Starting phenix.real_space_refine on Mon Apr 8 03:32:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8su9_40762/04_2024/8su9_40762_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8su9_40762/04_2024/8su9_40762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8su9_40762/04_2024/8su9_40762.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8su9_40762/04_2024/8su9_40762.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8su9_40762/04_2024/8su9_40762_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8su9_40762/04_2024/8su9_40762_updated.pdb" } resolution = 2.83 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= 0.002 sd= 0.099 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: 6 Type Number sf(0) Gaussians P 34 5.49 5 Mg 5 5.21 5 S 145 5.16 5 C 41764 2.51 5 N 11119 2.21 5 O 12318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 336": "NH1" <-> "NH2" Residue "Q PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 65385 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3185 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 1 Chain: "B" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3186 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 1 Chain: "C" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3185 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 1 Chain: "D" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3192 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} Chain breaks: 2 Chain: "E" Number of atoms: 3194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3194 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 388} Chain breaks: 1 Chain: "F" Number of atoms: 3198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3198 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} Chain breaks: 1 Chain: "G" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3119 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 379} Chain breaks: 2 Chain: "H" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3203 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 11, 'TRANS': 389} Chain breaks: 1 Chain: "I" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3145 Classifications: {'peptide': 394} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Chain breaks: 2 Chain: "J" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3199 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} Chain breaks: 1 Chain: "K" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3182 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 2 Chain: "L" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3199 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 11, 'TRANS': 388} Chain breaks: 1 Chain: "M" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4536 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 550} Chain breaks: 2 Chain: "N" Number of atoms: 4548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4548 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 551} Chain breaks: 2 Chain: "O" Number of atoms: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4637 Classifications: {'peptide': 585} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain breaks: 1 Chain: "P" Number of atoms: 4346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4346 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 526} Chain breaks: 4 Chain: "Q" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4389 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 530} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4170 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 19, 'TRANS': 504} Chain breaks: 3 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.56, per 1000 atoms: 0.39 Number of scatterers: 65385 At special positions: 0 Unit cell: (196.47, 184.26, 220.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 145 16.00 P 34 15.00 Mg 5 11.99 O 12318 8.00 N 11119 7.00 C 41764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.99 Conformation dependent library (CDL) restraints added in 9.3 seconds 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15054 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 363 helices and 52 sheets defined 39.8% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.82 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 removed outlier: 3.809A pdb=" N SER A 21 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 37 removed outlier: 3.722A pdb=" N SER A 37 " --> pdb=" O ALA A 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 34 through 37' Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 83 through 98 removed outlier: 3.699A pdb=" N ASP A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 123 removed outlier: 3.506A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 131 removed outlier: 4.262A pdb=" N ARG A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 131' Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 139 through 153 removed outlier: 3.509A pdb=" N LYS A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TYR A 143 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 144 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 146 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 147 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 153 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 180 Processing helix chain 'A' and resid 198 through 202 removed outlier: 4.005A pdb=" N PHE A 201 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 251 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.501A pdb=" N MET A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.538A pdb=" N ARG A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 317 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 removed outlier: 3.595A pdb=" N THR A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 360 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.841A pdb=" N GLU A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'B' and resid 12 through 24 removed outlier: 3.535A pdb=" N ARG B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 37 removed outlier: 3.616A pdb=" N SER B 37 " --> pdb=" O ALA B 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 34 through 37' Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 57 through 64 removed outlier: 3.816A pdb=" N GLY B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 77 No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 82 through 98 removed outlier: 3.966A pdb=" N ASP B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 123 removed outlier: 4.188A pdb=" N GLU B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 removed outlier: 4.232A pdb=" N ARG B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 139 through 153 removed outlier: 4.100A pdb=" N LYS B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR B 143 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS B 144 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 180 Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.587A pdb=" N PHE B 201 " --> pdb=" O PRO B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 251 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 283 through 295 removed outlier: 3.608A pdb=" N ILE B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 323 removed outlier: 3.600A pdb=" N LEU B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 321 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 350 through 359 removed outlier: 3.667A pdb=" N ALA B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 375 removed outlier: 3.652A pdb=" N ALA B 375 " --> pdb=" O GLY B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 377 through 383 Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.545A pdb=" N VAL B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 removed outlier: 4.153A pdb=" N GLN C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.522A pdb=" N TRP C 49 " --> pdb=" O MET C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 65 removed outlier: 4.519A pdb=" N ALA C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 82 through 98 Processing helix chain 'C' and resid 102 through 121 removed outlier: 3.502A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 130 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 139 through 153 removed outlier: 3.583A pdb=" N LYS C 142 " --> pdb=" O ASP C 139 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TYR C 143 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS C 144 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS C 145 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 147 " --> pdb=" O HIS C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 180 removed outlier: 3.732A pdb=" N ASP C 179 " --> pdb=" O TRP C 175 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.897A pdb=" N PHE C 201 " --> pdb=" O PRO C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 251 removed outlier: 3.740A pdb=" N ASP C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 257 No H-bonds generated for 'chain 'C' and resid 254 through 257' Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 312 through 323 removed outlier: 3.645A pdb=" N ALA C 321 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 345 Processing helix chain 'C' and resid 350 through 359 Processing helix chain 'C' and resid 377 through 380 No H-bonds generated for 'chain 'C' and resid 377 through 380' Processing helix chain 'C' and resid 397 through 406 removed outlier: 3.808A pdb=" N ALA C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.620A pdb=" N CYS D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 40 removed outlier: 3.798A pdb=" N SER D 37 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 38 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY D 39 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 72 through 77 Processing helix chain 'D' and resid 82 through 98 removed outlier: 3.711A pdb=" N ASP D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.817A pdb=" N LYS D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.792A pdb=" N PHE D 130 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG D 131 " --> pdb=" O GLU D 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 127 through 131' Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 139 through 153 removed outlier: 3.834A pdb=" N LYS D 142 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR D 143 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS D 144 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER D 153 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 178 Processing helix chain 'D' and resid 198 through 202 removed outlier: 3.971A pdb=" N PHE D 201 " --> pdb=" O PRO D 198 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP D 202 " --> pdb=" O GLN D 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 202' Processing helix chain 'D' and resid 245 through 251 removed outlier: 3.877A pdb=" N TYR D 249 " --> pdb=" O ALA D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 258 Processing helix chain 'D' and resid 283 through 296 removed outlier: 3.561A pdb=" N ARG D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU D 293 " --> pdb=" O ARG D 289 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 296 " --> pdb=" O GLY D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 323 removed outlier: 3.699A pdb=" N ILE D 318 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU D 319 " --> pdb=" O ASN D 315 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 322 " --> pdb=" O ILE D 318 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 350 through 360 removed outlier: 3.964A pdb=" N ALA D 354 " --> pdb=" O GLU D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 375 Processing helix chain 'D' and resid 377 through 383 Processing helix chain 'D' and resid 397 through 404 removed outlier: 3.851A pdb=" N ALA D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ALA D 404 " --> pdb=" O VAL D 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 24 removed outlier: 4.317A pdb=" N GLN E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 37 removed outlier: 3.596A pdb=" N SER E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 34 through 37' Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.993A pdb=" N LYS E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 65 Processing helix chain 'E' and resid 72 through 76 Processing helix chain 'E' and resid 82 through 99 removed outlier: 4.090A pdb=" N ILE E 86 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASP E 87 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG E 99 " --> pdb=" O ALA E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 123 removed outlier: 4.006A pdb=" N GLU E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU E 107 " --> pdb=" O ASP E 103 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 139 