 Angle : 0.590 10.520 92248 Z= 0.304 Chirality : 0.044 0.528 10616 Planarity : 0.004 0.079 11859 Dihedral : 7.841 168.622 10104 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.01 % Allowed : 0.58 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.09), residues: 8727 helix: -0.02 (0.08), residues: 4634 sheet: -1.39 (0.19), residues: 754 loop : -1.82 (0.10), residues: 3339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP L 450 HIS 0.012 0.001 HIS N 573 PHE 0.027 0.001 PHE L 291 TYR 0.024 0.001 TYR L 535 ARG 0.009 0.000 ARG P 400 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 958 time to evaluate : 5.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 182 MET cc_start: 0.5341 (tmm) cc_final: 0.4387 (ppp) REVERT: a 266 ARG cc_start: 0.5532 (mtt180) cc_final: 0.5105 (ttt180) REVERT: a 443 ASN cc_start: 0.8344 (m110) cc_final: 0.8115 (m-40) REVERT: a 728 ILE cc_start: 0.9215 (pt) cc_final: 0.8468 (mt) REVERT: a 796 MET cc_start: 0.7357 (ttm) cc_final: 0.6896 (mtt) REVERT: U 111 MET cc_start: 0.4301 (mmm) cc_final: 0.3972 (tpt) REVERT: U 341 TYR cc_start: 0.7904 (m-10) cc_final: 0.7648 (m-80) REVERT: U 424 LYS cc_start: 0.5703 (tttt) cc_final: 0.5120 (mtpt) REVERT: L 95 MET cc_start: 0.8952 (mmt) cc_final: 0.8663 (mmt) REVERT: L 131 ILE cc_start: 0.9081 (mm) cc_final: 0.8848 (mm) REVERT: L 544 MET cc_start: 0.7616 (mmm) cc_final: 0.7269 (mmm) REVERT: M 353 ARG cc_start: 0.7712 (mmp80) cc_final: 0.6892 (mmt90) REVERT: M 488 ASP cc_start: 0.7618 (m-30) cc_final: 0.7128 (m-30) REVERT: M 556 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7082 (mm-30) REVERT: M 574 MET cc_start: 0.8004 (mmt) cc_final: 0.7180 (mmt) REVERT: M 591 LYS cc_start: 0.7414 (mtpt) cc_final: 0.6922 (tttp) REVERT: M 613 ARG cc_start: 0.7230 (mtm180) cc_final: 0.6327 (tpm170) REVERT: N 139 LYS cc_start: 0.7648 (pptt) cc_final: 0.7294 (ptmt) REVERT: N 574 MET cc_start: 0.5225 (mtm) cc_final: 0.4933 (mmm) REVERT: O 135 SER cc_start: 0.8270 (p) cc_final: 0.7504 (t) REVERT: O 164 ILE cc_start: 0.8814 (mt) cc_final: 0.8461 (mm) REVERT: O 433 GLN cc_start: 0.8185 (tp-100) cc_final: 0.7787 (tt0) REVERT: P 433 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8048 (tm-30) REVERT: Q 54 ASN cc_start: 0.8408 (t0) cc_final: 0.8178 (t0) REVERT: D 86 ASN cc_start: 0.7544 (t0) cc_final: 0.7183 (t0) REVERT: b 68 LYS cc_start: 0.8715 (mttt) cc_final: 0.8266 (mtpp) REVERT: b 159 THR cc_start: 0.8923 (p) cc_final: 0.8258 (p) REVERT: b 161 ASN cc_start: 0.7456 (m110) cc_final: 0.7021 (m110) REVERT: d 21 GLN cc_start: 0.7410 (mm-40) cc_final: 0.6797 (mp10) REVERT: e 9 GLN cc_start: 0.7736 (mp10) cc_final: 0.6996 (mt0) REVERT: e 13 GLN cc_start: 0.6729 (pt0) cc_final: 0.6324 (pt0) REVERT: e 55 PHE cc_start: 0.5004 (t80) cc_final: 0.4672 (t80) REVERT: e 80 LYS cc_start: 0.7847 (mtmt) cc_final: 0.7594 (mtpt) REVERT: F 46 ASN cc_start: 0.7934 (p0) cc_final: 0.7457 (p0) REVERT: k 150 LEU cc_start: 0.8510 (tp) cc_final: 0.7978 (tp) REVERT: k 154 ILE cc_start: 0.8143 (mm) cc_final: 0.7745 (mt) REVERT: m 23 LEU cc_start: 0.8121 (mp) cc_final: 0.7844 (tp) REVERT: m 46 VAL cc_start: 0.9268 (p) cc_final: 0.9005 (t) REVERT: m 56 ILE cc_start: 0.9157 (tt) cc_final: 0.8945 (tt) REVERT: n 103 GLN cc_start: 0.7247 (tp40) cc_final: 0.6954 (tp40) REVERT: 1 30 ASP cc_start: 0.7673 (t0) cc_final: 0.7347 (t0) REVERT: 1 82 LYS cc_start: 0.8390 (mmmm) cc_final: 0.7812 (tppt) REVERT: 1 116 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7814 (mt-10) REVERT: 2 50 GLU cc_start: 0.7346 (pm20) cc_final: 0.7088 (pm20) REVERT: 3 134 ILE cc_start: 0.8573 (mm) cc_final: 0.8209 (mm) REVERT: 3 144 TYR cc_start: 0.8597 (m-10) cc_final: 0.8308 (m-10) REVERT: 4 23 MET cc_start: 0.8398 (tpt) cc_final: 0.8044 (tpp) REVERT: 6 83 ASP cc_start: 0.7801 (p0) cc_final: 0.7065 (p0) REVERT: 0 41 ILE cc_start: 0.8965 (mt) cc_final: 0.8661 (mm) outliers start: 1 outliers final: 0 residues processed: 959 average time/residue: 0.6358 time to fit residues: 1043.4386 Evaluate side-chains 823 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 823 time to evaluate : 5.