through 154 removed outlier: 3.550A pdb=" N LYS E 142 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR E 143 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS E 144 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS E 145 " --> pdb=" O LYS E 142 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER E 153 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN E 154 " --> pdb=" O LEU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 180 removed outlier: 3.594A pdb=" N ASP E 179 " --> pdb=" O TRP E 175 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU E 180 " --> pdb=" O ALA E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 removed outlier: 4.122A pdb=" N PHE E 201 " --> pdb=" O PRO E 198 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP E 202 " --> pdb=" O GLN E 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 202' Processing helix chain 'E' and resid 245 through 251 Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.628A pdb=" N GLU E 286 " --> pdb=" O PHE E 282 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE E 295 " --> pdb=" O PHE E 291 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER E 296 " --> pdb=" O GLY E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 322 removed outlier: 3.634A pdb=" N LEU E 322 " --> pdb=" O ILE E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 345 removed outlier: 3.765A pdb=" N LYS E 342 " --> pdb=" O GLU E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 359 Processing helix chain 'E' and resid 372 through 375 Processing helix chain 'E' and resid 377 through 382 removed outlier: 3.645A pdb=" N VAL E 381 " --> pdb=" O PHE E 377 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU E 382 " --> pdb=" O ASN E 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 377 through 382' Processing helix chain 'E' and resid 396 through 405 Processing helix chain 'F' and resid 12 through 23 removed outlier: 3.517A pdb=" N CYS F 23 " --> pdb=" O VAL F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 57 through 65 removed outlier: 3.725A pdb=" N GLY F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 76 Processing helix chain 'F' and resid 83 through 98 removed outlier: 3.971A pdb=" N ASP F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 123 removed outlier: 3.517A pdb=" N GLU F 107 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 131 removed outlier: 4.150A pdb=" N ARG F 131 " --> pdb=" O GLU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 140 through 153 removed outlier: 4.721A pdb=" N TYR F 143 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N HIS F 144 " --> pdb=" O PHE F 141 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS F 145 " --> pdb=" O LYS F 142 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER F 153 " --> pdb=" O LYS F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 180 removed outlier: 3.519A pdb=" N ASP F 179 " --> pdb=" O TRP F 175 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 202 removed outlier: 3.838A pdb=" N PHE F 201 " --> pdb=" O PRO F 198 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP F 202 " --> pdb=" O GLN F 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 198 through 202' Processing helix chain 'F' and resid 245 through 251 Processing helix chain 'F' and resid 253 through 258 Processing helix chain 'F' and resid 283 through 296 removed outlier: 3.755A pdb=" N ILE F 295 " --> pdb=" O PHE F 291 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER F 296 " --> pdb=" O GLY F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 323 removed outlier: 3.559A pdb=" N LEU F 319 " --> pdb=" O ASN F 315 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY F 320 " --> pdb=" O ARG F 316 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU F 322 " --> pdb=" O ILE F 318 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU F 323 " --> pdb=" O LEU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 344 removed outlier: 3.585A pdb=" N LYS F 342 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER F 344 " --> pdb=" O ILE F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 359 removed outlier: 4.072A pdb=" N ILE F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 375 removed outlier: 3.589A pdb=" N ALA F 375 " --> pdb=" O GLY F 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 372 through 375' Processing helix chain 'F' and resid 377 through 383 removed outlier: 3.606A pdb=" N GLU F 382 " --> pdb=" O ASN F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 406 removed outlier: 4.266A pdb=" N LEU F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 402 through 406' Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.553A pdb=" N TYR G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN G 24 " --> pdb=" O TYR G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 40 removed outlier: 3.727A pdb=" N SER G 37 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL G 38 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY G 39 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 53 Processing helix chain 'G' and resid 62 through 65 No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 102 through 124 removed outlier: 3.634A pdb=" N GLU G 107 " --> pdb=" O ASP G 103 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE G 108 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER G 113 " --> pdb=" O ARG G 109 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS G 121 " --> pdb=" O LYS G 117 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA G 122 " --> pdb=" O GLU G 118 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA G 123 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU G 124 " --> pdb=" O THR G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 131 removed outlier: 3.758A pdb=" N PHE G 130 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG G 131 " --> pdb=" O GLU G 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 127 through 131' Processing helix chain 'G' and resid 135 through 137 No H-bonds generated for 'chain 'G' and resid 135 through 137' Processing helix chain 'G' and resid 143 through 152 removed outlier: 3.702A pdb=" N LEU G 147 " --> pdb=" O TYR G 143 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE G 148 " --> pdb=" O HIS G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 180 removed outlier: 3.999A pdb=" N ALA G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 202 removed outlier: 3.644A pdb=" N PHE G 201 " --> pdb=" O PRO G 198 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP G 202 " --> pdb=" O GLN G 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 202' Processing helix chain 'G' and resid 245 through 251 Processing helix chain 'G' and resid 253 through 257 removed outlier: 3.672A pdb=" N ILE G 257 " --> pdb=" O ILE G 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 253 through 257' Processing helix chain 'G' and resid 281 through 295 removed outlier: 3.643A pdb=" N GLU G 286 " --> pdb=" O PHE G 282 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET G 287 " --> pdb=" O VAL G 283 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE G 288 " --> pdb=" O TYR G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 323 removed outlier: 3.816A pdb=" N LEU G 322 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU G 323 " --> pdb=" O LEU G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 344 removed outlier: 3.529A pdb=" N LYS G 342 " --> pdb=" O GLU G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 360 removed outlier: 3.536A pdb=" N LEU G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS G 359 " --> pdb=" O ILE G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 383 removed outlier: 3.645A pdb=" N GLU G 382 " --> pdb=" O ASN G 378 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS G 383 " --> pdb=" O SER G 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 405 Processing helix chain 'H' and resid 12 through 24 removed outlier: 3.563A pdb=" N CYS H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 40 removed outlier: 3.920A pdb=" N SER H 37 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL H 38 " --> pdb=" O GLY H 35 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLY H 39 " --> pdb=" O ALA H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 53 Processing helix chain 'H' and resid 57 through 65 Processing helix chain 'H' and resid 72 through 77 removed outlier: 3.855A pdb=" N ASP H 76 " --> pdb=" O GLN H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 98 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.573A pdb=" N ARG H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR H 116 " --> pdb=" O LEU H 112 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL H 119 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 122 " --> pdb=" O GLU H 118 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA H 123 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 131 removed outlier: 4.137A pdb=" N ARG H 131 " --> pdb=" O GLU H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 137 No H-bonds generated for 'chain 'H' and resid 135 through 137' Processing helix chain 'H' and resid 139 through 153 removed outlier: 3.832A pdb=" N LYS H 142 " --> pdb=" O ASP H 139 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TYR H 143 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS H 144 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER H 153 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 178 removed outlier: 3.752A pdb=" N ALA H 176 " --> pdb=" O ALA H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 201 removed outlier: 3.923A pdb=" N PHE H 201 " --> pdb=" O PRO H 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 198 through 201' Processing helix chain 'H' and resid 245 through 251 Processing helix chain 'H' and resid 283 through 296 removed outlier: 3.790A pdb=" N ILE H 295 " --> pdb=" O PHE H 291 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER H 296 " --> pdb=" O GLY H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 323 removed outlier: 3.898A pdb=" N LEU H 322 " --> pdb=" O ILE H 318 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU H 323 " --> pdb=" O LEU H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 345 removed outlier: 3.778A pdb=" N LYS H 345 " --> pdb=" O THR H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 360 removed outlier: 3.657A pdb=" N ALA H 354 " --> pdb=" O GLU H 350 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE H 355 " --> pdb=" O ALA H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 375 removed outlier: 3.661A pdb=" N ALA H 375 " --> pdb=" O GLY H 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 372 through 375' Processing helix chain 'H' and resid 377 through 383 Processing helix chain 'H' and resid 397 through 404 Processing helix chain 'I' and resid 12 through 24 removed outlier: 3.530A pdb=" N CYS I 23 " --> pdb=" O VAL I 19 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 36 No H-bonds generated for 'chain 'I' and resid 34 through 36' Processing helix chain 'I' and resid 38 through 40 No H-bonds generated for 'chain 'I' and resid 38 through 40' Processing helix chain 'I' and resid 45 through 55 removed outlier: 3.991A pdb=" N GLN I 54 " --> pdb=" O LYS I 50 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN I 55 " --> pdb=" O SER I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 65 removed outlier: 3.674A pdb=" N LEU I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 77 Processing helix chain 'I' and resid 82 through 99 removed outlier: 3.855A pdb=" N LYS I 91 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER I 94 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 123 removed outlier: 3.848A pdb=" N LYS I 110 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU I 112 " --> pdb=" O PHE I 108 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS I 121 " --> pdb=" O LYS I 117 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA I 123 " --> pdb=" O VAL I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 131 removed outlier: 3.648A pdb=" N PHE I 130 " --> pdb=" O GLY I 127 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG I 131 " --> pdb=" O GLU I 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 127 through 131' Processing helix chain 'I' and resid 135 through 137 No H-bonds generated for 'chain 'I' and resid 135 through 137' Processing helix chain 'I' and resid 139 through 154 removed outlier: 5.010A pdb=" N TYR I 143 " --> pdb=" O ALA I 140 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS I 144 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS I 145 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU I 146 " --> pdb=" O TYR I 143 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU I 147 " --> pdb=" O HIS I 144 