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 513 optimal weight: 8.9990 chunk 826 optimal weight: 7.9990 chunk 504 optimal weight: 8.9990 chunk 391 optimal weight: 4.9990 chunk 574 optimal weight: 40.0000 chunk 866 optimal weight: 8.9990 chunk 797 optimal weight: 5.9990 chunk 690 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 533 optimal weight: 6.9990 chunk 423 optimal weight: 4.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 GLN L 449 ASN L 573 HIS ** N 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 63 GLN d 139 GLN e 6 GLN ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 124 GLN 6 51 GLN ** 6 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 68144 Z= 0.392 Angle : 0.673 11.247 92248 Z= 0.346 Chirality : 0.048 0.572 10616 Planarity : 0.004 0.074 11859 Dihedral : 8.062 176.371 10104 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.01 % Allowed : 0.45 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.09), residues: 8727 helix: -0.21 (0.08), residues: 4655 sheet: -1.40 (0.19), residues: 741 loop : -1.93 (0.10), residues: 3331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 450 HIS 0.009 0.001 HIS N 573 PHE 0.028 0.002 PHE L 291 TYR 0.029 0.002 TYR O 371 ARG 0.009 0.001 ARG F 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 929 time to evaluate : 5.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 182 MET cc_start: 0.5338 (tmm) cc_final: 0.4372 (ppp) REVERT: a 266 ARG cc_start: 0.5573 (mtt180) cc_final: 0.5105 (ttt180) REVERT: a 310 ASN cc_start: 0.7592 (m110) cc_final: 0.7350 (m110) REVERT: a 728 ILE cc_start: 0.9208 (pt) cc_final: 0.8446 (mt) REVERT: a 821 ASP cc_start: 0.7684 (m-30) cc_final: 0.7393 (m-30) REVERT: U 111 MET cc_start: 0.4225 (mmm) cc_final: 0.3947 (tpt) REVERT: U 341 TYR cc_start: 0.7990 (m-10) cc_final: 0.7735 (m-10) REVERT: L 95 MET cc_start: 0.8984 (mmt) cc_final: 0.8649 (mmt) REVERT: L 450 TRP cc_start: 0.7617 (p90) cc_final: 0.7316 (p90) REVERT: L 544 MET cc_start: 0.7598 (mmm) cc_final: 0.7231 (mmm) REVERT: M 488 ASP cc_start: 0.7424 (m-30) cc_final: 0.7132 (m-30) REVERT: M 574 MET cc_start: 0.7984 (mmt) cc_final: 0.7236 (mmt) REVERT: M 613 ARG cc_start: 0.7250 (mtm180) cc_final: 0.6382 (tpm170) REVERT: N 139 LYS cc_start: 0.7660 (pptt) cc_final: 0.7327 (ptmt) REVERT: N 574 MET cc_start: 0.4976 (mtm) cc_final: 0.4577 (mmm) REVERT: N 606 GLU cc_start: 0.5996 (mm-30) cc_final: 0.5792 (mm-30) REVERT: O 164 ILE cc_start: 0.8822 (mt) cc_final: 0.8476 (mm) REVERT: O 270 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7011 (mt-10) REVERT: O 433 GLN cc_start: 0.8111 (tp-100) cc_final: 0.7825 (tt0) REVERT: P 250 GLU cc_start: 0.7149 (tt0) cc_final: 0.6826 (tt0) REVERT: P 433 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8087 (tm-30) REVERT: Q 54 ASN cc_start: 0.8461 (t0) cc_final: 0.8223 (t0) REVERT: D 86 ASN cc_start: 0.7627 (t0) cc_final: 0.7357 (t0) REVERT: D 99 ASP cc_start: 0.7082 (t0) cc_final: 0.6878 (t0) REVERT: b 68 LYS cc_start: 0.8720 (mttt) cc_final: 0.8307 (mtpp) REVERT: b 159 THR cc_start: 0.8933 (p) cc_final: 0.8315 (p) REVERT: b 161 ASN cc_start: 0.7521 (m110) cc_final: 0.7080 (m110) REVERT: d 21 GLN cc_start: 0.7466 (mm-40) cc_final: 0.6781 (mp10) REVERT: e 9 GLN cc_start: 