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU I 151 " --> pdb=" O ILE I 148 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE I 152 " --> pdb=" O SER I 149 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER I 153 " --> pdb=" O LYS I 150 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN I 154 " --> pdb=" O LEU I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 180 removed outlier: 3.842A pdb=" N ALA I 176 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA I 177 " --> pdb=" O LEU I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 202 removed outlier: 3.644A pdb=" N PHE I 201 " --> pdb=" O PRO I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 245 through 251 Processing helix chain 'I' and resid 253 through 258 Processing helix chain 'I' and resid 281 through 296 removed outlier: 3.890A pdb=" N ILE I 295 " --> pdb=" O PHE I 291 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER I 296 " --> pdb=" O GLY I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 312 through 323 removed outlier: 3.914A pdb=" N LEU I 322 " --> pdb=" O ILE I 318 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU I 323 " --> pdb=" O LEU I 319 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 345 removed outlier: 3.804A pdb=" N LYS I 345 " --> pdb=" O THR I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 359 Processing helix chain 'I' and resid 377 through 383 removed outlier: 3.579A pdb=" N GLU I 382 " --> pdb=" O ASN I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 405 Processing helix chain 'J' and resid 12 through 24 removed outlier: 3.679A pdb=" N SER J 17 " --> pdb=" O ASP J 13 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN J 24 " --> pdb=" O TYR J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 40 removed outlier: 3.611A pdb=" N SER J 37 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY J 39 " --> pdb=" O ALA J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 55 removed outlier: 3.575A pdb=" N TRP J 49 " --> pdb=" O MET J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 62 removed outlier: 3.565A pdb=" N ALA J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 77 Processing helix chain 'J' and resid 82 through 99 removed outlier: 3.677A pdb=" N ILE J 86 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP J 87 " --> pdb=" O GLU J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 123 removed outlier: 3.688A pdb=" N GLU J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU J 107 " --> pdb=" O ASP J 103 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE J 111 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU J 112 " --> pdb=" O PHE J 108 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER J 113 " --> pdb=" O ARG J 109 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL J 119 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR J 120 " --> pdb=" O TYR J 116 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS J 121 " --> pdb=" O LYS J 117 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 131 removed outlier: 4.209A pdb=" N ARG J 131 " --> pdb=" O GLU J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 137 No H-bonds generated for 'chain 'J' and resid 135 through 137' Processing helix chain 'J' and resid 139 through 154 removed outlier: 4.012A pdb=" N LYS J 142 " --> pdb=" O ASP J 139 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR J 143 " --> pdb=" O ALA J 140 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS J 144 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU J 147 " --> pdb=" O HIS J 144 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU J 151 " --> pdb=" O ILE J 148 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE J 152 " --> pdb=" O SER J 149 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER J 153 " --> pdb=" O LYS J 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN J 154 " --> pdb=" O LEU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 180 removed outlier: 3.583A pdb=" N ASP J 179 " --> pdb=" O TRP J 175 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU J 180 " --> pdb=" O ALA J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 201 removed outlier: 3.929A pdb=" N PHE J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 198 through 201' Processing helix chain 'J' and resid 245 through 251 removed outlier: 3.700A pdb=" N TYR J 249 " --> pdb=" O ALA J 245 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP J 250 " --> pdb=" O SER J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 258 Processing helix chain 'J' and resid 282 through 295 removed outlier: 3.760A pdb=" N GLU J 286 " --> pdb=" O PHE J 282 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE J 295 " --> pdb=" O PHE J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 323 removed outlier: 3.873A pdb=" N LEU J 322 " --> pdb=" O ILE J 318 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU J 323 " --> pdb=" O LEU J 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 344 removed outlier: 3.888A pdb=" N THR J 341 " --> pdb=" O LYS J 337 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS J 342 " --> pdb=" O GLU J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 359 Processing helix chain 'J' and resid 372 through 375 Processing helix chain 'J' and resid 377 through 383 Processing helix chain 'J' and resid 395 through 407 removed outlier: 3.709A pdb=" N VAL J 400 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA J 404 " --> pdb=" O VAL J 400 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN J 405 " --> pdb=" O GLU J 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 24 removed outlier: 3.768A pdb=" N CYS K 23 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN K 24 " --> pdb=" O TYR K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 40 No H-bonds generated for 'chain 'K' and resid 38 through 40' Processing helix chain 'K' and resid 45 through 55 Processing helix chain 'K' and resid 58 through 65 removed outlier: 3.784A pdb=" N GLY K 61 " --> pdb=" O GLU K 58 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA K 62 " --> pdb=" O LEU K 59 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP K 65 " --> pdb=" O ALA K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 77 Processing helix chain 'K' and resid 82 through 99 removed outlier: 3.869A pdb=" N LYS K 91 " --> pdb=" O ASP K 87 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER K 94 " --> pdb=" O THR K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 120 removed outlier: 3.591A pdb=" N ARG K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS K 110 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 131 removed outlier: 3.600A pdb=" N PHE K 130 " --> pdb=" O GLY K 127 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG K 131 " --> pdb=" O GLU K 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 127 through 131' Processing helix chain 'K' and resid 135 through 137 No H-bonds generated for 'chain 'K' and resid 135 through 137' Processing helix chain 'K' and resid 139 through 154 removed outlier: 3.589A pdb=" N LYS K 142 " --> pdb=" O ASP K 139 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR K 143 " --> pdb=" O ALA K 140 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N HIS K 144 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS K 145 " --> pdb=" O LYS K 142 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER K 153 " --> pdb=" O LYS K 150 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN K 154 " --> pdb=" O LEU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 180 Processing helix chain 'K' and resid 200 through 202 No H-bonds generated for 'chain 'K' and resid 200 through 202' Processing helix chain 'K' and resid 245 through 251 Processing helix chain 'K' and resid 253 through 257 removed outlier: 3.579A pdb=" N ILE K 257 " --> pdb=" O ILE K 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 253 through 257' Processing helix chain 'K' and resid 281 through 296 removed outlier: 3.747A pdb=" N PHE K 291 " --> pdb=" O MET K 287 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY K 292 " --> pdb=" O PHE K 288 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU K 293 " --> pdb=" O ARG K 289 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE K 295 " --> pdb=" O PHE K 291 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER K 296 " --> pdb=" O GLY K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 312 through 323 removed outlier: 3.517A pdb=" N ALA K 321 " --> pdb=" O ILE K 317 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU K 322 " --> pdb=" O ILE K 318 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU K 323 " --> pdb=" O LEU K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 345 removed outlier: 3.866A pdb=" N LYS K 345 " --> pdb=" O THR K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 360 Processing helix chain 'K' and resid 373 through 375 No H-bonds generated for 'chain 'K' and resid 373 through 375' Processing helix chain 'K' and resid 377 through 383 removed outlier: 3.720A pdb=" N GLU K 382 " --> pdb=" O ASN K 378 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS K 383 " --> pdb=" O SER K 379 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 405 Processing helix chain 'L' and resid 12 through 22 removed outlier: 3.667A pdb=" N SER L 17 " --> pdb=" O ASP L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 37 removed outlier: 3.811A pdb=" N SER L 37 " --> pdb=" O ALA L 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 34 through 37' Processing helix chain 'L' and resid 45 through 55 removed outlier: 3.973A pdb=" N TRP L 49 " --> pdb=" O MET L 45 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS L 50 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 65 Processing helix chain 'L' and resid 72 through 76 Processing helix chain 'L' and resid 82 through 98 Processing helix chain 'L' and resid 103 through 123 removed outlier: 3.969A pdb=" N GLU L 107 " --> pdb=" O ASP L 103 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA L 122 " --> pdb=" O GLU L 118 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA L 123 " --> pdb=" O VAL L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 131 removed outlier: 3.669A pdb=" N PHE L 130 " --> pdb=" O GLY L 127 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 131' Processing helix chain 'L' and resid 135 through 137 No H-bonds generated for 'chain 'L' and resid 135 through 137' Processing helix chain 'L' and resid 139 through 154 removed outlier: 3.570A pdb=" N LYS L 142 " --> pdb=" O ASP L 139 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N TYR L 143 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS L 144 " --> pdb=" O PHE L 141 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS L 145 " --> pdb=" O LYS L 142 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE L 152 " --> pdb=" O SER L 149 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER L 153 " --> pdb=" O LYS L 150 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN L 154 " --> pdb=" O LEU L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 179 Processing helix chain 'L' and resid 198 through 201 removed outlier: 3.712A pdb=" N PHE L 201 " --> pdb=" O PRO L 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 198 through 201' Processing helix chain 'L' and resid 245 through 251 Processing helix chain 'L' and resid 253 through 258 Processing helix chain 'L' and resid 283 through 295 removed outlier: 3.629A pdb=" N PHE L 288 " --> pdb=" O TYR L 284 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE L 295 " --> pdb=" O PHE L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 323 removed outlier: 3.825A pdb=" N LEU L 322 " --> pdb=" O ILE L 318 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU L 323 " --> pdb=" O LEU L 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 337 through 344 Processing helix chain 'L' and resid 350 through 360 Processing helix chain 'L' and resid 372 through 375 Processing helix chain 'L' and resid 377 through 383 Processing helix chain 'L' and resid 396 through 401 Processing helix chain 'L' and resid 404 through 407 No H-bonds generated for 'chain 'L' and resid 404 through 407' Processing helix chain 'M' and resid 130 through 136 removed outlier: 3.637A pdb=" N ILE M 135 " --> pdb=" O ASP M 131 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE M 136 " --> pdb=" O PHE M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 146 Proline residue: M 145 - end of helix Processing helix chain 'M' and resid 165 through 168 No H-bonds generated for 'chain 'M' and resid 165 through 168' Processing helix chain 'M' and resid 183 through 195 removed outlier: 3.516A pdb=" N VAL M 194 " --> pdb=" O LEU M 190 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER M 195 " --> pdb=" O THR M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 270 removed outlier: 3.730A pdb=" N LEU M 261 " --> pdb=" O TYR M 258 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY M 262 " --> pdb=" O GLN M 259 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N PHE M 263 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ALA M 264 " --> pdb=" O LEU M 261 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY M 265 " --> pdb=" O GLY M 262 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU M 266 " --> pdb=" O PHE M 263 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU M 270 " --> pdb=" O ILE M 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 290 removed outlier: 3.879A pdb=" N ILE M 288 " --> pdb=" O ALA M 284 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN M 289 " --> pdb=" O LEU M 285 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ARG M 290 " --> pdb=" O SER M 286 " (cutoff:3.500A) Processing helix chain 'M' and resid 323 through 330 Processing helix chain 'M' and resid 343 through 355 removed outlier: 3.509A pdb=" N LEU M 346 " --> pdb=" O PHE M 343 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU M 349 " --> pdb=" O LEU M 346 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL M 350 " --> pdb=" O ALA M 347 " (cutoff:3.500A) Processing helix chain 'M' and resid 369 through 385 removed outlier: 4.363A pdb=" N ASN M 373 " --> pdb=" O PHE M 369 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL M 374 " --> pdb=" O GLY M 370 " (cutoff:3.500A) Proline residue: M 376 - end of helix removed outlier: 3.542A pdb=" N ALA M 385 " --> pdb=" O ILE M 381 " (cutoff:3.500A) Processing helix chain 'M' and resid 388 through 391 No H-bonds generated for 'chain 'M' and resid 388 through 391' Processing helix chain 'M' and resid 408 through 421 removed outlier: 4.509A pdb=" N ALA M 412 " --> pdb=" O HIS M 408 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET M 413 " --> pdb=" O TRP M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 446 through 464 removed outlier: 4.219A pdb=" N SER M 451 " --> pdb=" O PRO M 447 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA M 452 " --> pdb=" O MET M 448 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU M 453 " --> pdb=" O LEU M 449 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU M 454 " --> pdb=" O LEU M 450 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU M 455 " --> pdb=" O SER M 451 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG M 463 " --> pdb=" O GLU M 459 " (cutoff:3.500A) Processing helix chain 'M' and resid 466 through 468 No H-bonds generated for 'chain 'M' and resid 466 through 468' Processing helix chain 'M' and resid 479 through 481 No H-bonds generated for 'chain 'M' and resid 479 through 481' Processing helix chain 'M' and resid 523 through 527 Processing helix chain 'M' and resid 540 through 549 removed outlier: 3.774A pdb=" N GLN M 544 " --> pdb=" O GLU M 540 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA M 545 " --> pdb=" O ARG M 541 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU M 546 " --> pdb=" O ASP M 542 " (cutoff:3.500A) Processing helix chain 'M' and resid 559 through 563 removed outlier: 3.598A pdb=" N SER M 562 " --> pdb=" O LYS M 559 " (cutoff:3.500A) Processing helix chain 'M' and resid 598 through 603 Processing helix chain 'N' and resid 30 through 33 Processing helix chain 'N' and resid 130 through 136 removed outlier: 3.506A pdb=" N ILE N 135 " --> pdb=" O ASP N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 146 No H-bonds generated for 'chain 'N' and resid 144 through 146' Processing helix chain 'N' and resid 165 through 168 No H-bonds generated for 'chain 'N' and resid 165 through 168' Processing helix chain 'N' and resid 183 through 197 removed outlier: 3.909A pdb=" N LYS N 197 " --> pdb=" O LYS N 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 216 No H-bonds generated for 'chain 'N' and resid 214 through 216' Processing helix chain 'N' and resid 258 through 260 No H-bonds generated for 'chain 'N' and resid 258 through 260' Processing helix chain 'N' and resid 263 through 270 removed outlier: 3.703A pdb=" N ILE N 267 " --> pdb=" O PHE N 263 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU N 269 " --> pdb=" O GLY N 265 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU N 270 " --> pdb=" O LEU N 266 " (cutoff:3.500A) Processing helix chain 'N' and resid 278 through 290 removed outlier: 3.561A pdb=" N ALA N 287 " --> pdb=" O ASN N 283 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE N 288 " --> pdb=" O ALA N 284 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASN N 289 " --> pdb=" O LEU N 285 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG N 290 " --> pdb=" O SER N 286 " (cutoff:3.500A) Processing helix chain 'N' and resid 323 through 330 Processing helix chain 'N' and resid 343 through 355 removed outlier: 3.558A pdb=" N ALA N 347 " --> pdb=" O LYS N 344 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR N 348 " --> pdb=" O SER N 345 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU N 349 " --> pdb=" O LEU N 346 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS N 355 " --> pdb=" O GLU N 352 " (cutoff:3.500A) Processing helix chain 'N' and resid 375 through 384 Processing helix chain 'N' and resid 408 through 421 removed outlier: 3.770A pdb=" N ALA N 412 " --> pdb=" O HIS N 408 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU N 416 " --> pdb=" O ALA N 412 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL N 417 " --> pdb=" O MET N 413 " (cutoff:3.500A) Processing helix chain 'N' and resid 446 through 464 removed outlier: 3.629A pdb=" N ALA N 458 " --> pdb=" O LEU N 454 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU N 459 " --> pdb=" O GLU N 455 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE N 460 " --> pdb=" O MET N 456 " (cutoff:3.500A) Processing helix chain 'N' and resid 479 through 481 No H-bonds generated for 'chain 'N' and resid 479 through 481' Processing helix chain 'N' and resid 499 through 502 No H-bonds generated for 'chain 'N' and resid 499 through 502' Processing helix chain 'N' and resid 518 through 520 No H-bonds generated for 'chain 'N' and resid 518 through 520' Processing helix chain 'N' and resid 523 through 528 removed outlier: 3.645A pdb=" N MET N 528 " --> pdb=" O THR N 524 " (cutoff:3.500A) Processing helix chain 'N' and resid 540 through 549 removed outlier: 3.605A pdb=" N ALA N 545 " --> pdb=" O ARG N 541 " (cutoff:3.500A) Processing helix chain 'N' and resid 558 through 563 removed outlier: 3.574A pdb=" N ILE N 561 " --> pdb=" O LEU N 558 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER N 562 " --> pdb=" O LYS N 559 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 136 Processing helix chain 'O' and resid 141 through 146 removed outlier: 3.570A pdb=" N LEU O 144 " --> pdb=" O LYS O 141 " (cutoff:3.500A) Proline residue: O 145 - end of helix No H-bonds generated for 'chain 'O' and resid 141 through 146' Processing helix chain 'O' and resid 165 through 169 Processing helix chain 'O' and resid 183 through 197 Processing helix chain 'O' and resid 214 through 216 No H-bonds generated for 'chain 'O' and resid 214 through 216' Processing helix chain 'O' and resid 262 through 270 Processing helix chain 'O' and resid 278 through 290 removed outlier: 3.555A pdb=" N ALA O 287 " --> pdb=" O ASN O 283 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE O 288 " --> pdb=" O ALA O 284 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ASN O 289 " --> pdb=" O LEU O 285 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG O 290 " --> pdb=" O SER O 286 " (cutoff:3.500A) Processing helix chain 'O' and resid 322 through 331 Processing helix chain 'O' and resid 343 through 354 removed outlier: 3.668A pdb=" N THR O 348 " --> pdb=" O SER O 345 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU O 349 " --> pdb=" O LEU O 346 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL O 350 " --> pdb=" O ALA O 347 " (cutoff:3.500A) Processing helix chain 'O' and resid 369 through 385 Proline residue: O 376 - end of helix Processing helix chain 'O' and resid 410 through 420 removed outlier: 3.701A pdb=" N PHE O 420 " --> pdb=" O GLU O 416 " (cutoff:3.500A) Processing helix chain 'O' and resid 446 through 464 removed outlier: 3.644A pdb=" N SER O 451 " --> pdb=" O PRO O 447 " (cutoff:3.500A) Processing helix chain 'O' and resid 479 through 481 No H-bonds generated for 'chain 'O' and resid 479 through 481' Processing helix chain 'O' and resid 491 through 493 No H-bonds generated for 'chain 'O' and resid 491 through 493' Processing helix chain 'O' and resid 497 through 506 Processing helix chain 'O' and resid 518 through 520 No H-bonds generated for 'chain 'O' and resid 518 through 520' Processing helix chain 'O' and resid 523 through 526 No H-bonds generated for 'chain 'O' and resid 523 through 526' Processing helix chain 'O' and resid 540 through 549 removed outlier: 3.654A pdb=" N ALA O 545 " --> pdb=" O ARG O 541 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA O 549 " --> pdb=" O ALA O 545 " (cutoff:3.500A) Processing helix chain 'O' and resid 555 through 560 removed outlier: 3.611A pdb=" N LYS O 559 " --> pdb=" O GLU O 555 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLN O 560 " --> pdb=" O GLN O 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 555 through 560' Processing helix chain 'O' and resid 598 through 602 Processing helix chain 'P' and resid 30 through 33 removed outlier: 3.609A pdb=" N GLY P 33 " --> pdb=" O GLY P 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 30 through 33' Processing helix chain 'P' and resid 130 through 136 Processing helix chain 'P' and resid 141 through 143 No H-bonds generated for 'chain 'P' and resid 141 through 143' Processing helix chain 'P' and resid 165 through 168 No H-bonds generated for 'chain 'P' and resid 165 through 168' Processing helix chain 'P' and resid 183 through 197 Processing helix chain 'P' and resid 214 through 216 No H-bonds generated for 'chain 'P' and resid 214 through 216' Processing helix chain 'P' and resid 262 through 269 removed outlier: 3.581A pdb=" N LEU P 266 " --> pdb=" O GLY P 262 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE P 267 " --> pdb=" O PHE P 263 " (cutoff:3.500A) Processing helix chain 'P' and resid 278 through 286 Processing helix chain 'P' and resid 343 through 352 removed outlier: 3.525A pdb=" N LEU P 346 " --> pdb=" O PHE P 343 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU P 349 " --> pdb=" O LEU P 346 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL P 350 " --> pdb=" O ALA P 347 " (cutoff:3.500A) Processing helix chain 'P' and resid 375 through 385 removed outlier: 3.682A pdb=" N GLN P 382 " --> pdb=" O VAL P 378 " (cutoff:3.500A) Processing helix chain 'P' and resid 388 through 392 Processing helix chain 'P' and resid 408 through 417 Processing helix chain 'P' and resid 446 through 464 removed outlier: 3.874A pdb=" N PHE P 462 " --> pdb=" O ALA P 458 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG P 463 " --> pdb=" O GLU P 459 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG P 464 " --> pdb=" O ILE P 460 " (cutoff:3.500A) Processing helix chain 'P' and resid 479 through 481 No H-bonds generated for 'chain 'P' and resid 479 through 481' Processing helix chain 'P' and resid 498 through 503 Processing helix chain 'P' and resid 505 through 507 No H-bonds generated for 'chain 'P' and resid 505 through 507' Processing helix chain 'P' and resid 518 through 520 No H-bonds generated for 'chain 'P' and resid 518 through 520' Processing helix chain 'P' and resid 526 through 528 No H-bonds generated for 'chain 'P' and resid 526 through 528' Processing helix chain 'P' and resid 540 through 549 removed outlier: 4.295A pdb=" N ALA P 549 " --> pdb=" O ALA P 545 " (cutoff:3.500A) Processing helix chain 'P' and resid 561 through 563 No H-bonds generated for 'chain 'P' and resid 561 through 563' Processing helix chain 'P' and resid 599 through 601 No H-bonds generated for 'chain 'P' and resid 599 through 601' Processing helix chain 'Q' and resid 130 through 136 removed outlier: 3.655A pdb=" N ASN Q 134 " --> pdb=" O SER Q 130 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE Q 135 " --> pdb=" O ASP Q 131 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 146 No H-bonds generated for 'chain 'Q' and resid 144 through 146' Processing helix chain 'Q' and resid 183 through 197 Processing helix chain 'Q' and resid 259 through 261 No H-bonds generated for 'chain 'Q' and resid 259 through 261' Processing helix chain 'Q' and resid 263 through 269 Processing helix chain 'Q' and resid 278 through 287 Processing helix chain 'Q' and resid 322 through 330 Processing helix chain 'Q' and resid 343 through 354 removed outlier: 3.594A pdb=" N THR