0.7744 (mp10) cc_final: 0.7004 (mt0) REVERT: e 10 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7522 (mm-40) REVERT: F 46 ASN cc_start: 0.8019 (p0) cc_final: 0.7560 (p0) REVERT: F 47 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7232 (mm-30) REVERT: F 75 ARG cc_start: 0.7814 (tpp80) cc_final: 0.7503 (mmm-85) REVERT: k 38 GLN cc_start: 0.7323 (pm20) cc_final: 0.7082 (pm20) REVERT: k 150 LEU cc_start: 0.8547 (tp) cc_final: 0.7848 (tp) REVERT: k 154 ILE cc_start: 0.8165 (mm) cc_final: 0.7765 (mt) REVERT: m 23 LEU cc_start: 0.8139 (mp) cc_final: 0.7875 (tp) REVERT: m 46 VAL cc_start: 0.9309 (p) cc_final: 0.9005 (t) REVERT: m 69 LYS cc_start: 0.8888 (ptmt) cc_final: 0.8532 (ttpt) REVERT: s 399 ASP cc_start: 0.8795 (m-30) cc_final: 0.8587 (m-30) REVERT: s 436 MET cc_start: 0.8179 (mmm) cc_final: 0.7634 (mtm) REVERT: 1 30 ASP cc_start: 0.7664 (t0) cc_final: 0.7336 (t0) REVERT: 1 36 ASP cc_start: 0.8378 (t0) cc_final: 0.8127 (t0) REVERT: 1 82 LYS cc_start: 0.8427 (mmmm) cc_final: 0.7798 (tppt) REVERT: 1 116 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7868 (mt-10) REVERT: 1 197 GLN cc_start: 0.8403 (mt0) cc_final: 0.8039 (mt0) REVERT: 2 50 GLU cc_start: 0.7382 (pm20) cc_final: 0.7088 (pm20) REVERT: 3 134 ILE cc_start: 0.8609 (mm) cc_final: 0.8209 (mm) REVERT: 3 144 TYR cc_start: 0.8679 (m-10) cc_final: 0.8379 (m-10) REVERT: 4 23 MET cc_start: 0.8380 (tpt) cc_final: 0.8028 (tpp) REVERT: 5 83 ASP cc_start: 0.7169 (m-30) cc_final: 0.6650 (p0) REVERT: 6 83 ASP cc_start: 0.7881 (p0) cc_final: 0.7108 (p0) REVERT: 0 41 ILE cc_start: 0.8942 (mt) cc_final: 0.8620 (mm) outliers start: 1 outliers final: 0 residues processed: 930 average time/residue: 0.6371 time to fit residues: 1013.8916 Evaluate side-chains 804 residues out of total 7420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 804 time to evaluate : 5.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 870 random chunks: chunk 548 optimal weight: 9.9990 chunk 735 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 636 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 691 optimal weight: 4.9990 chunk 289 optimal weight: 0.6980 chunk 709 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 127 optimal weight: 0.0270 overall best weight: 1.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 444 HIS L 449 ASN L 573 HIS ** N 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 205 GLN P 209 GLN ** P 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 14 HIS d 139 GLN ** e 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 HIS k 145 GLN ** k 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 124 GLN 6 123 GLN ** 6 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.092722 restraints weight = 115418.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.092032 restraints weight = 154773.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093371 restraints weight = 123555.301| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 68144 Z= 0.184 Angle : 0.563 9.289 92248 Z= 0.290 Chirality : 0.043 0.430 10616 Planarity : 0.004 0.077 11859 Dihedral : 7.544 163.298 10104 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.03 % Allowed : 0.43 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.09), residues: 8727 helix: 0.24 (0.08), residues: 4578 sheet: -1.36 (0.19), residues: 764 loop : -1.76 (0.10), residues: 3385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 450 HIS 0.008 0.001 HIS N 573 PHE 0.032 0.001 PHE L 291 TYR 0.024 0.001 TYR L 535 ARG 0.011 0.000 ARG Q 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18398.32 seconds wall clock time: 316 minutes 48.91 seconds (19008.91 seconds total)