Q 348 " --> pdb=" O SER Q 345 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 373 removed outlier: 3.767A pdb=" N SER Q 372 " --> pdb=" O ALA Q 368 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN Q 373 " --> pdb=" O PHE Q 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 368 through 373' Processing helix chain 'Q' and resid 375 through 385 Processing helix chain 'Q' and resid 388 through 393 removed outlier: 3.970A pdb=" N ILE Q 393 " --> pdb=" O ARG Q 389 " (cutoff:3.500A) Processing helix chain 'Q' and resid 410 through 420 Processing helix chain 'Q' and resid 446 through 464 removed outlier: 3.856A pdb=" N ARG Q 463 " --> pdb=" O GLU Q 459 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG Q 464 " --> pdb=" O ILE Q 460 " (cutoff:3.500A) Processing helix chain 'Q' and resid 479 through 481 No H-bonds generated for 'chain 'Q' and resid 479 through 481' Processing helix chain 'Q' and resid 499 through 503 Processing helix chain 'Q' and resid 518 through 520 No H-bonds generated for 'chain 'Q' and resid 518 through 520' Processing helix chain 'Q' and resid 523 through 528 removed outlier: 3.816A pdb=" N MET Q 528 " --> pdb=" O THR Q 524 " (cutoff:3.500A) Processing helix chain 'Q' and resid 540 through 549 removed outlier: 3.735A pdb=" N ALA Q 545 " --> pdb=" O ARG Q 541 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA Q 549 " --> pdb=" O ALA Q 545 " (cutoff:3.500A) Processing helix chain 'Q' and resid 557 through 559 No H-bonds generated for 'chain 'Q' and resid 557 through 559' Processing helix chain 'Q' and resid 561 through 563 No H-bonds generated for 'chain 'Q' and resid 561 through 563' Processing helix chain 'R' and resid 130 through 136 removed outlier: 3.663A pdb=" N ILE R 135 " --> pdb=" O ASP R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 146 No H-bonds generated for 'chain 'R' and resid 144 through 146' Processing helix chain 'R' and resid 165 through 169 Processing helix chain 'R' and resid 183 through 195 Processing helix chain 'R' and resid 262 through 270 removed outlier: 3.609A pdb=" N LEU R 266 " --> pdb=" O GLY R 262 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE R 267 " --> pdb=" O PHE R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 285 Processing helix chain 'R' and resid 319 through 330 removed outlier: 4.792A pdb=" N ALA R 323 " --> pdb=" O SER R 320 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG R 330 " --> pdb=" O ASP R 327 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 352 Processing helix chain 'R' and resid 368 through 373 Processing helix chain 'R' and resid 375 through 385 removed outlier: 3.555A pdb=" N GLN R 383 " --> pdb=" O LYS R 379 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU R 384 " --> pdb=" O ILE R 380 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA R 385 " --> pdb=" O ILE R 381 " (cutoff:3.500A) Processing helix chain 'R' and resid 408 through 420 removed outlier: 4.022A pdb=" N ALA R 412 " --> pdb=" O HIS R 408 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET R 413 " --> pdb=" O TRP R 409 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU R 416 " --> pdb=" O ALA R 412 " (cutoff:3.500A) Processing helix chain 'R' and resid 443 through 464 Proline residue: R 447 - end of helix removed outlier: 3.622A pdb=" N SER R 451 " --> pdb=" O PRO R 447 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA R 452 " --> pdb=" O MET R 448 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU R 453 " --> pdb=" O LEU R 449 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU R 454 " --> pdb=" O LEU R 450 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU R 455 " --> pdb=" O SER R 451 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET R 456 " --> pdb=" O ALA R 452 " (cutoff:3.500A) Processing helix chain 'R' and resid 479 through 482 No H-bonds generated for 'chain 'R' and resid 479 through 482' Processing helix chain 'R' and resid 492 through 506 removed outlier: 3.518A pdb=" N GLY R 504 " --> pdb=" O LEU R 500 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG R 505 " --> pdb=" O ALA R 501 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS R 506 " --> pdb=" O LYS R 502 " (cutoff:3.500A) Processing helix chain 'R' and resid 523 through 527 Processing helix chain 'R' and resid 540 through 548 Processing helix chain 'R' and resid 555 through 563 removed outlier: 3.545A pdb=" N GLN R 560 " --> pdb=" O GLN R 556 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE R 561 " --> pdb=" O ILE R 557 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N SER R 562 " --> pdb=" O LEU R 558 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLY R 563 " --> pdb=" O LYS R 559 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 8.816A pdb=" N THR A 367 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 329 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VAL A 369 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 331 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A 300 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N VAL A 330 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 302 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TYR A 332 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE A 304 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN A 27 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N PHE A 303 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY A 29 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ASN A 305 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU A 31 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA A 163 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LEU A 32 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE A 165 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N ILE A 164 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N THR A 166 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR A 224 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN A 183 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEU A 223 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE A 185 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LYS A 225 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 3 through 5 removed outlier: 8.638A pdb=" N THR B 367 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 329 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N VAL B 369 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE B 331 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR B 300 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N VAL B 330 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 302 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N TYR B 332 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE B 304 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN B 27 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N PHE B 303 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY B 29 " --> pdb=" O PHE B 303 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ASN B 305 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU B 31 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA B 163 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N LEU B 32 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE B 165 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N ILE B 164 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR B 222 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR B 166 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR B 224 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN B 183 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B 223 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE B 185 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LYS B 225 " --> pdb=" O PHE B 185 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 232 through 234 Processing sheet with id= D, first strand: chain 'C' and resid 3 through 5 removed outlier: 8.687A pdb=" N THR C 367 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL C 329 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL C 369 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE C 331 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 300 " --> pdb=" O HIS C 328 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N VAL C 330 " --> pdb=" O THR C 300 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU C 302 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N TYR C 332 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE C 304 " --> pdb=" O TYR C 332 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN C 27 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N PHE C 303 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY C 29 " --> pdb=" O PHE C 303 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ASN C 305 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 31 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA C 163 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU C 32 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE C 165 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N ILE C 164 " --> pdb=" O HIS C 220 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N THR C 166 " --> pdb=" O TYR C 222 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR C 224 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN C 183 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU C 223 " --> pdb=" O GLN C 183 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE C 185 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LYS C 225 " --> pdb=" O PHE C 185 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 232 through 234 Processing sheet with id= F, first strand: chain 'D' and resid 8 through 10 removed outlier: 3.560A pdb=" N ASN D 8 " --> pdb=" O GLN D 5 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE D 3 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N THR D 367 " --> pdb=" O PHE D 327 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL D 329 " --> pdb=" O THR D 367 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL D 369 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE D 331 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR D 300 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N VAL D 330 " --> pdb=" O THR D 300 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU D 302 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N TYR D 332 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE D 304 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN D 27 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N PHE D 303 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY D 29 " --> pdb=" O PHE D 303 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ASN D 305 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU D 31 " --> pdb=" O ASN D 305 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA D 163 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N LEU D 32 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE D 165 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N ILE D 164 " --> pdb=" O HIS D 220 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR D 222 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N THR D 166 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR D 224 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLN D 183 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU D 223 " --> pdb=" O GLN D 183 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE D 185 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LYS D 225 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 232 through 234 Processing sheet with id= H, first strand: chain 'E' and resid 3 through 5 removed outlier: 8.476A pdb=" N THR E 367 " --> pdb=" O PHE E 327 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL E 329 " --> pdb=" O THR E 367 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N VAL E 369 " --> pdb=" O VAL E 329 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE E 331 " --> pdb=" O VAL E 369 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR E 300 " --> pdb=" O HIS E 328 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N VAL E 330 " --> pdb=" O THR E 300 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU E 302 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N TYR E 332 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE E 304 " --> pdb=" O TYR E 332 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN E 27 " --> pdb=" O ALA E 301 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N PHE E 303 " --> pdb=" O ASN E 27 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY E 29 " --> pdb=" O PHE E 303 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASN E 305 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU E 31 " --> pdb=" O ASN E 305 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA E 163 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N LEU E 32 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE E 165 " --> pdb=" O LEU E 32 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N ILE E 164 " --> pdb=" O HIS E 220 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR E 222 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N THR E 166 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TYR E 224 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN E 183 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU E 223 " --> pdb=" O GLN E 183 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE E 185 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LYS E 225 " --> pdb=" O PHE E 185 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 232 through 234 Processing sheet with id= J, first strand: chain 'F' and resid 3 through 5 removed outlier: 8.524A pdb=" N THR F 367 " --> pdb=" O PHE F 327 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL F 329 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL F 369 " --> pdb=" O VAL F 329 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE F 331 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR F 300 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N VAL F 330 " --> pdb=" O THR F 300 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU F 302 " --> pdb=" O VAL F 330 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TYR F 332 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE F 304 " --> pdb=" O TYR F 332 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN F 27 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N PHE F 303 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY F 29 " --> pdb=" O PHE F 303 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN F 305 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU F 31 " --> pdb=" O ASN F 305 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA F 163 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU F 32 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE F 165 " --> pdb=" O LEU F 32 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ILE F 164 " --> pdb=" O HIS F 220 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR F 222 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR F 166 " --> pdb=" O TYR F 222 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR F 224 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN F 183 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU F 223 " --> pdb=" O GLN F 183 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N PHE F 185 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LYS F 225 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 232 through 234 Processing sheet with id= L, first strand: chain 'G' and resid 183 through 185 Processing sheet with id= M, first strand: chain 'G' and resid 232 through 234 Processing sheet with id= N, first strand: chain 'H' and resid 3 through 5 removed outlier: 8.485A pdb=" N THR H 367 " --> pdb=" O PHE H 327 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL H 329 " --> pdb=" O THR H 367 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL H 369 " --> pdb=" O VAL H 329 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE H 331 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR H 300 " --> pdb=" O HIS H 328 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N VAL H 330 " --> pdb=" O THR H 300 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU H 302 " --> pdb=" O VAL H 330 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N TYR H 332 " --> pdb=" O LEU H 302 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE H 304 " --> pdb=" O TYR H 332 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN H 27 " --> pdb=" O ALA H 301 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N PHE H 303 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY H 29 " --> pdb=" O PHE H 303 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ASN H 305 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU H 31 " --> pdb=" O ASN H 305 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA H 163 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N LEU H 32 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE H 165 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N ILE H 164 " --> pdb=" O HIS H 220 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR H 222 " --> pdb=" O ILE H 164 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N THR H 166 " --> pdb=" O TYR H 222 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR H 224 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN H 183 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU H 223 " --> pdb=" O GLN H 183 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE H 185 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LYS H 225 " --> pdb=" O PHE H 185 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 232 through 234 Processing sheet with id= P, first strand: chain 'I' and resid 8 through 10 removed outlier: 3.829A pdb=" N ASN I 8 " --> pdb=" O GLN I 5 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE I 3 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N THR I 367 " --> pdb=" O PHE I 327 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL I 329 " --> pdb=" O THR I 367 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N VAL I 369 " --> pdb=" O VAL I 329 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE I 331 " --> pdb=" O VAL I 369 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR I 300 " --> pdb=" O HIS I 328 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N VAL I 330 " --> pdb=" O THR I 300 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU I 302 " --> pdb=" O VAL I 330 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N TYR I 332 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE I 304 " --> pdb=" O TYR I 332 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN I 27 " --> pdb=" O ALA I 301 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N PHE I 303 " --> pdb=" O ASN I 27 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY I 29 " --> pdb=" O PHE I 303 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ASN I 305 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU I 31 " --> pdb=" O ASN I 305 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA I 163 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N LEU I 32 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE I 165 " --> pdb=" O LEU I 32 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N ILE I 164 " --> pdb=" O HIS I 220 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR I 222 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N THR I 166 " --> pdb=" O TYR I 222 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TYR I 224 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN I 183 " --> pdb=" O ALA I 221 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU I 223 " --> pdb=" O GLN I 183 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE I 185 " --> pdb=" O LEU I 223 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LYS I 225 " --> pdb=" O PHE I 185 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 3 through 5 removed outlier: 8.687A pdb=" N THR J 367 " --> pdb=" O PHE J 327 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL J 329 " --> pdb=" O THR J 367 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N VAL J 369 " --> pdb=" O VAL J 329 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE J 331 " --> pdb=" O VAL J 369 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR J 300 " --> pdb=" O HIS J 328 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N VAL J 330 " --> pdb=" O THR J 300 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU J 302 " --> pdb=" O VAL J 330 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N TYR J 332 " --> pdb=" O LEU J 302 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE J 304 " --> pdb=" O TYR J 332 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN J 27 " --> pdb=" O ALA J 301 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N PHE J 303 " --> pdb=" O ASN J 27 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY J 29 " --> pdb=" O PHE J 303 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N ASN J 305 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU J 31 " --> pdb=" O ASN J 305 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA J 163 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N LEU J 32 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE J 165 " --> pdb=" O LEU J 32 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N ILE J 164 " --> pdb=" O HIS J 220 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR J 222 " --> pdb=" O ILE J 164 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR J 166 " --> pdb=" O TYR J 222 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR J 224 " --> pdb=" O THR J 166 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN J 183 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU J 223 " --> pdb=" O GLN J 183 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE J 185 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LYS J 225 " --> pdb=" O PHE J 185 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 232 through 234 Processing sheet with id= S, first strand: chain 'K' and resid 3 through 5 removed outlier: 8.720A pdb=" N THR K 367 " --> pdb=" O PHE K 327 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL K 329 " --> pdb=" O THR K 367 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N VAL K 369 " --> pdb=" O VAL K 329 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE K 331 " --> pdb=" O VAL K 369 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR K 300 " --> pdb=" O HIS K 328 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N VAL K 330 " --> pdb=" O THR K 300 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU K 302 " --> pdb=" O VAL K 330 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N TYR K 332 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE K 304 " --> pdb=" O TYR K 332 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASN K 27 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N PHE K 303 " --> pdb=" O ASN K 27 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY K 29 " --> pdb=" O PHE K 303 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ASN K 305 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU K 31 " --> pdb=" O ASN K 305 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA K 163 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LEU K 32 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE K 165 " --> pdb=" O LEU K 32 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N ILE K 164 " --> pdb=" O HIS K 220 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR K 222 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N THR K 166 " --> pdb=" O TYR K 222 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR K 224 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN K 183 " --> pdb=" O ALA K 221 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU K 223 " --> pdb=" O GLN K 183 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE K 185 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LYS K 225 " --> pdb=" O PHE K 185 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 232 through 234 Processing sheet with id= U, first strand: chain 'L' and resid 8 through 10 removed outlier: 3.618A pdb=" N ASN L 8 " --> pdb=" O GLN L 5 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE L 3 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR L 367 " --> pdb=" O PHE L 327 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL L 329 " --> pdb=" O THR L 367 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL L 369 " --> pdb=" O VAL L 329 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE L 331 " --> pdb=" O VAL L 369 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR L 300 " --> pdb=" O HIS L 328 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N VAL L 330 " --> pdb=" O THR L 300 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU L 302 " --> pdb=" O VAL L 330 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N TYR L 332 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE L 304 " --> pdb=" O TYR L 332 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASN L 27 " --> pdb=" O ALA L 301 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N PHE L 303 " --> pdb=" O ASN L 27 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY L 29 " --> pdb=" O PHE L 303 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASN L 305 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU L 31 " --> pdb=" O ASN L 305 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA L 163 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LEU L 32 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE L 165 " --> pdb=" O LEU L 32 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N ILE L 164 " --> pdb=" O HIS L 220 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR L 222 " --> pdb=" O ILE L 164 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR L 166 " --> pdb=" O TYR L 222 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR L 224 " --> pdb=" O THR L 166 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN L 183 " --> pdb=" O ALA L 221 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU L 223 " --> pdb=" O GLN L 183 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE L 185 " --> pdb=" O LEU L 223 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LYS L 225 " --> pdb=" O PHE L 185 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 232 through 234 Processing sheet with id= W, first strand: chain 'M' and resid 67 through 70 removed outlier: 3.563A pdb=" N ASP M 67 " --> pdb=" O ILE M 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE M 95 " --> pdb=" O ASP M 67 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA M 69 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ARG M 92 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU M 27 " --> pdb=" O ARG M 92 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY M 17 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN M 26 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL M 15 " --> pdb=" O ASN M 26 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'M' and resid 35 through 38 Processing sheet with id= Y, first strand: chain 'M' and resid 125 through 127 removed outlier: 3.949A pdb=" N GLY M 100 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG M 64 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA M 98 " --> pdb=" O ARG M 64 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 147 through 149 Processing sheet with id= AA, first strand: chain 'M' and resid 151 through 153 removed outlier: 7.739A pdb=" N HIS M 172 " --> pdb=" O SER M 530 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP M 532 " --> pdb=" O HIS M 172 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA M 174 " --> pdb=" O TRP M 532 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N SER M 534 " --> pdb=" O ALA M 174 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU M 176 " --> pdb=" O SER M 534 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR M 472 " --> pdb=" O SER M 510 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE M 512 " --> pdb=" O THR M 472 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU M 474 " --> pdb=" O ILE M 512 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N SER M 514 " --> pdb=" O LEU M 474 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU M 476 " --> pdb=" O SER M 514 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG M 202 " --> pdb=" O VAL M 473 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU M 475 " --> pdb=" O ARG M 202 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL M 204 " --> pdb=" O LEU M 475 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLU M 477 " --> pdb=" O VAL M 204 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE M 206 " --> pdb=" O GLU M 477 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU M 227 " --> pdb=" O ASN M 437 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N CYS M 252 " --> pdb=" O ILE M 226 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'M' and resid 299 through 301 Processing sheet with id= AC, first strand: chain 'M' and resid 356 through 359 removed outlier: 3.959A pdb=" N GLY M 363 " --> pdb=" O ASP M 359 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'N' and resid 67 through 70 removed outlier: 3.607A pdb=" N ASP N 67 " --> pdb=" O ILE N 95 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA N 69 " --> pdb=" O GLN N 93 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ARG N 92 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY N 17 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN N 26 " --> pdb=" O VAL N 15 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL N 15 " --> pdb=" O ASN N 26 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 35 through 38 Processing sheet with id= AF, first strand: chain 'N' and resid 125 through 127 removed outlier: 3.792A pdb=" N ILE N 59 " --> pdb=" O ALA N 56 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY N 100 " --> pdb=" O VAL N 62 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG N 64 " --> pdb=" O ALA N 98 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ALA N 98 " --> pdb=" O ARG N 64 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 222 through 226 removed outlier: 6.558A pdb=" N VAL N 433 " --> pdb=" O LYS N 223 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N THR N 225 " --> pdb=" O VAL N 433 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE N 435 " --> pdb=" O THR N 225 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE N 203 " --> pdb=" O HIS N 434 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL N 436 " --> pdb=" O ILE N 203 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE N 205 " --> pdb=" O VAL N 436 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL N 473 " --> pdb=" O VAL N 204 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE N 206 " --> pdb=" O VAL N 473 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU N 475 " --> pdb=" O PHE N 206 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU N 173 " --> pdb=" O VAL N 513 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N THR N 515 " --> pdb=" O LEU N 173 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL N 175 " --> pdb=" O THR N 515 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA N 174 " --> pdb=" O SER N 530 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TRP N 532 " --> pdb=" O ALA N 174 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU N 176 " --> pdb=" O TRP N 532 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER N 534 " --> pdb=" O LEU N 176 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE N 161 " --> pdb=" O LEU N 150 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'N' and resid 299 through 301 removed outlier: 3.661A pdb=" N PHE N 308 " --> pdb=" O LEU N 300 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 356 through 358 removed outlier: 3.718A pdb=" N LYS N 365 " --> pdb=" O ALA N 357 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'O' and resid 67 through 70 removed outlier: 3.535A pdb=" N ASP O 67 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA O 69 " --> pdb=" O GLN O 93 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ARG O 92 " --> pdb=" O LEU O 27 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY O 17 " --> pdb=" O ARG O 24 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN O 26 " --> pdb=" O VAL O 15 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL O 15 " --> pdb=" O ASN O 26 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA O 125 " --> pdb=" O ILE O 12 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER O 124 " --> pdb=" O ASP O 55 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY O 100 " --> pdb=" O VAL O 62 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG O 64 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA O 98 " --> pdb=" O ARG O 64 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'O' and resid 35 through 37 Processing sheet with id= AL, first strand: chain 'O' and resid 222 through 226 removed outlier: 6.565A pdb=" N VAL O 433 " --> pdb=" O LYS O 223 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N THR O 225 " --> pdb=" O VAL O 433 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE O 435 " --> pdb=" O THR O 225 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE O 203 " --> pdb=" O HIS O 434 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL O 436 " --> pdb=" O ILE O 203 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE O 205 " --> pdb=" O VAL O 436 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL O 473 " --> pdb=" O VAL O 204 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N PHE O 206 " --> pdb=" O VAL O 473 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU O 475 " --> pdb=" O PHE O 206 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU O 173 " --> pdb=" O VAL O 513 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N THR O 515 " --> pdb=" O LEU O 173 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL O 175 " --> pdb=" O THR O 515 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN O 531 " --> pdb=" O ALA O 174 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N LEU O 176 " --> pdb=" O ASN O 531 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE O 533 " --> pdb=" O LEU O 176 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE O 161 " --> pdb=" O LEU O 150 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'O' and resid 299 through 301 removed outlier: 3.678A pdb=" N PHE O 308 " --> pdb=" O LEU O 300 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'P' and resid 67 through 70 removed outlier: 3.679A pdb=" N ASP P 67 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA P 69 " --> pdb=" O GLN P 93 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ARG P 92 " --> pdb=" O LEU P 27 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY P 17 " --> pdb=" O ARG P 24 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASN P 26 " --> pdb=" O VAL P 15 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL P 15 " --> pdb=" O ASN P 26 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'P' and resid 35 through 38 removed outlier: 3.642A pdb=" N GLY P 41 " --> pdb=" O HIS P 38 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'P' and resid 125 through 127 removed outlier: 3.914A pdb=" N ILE P 59 " --> pdb=" O ALA P 56 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY P 100 " --> pdb=" O VAL P 62 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ARG P 64 " --> pdb=" O ALA P 98 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ALA P 98 " --> pdb=" O ARG P 64 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'P' and resid 222 through 226 removed outlier: 6.542A pdb=" N VAL P 433 " --> pdb=" O LYS P 223 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N THR P 225 " --> pdb=" O VAL P 433 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE P 435 " --> pdb=" O THR P 225 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE P 203 " --> pdb=" O HIS P 434 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL P 436 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE P 205 " --> pdb=" O VAL P 436 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL P 473 " --> pdb=" O ARG P 202 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU P 173 " --> pdb=" O VAL P 513 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N THR P 515 " --> pdb=" O LEU P 173 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL P 175 " --> pdb=" O THR P 515 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ALA P 174 " --> pdb=" O SER P 530 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TRP P 532 " --> pdb=" O ALA P 174 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU P 176 " --> pdb=" O TRP P 532 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER P 534 " --> pdb=" O LEU P 176 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE P 161 " --> pdb=" O LEU P 150 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Q' and resid 67 through 70 removed outlier: 3.580A pdb=" N ASP Q 67 " --> pdb=" O ILE Q 95 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA Q 69 " --> pdb=" O GLN Q 93 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ARG Q 92 " --> pdb=" O LEU Q 27 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY Q 17 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASN Q 26 " --> pdb=" O VAL Q 15 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL Q 15 " --> pdb=" O ASN Q 26 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'Q' and resid 125 through 127 removed outlier: 3.713A pdb=" N GLY Q 100 " --> pdb=" O VAL Q 62 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG Q 64 " --> pdb=" O ALA Q 98 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ALA Q 98 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 222 through 226 removed outlier: 7.113A pdb=" N VAL Q 433 " --> pdb=" O LYS Q 223 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N THR Q 225 " --> pdb=" O VAL Q 433 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE Q 435 " --> pdb=" O THR Q 225 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE Q 203 " --> pdb=" O HIS Q 434 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL Q 436 " --> pdb=" O ILE Q 203 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE Q 205 " --> pdb=" O VAL Q 436 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL Q 473 " --> pdb=" O VAL Q 204 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE Q 206 " --> pdb=" O VAL Q 473 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU Q 475 " --> pdb=" O PHE Q 206 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER Q 510 " --> pdb=" O LEU Q 474 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU Q 476 " --> pdb=" O SER Q 510 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE Q 512 " --> pdb=" O LEU Q 476 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU Q 173 " --> pdb=" O VAL Q 513 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR Q 515 " --> pdb=" O LEU Q 173 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL Q 175 " --> pdb=" O THR Q 515 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE Q 161 " --> pdb=" O LEU Q 150 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'R' and resid 13 through 19 removed outlier: 7.211A pdb=" N ARG R 24 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU R 18 " --> pdb=" O ARG R 22 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL R 62 " --> pdb=" O ILE R 99 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE R 101 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU R 60 " --> pdb=" O PHE R 101 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'R' and resid 101 through 104 Processing sheet with id= AW, first strand: chain 'R' and resid 512 through 515 removed outlier: 6.843A pdb=" N LEU R 173 " --> pdb=" O VAL R 513 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N THR R 515 " --> pdb=" O LEU R 173 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL R 175 " --> pdb=" O THR R 515 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'R' and resid 203 through 206 removed outlier: 3.734A pdb=" N THR R 225 " --> pdb=" O ILE R 435 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN R 437 " --> pdb=" O THR R 225 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'R' and resid 356 through 358 Processing sheet with id= AZ, first strand: chain 'R' and resid 147 through 152 removed outlier: 7.182A pdb=" N ILE R 161 " --> pdb=" O LEU R 150 " (cutoff:3.500A) 1731 hydrogen bonds defined for protein. 4659 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: 26.04 Time building geometry restraints manager: 20.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 10852 1.30 - 1.43: 17971 1.43 - 1.56: 37712 1.56 - 1.68: 66 1.68 - 1.81: 223 Bond restraints: 66824 Sorted by residual: bond pdb=" N TYR A 270 " pdb=" CA TYR A 270 " ideal model delta sigma weight residual 1.456 1.490 -0.033 9.40e-03 1.13e+04 1.25e+01 bond pdb=" N ASP P 316 " pdb=" CA ASP P 316 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.28e-02 6.10e+03 1.16e+01 bond pdb=" CA ALA A 273 " pdb=" CB ALA A 273 " ideal model delta sigma weight residual 1.532 1.479 0.053 1.59e-02 3.96e+03 1.10e+01 bond pdb=" N ILE A 269 " pdb=" CA ILE A 269 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" C PRO A 271 " pdb=" O PRO A 271 " ideal model delta sigma weight residual 1.228 1.176 0.052 2.00e-02 2.50e+03 6.87e+00 ... (remaining 66819 not shown) Histogram of bond angle deviations from ideal: 92.29 - 101.08: 112 101.08 - 109.86: 7473 109.86 - 118.64: 45308 118.64 - 127.42: 36936 127.42 - 136.21: 564 Bond angle restraints: 90393 Sorted by residual: angle pdb=" CA TYR A 270 " pdb=" C TYR A 270 " pdb=" N PRO A 271 " ideal model delta sigma weight residual 117.82 124.92 -7.10 7.80e-01 1.64e+00 8.28e+01 angle pdb=" N SER P 320 " pdb=" CA SER P 320 " pdb=" C SER P 320 " ideal model delta sigma weight residual 112.88 101.54 11.34 1.29e+00 6.01e-01 7.73e+01 angle pdb=" N ALA P 323 " pdb=" CA ALA P 323 " pdb=" C ALA P 323 " ideal model delta sigma weight residual 110.53 99.73 10.80 1.29e+00 6.01e-01 7.02e+01 angle pdb=" N LEU P 322 " pdb=" CA LEU P 322 " pdb=" C LEU P 322 " ideal model delta sigma weight residual 113.41 104.23 9.18 1.22e+00 6.72e-01 5.67e+01 angle pdb=" N TYR A 270 " pdb=" CA TYR A 270 " pdb=" C TYR A 270 " ideal model delta sigma weight residual 108.07 102.27 5.80 8.90e-01 1.26e+00 4.25e+01 ... (remaining 90388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.91: 38787 31.91 - 63.82: 1077 63.82 - 95.73: 124 95.73 - 127.65: 6 127.65 - 159.56: 2 Dihedral angle restraints: 39996 sinusoidal: 16468 harmonic: 23528 Sorted by residual: dihedral pdb=" CA TYR A 270 " pdb=" C TYR A 270 " pdb=" N PRO A 271 " pdb=" CA PRO A 271 " ideal model delta harmonic sigma weight residual 0.00 -41.91 41.91 0 5.00e+00 4.00e-02 7.03e+01 dihedral pdb=" O1B ADP N 701 " pdb=" O3A ADP N 701 " pdb=" PB ADP N 701 " pdb=" PA ADP N 701 " ideal model delta sinusoidal sigma weight residual -60.00 -166.04 106.03 1 2.00e+01 2.50e-03 3.06e+01 dihedral pdb=" C5' ADP P 701 " pdb=" O5' ADP P 701 " pdb=" PA ADP P 701 " pdb=" O2A ADP P 701 " ideal model delta sinusoidal sigma weight residual -60.00 -159.48 99.49 1 2.00e+01 2.50e-03 2.80e+01 ... (remaining 39993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 9114 0.076 - 0.152: 716 0.152 - 0.228: 6 0.228 - 0.304: 0 0.304 - 0.380: 1 Chirality restraints: 9837 Sorted by residual: chirality pdb=" CA ARG P 315 " pdb=" N ARG P 315 " pdb=" C ARG P 315 " pdb=" CB ARG P 315 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA ALA P 323 " pdb=" N ALA P 323 " pdb=" C ALA P 323 " pdb=" CB ALA P 323 " both_signs ideal model delta sigma weight residual False 2.48 2.71 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ASN P 318 " pdb=" N ASN P 318 " pdb=" C ASN P 318 " pdb=" CB ASN P 318 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 9834 not shown) Planarity restraints: 11590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 290 " 0.632 9.50e-02 1.11e+02 2.83e-01 4.90e+01 pdb=" NE ARG P 290 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG P 290 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG P 290 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG P 290 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 322 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C LEU P 322 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU P 322 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA P 323 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS P 314 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C CYS P 314 " 0.044 2.00e-02 2.50e+03 pdb=" O CYS P 314 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG P 315 " -0.014 2.00e-02 2.50e+03 ... (remaining 11587 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 259 2.59 - 3.17: 49199 3.17 - 3.75: 87648 3.75 - 4.32: 123444 4.32 - 4.90: 215042 Nonbonded interactions: 475592 Sorted by model distance: nonbonded pdb=" O3B ADP N 701 " pdb="MG MG N 702 " model vdw 2.013 2.170 nonbonded pdb=" O3B ADP M 701 " pdb="MG MG M 702 " model vdw 2.014 2.170 nonbonded pdb=" O2B ADP Q 701 " pdb="MG MG Q 702 " model vdw 2.019 2.170 nonbonded pdb=" O ARG Q 296 " pdb=" OD1 ASN Q 297 " model vdw 2.086 3.040 nonbonded pdb=" O3B ADP O 701 " pdb="MG MG O 702 " model vdw 2.120 2.170 ... (remaining 475587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'B' and (resid 2 through 387 or resid 395 through 406 or resid 501)) selection = (chain 'C' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'D' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'E' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'F' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'G' and (resid 2 through 208 or resid 218 through 406 or resid 501)) selection = (chain 'H' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'I' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'J' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'K' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) selection = (chain 'L' and (resid 2 through 208 or resid 218 through 387 or resid 395 throug \ h 406 or resid 501)) } ncs_group { reference = (chain 'M' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 584)) selection = (chain 'N' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 584)) selection = (chain 'O' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 584)) selection = (chain 'P' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 355 or resid 375 through 484 or resid 498 through 584)) selection = (chain 'Q' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 584)) selection = (chain 'R' and (resid 10 through 227 or resid 238 through 328 or resid 336 throu \ gh 355 or resid 375 through 484 or resid 498 through 584)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 9.400 Check model and map are aligned: 0.740 Set scattering table: 0.450 Process input model: 135.800 Find NCS groups from input model: 4.390 Set up NCS constraints: 0.270 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: 0.020 Load rotamer database and sin/cos tables:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.003 0.053 66824 Z= 0.175 Angle : 0.558 11.343 90393 Z= 0.313 Chirality : 0.041 0.380 9837 Planarity : 0.004 0.283 11590 Dihedral : 14.790 159.557 24942 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.86 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.09), residues: 8032 helix: 0.12 (0.10), residues: 3157 sheet: 0.40 (0.16), residues: 1018 loop : -1.59 (0.09), residues: 3857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 409 HIS 0.006 0.001 HIS B 313 PHE 0.022 0.001 PHE I 363 TYR 0.022 0.001 TYR R 497 ARG 0.004 0.000 ARG P 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 957 time to evaluate : 5.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 LYS cc_start: 0.8340 (mttt) cc_final: 0.8126 (mtmm) REVERT: B 342 LYS cc_start: 0.8001 (mttm) cc_final: 0.7722 (mtpm) REVERT: B 378 ASN cc_start: 0.7767 (m-40) cc_final: 0.7490 (m-40) REVERT: B 382 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7611 (tt0) REVERT: C 24 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7730 (mt0) REVERT: C 90 THR cc_start: 0.8707 (m) cc_final: 0.8371 (p) REVERT: C 102 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7831 (mm-30) REVERT: D 378 ASN cc_start: 0.8330 (m-40) cc_final: 0.8060 (m-40) REVERT: E 13 ASP cc_start: 0.6800 (m-30) cc_final: 0.6238 (t0) REVERT: F 206 ARG cc_start: 0.6728 (tmm-80) cc_final: 0.6429 (ttm170) REVERT: F 316 ARG cc_start: 0.7983 (tpp-160) cc_final: 0.7439 (mmm160) REVERT: G 239 THR cc_start: 0.8068 (p) cc_final: 0.7764 (t) REVERT: H 110 LYS cc_start: 0.8312 (mtmm) cc_final: 0.8112 (ttmm) REVERT: H 207 ASN cc_start: 0.7160 (m-40) cc_final: 0.6891 (m-40) REVERT: H 270 TYR cc_start: 0.6855 (m-80) cc_final: 0.6398 (m-80) REVERT: H 316 ARG cc_start: 0.8331 (mmm160) cc_final: 0.7878 (mmp-170) REVERT: I 79 LEU cc_start: 0.8770 (mt) cc_final: 0.8524 (mt) REVERT: I 231 THR cc_start: 0.8443 (m) cc_final: 0.8008 (p) REVERT: I 337 LYS cc_start: 0.7207 (mmtt) cc_final: 0.6996 (mmtt) REVERT: J 74 ASP cc_start: 0.7658 (m-30) cc_final: 0.7261 (m-30) REVERT: J 103 ASP cc_start: 0.8340 (m-30) cc_final: 0.8077 (m-30) REVERT: J 106 GLU cc_start: 0.7720 (tp30) cc_final: 0.7358 (mm-30) REVERT: J 263 TYR cc_start: 0.7154 (t80) cc_final: 0.6777 (t80) REVERT: K 26 ASP cc_start: 0.8547 (m-30) cc_final: 0.8331 (m-30) REVERT: K 146 GLU cc_start: 0.8235 (tt0) cc_final: 0.8018 (tt0) REVERT: K 338 GLU cc_start: 0.7936 (mp0) cc_final: 0.7720 (mp0) REVERT: N 141 LYS cc_start: 0.6938 (ptmm) cc_final: 0.6707 (ptpt) REVERT: N 383 GLN cc_start: 0.8448 (mt0) cc_final: 0.8205 (mt0) REVERT: N 528 MET cc_start: 0.8820 (mtp) cc_final: 0.8610 (mtp) REVERT: N 540 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7263 (mm-30) REVERT: N 592 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7490 (tppp) REVERT: O 34 ARG cc_start: 0.6891 (ttp-170) cc_final: 0.6676 (ttm-80) REVERT: O 238 LYS cc_start: 0.7215 (tptp) cc_final: 0.6575 (tppt) REVERT: P 144 LEU cc_start: 0.8124 (mt) cc_final: 0.7877 (mp) REVERT: P 503 GLU cc_start: 0.8177 (pp20) cc_final: 0.7923 (pp20) REVERT: Q 5 LYS cc_start: 0.6031 (mmmt) cc_final: 0.5760 (ttmt) REVERT: Q 8 GLU cc_start: 0.5559 (mm-30) cc_final: 0.4809 (pm20) REVERT: Q 550 MET cc_start: 0.8444 (ptp) cc_final: 0.8157 (ptm) REVERT: Q 592 LYS cc_start: 0.7211 (mtmt) cc_final: 0.6969 (tttp) REVERT: R 300 LEU cc_start: 0.7438 (mp) cc_final: 0.7084 (tm) outliers start: 0 outliers final: 2 residues processed: 957 average time/residue: 1.5652 time to fit residues: 1887.3953 Evaluate side-chains 531 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 529 time to evaluate : 5.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain O residue 578 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 681 optimal weight: 6.9990 chunk 611 optimal weight: 0.8980 chunk 339 optimal weight: 8.9990 chunk 208 optimal weight: 8.9990 chunk 412 optimal weight: 5.9990 chunk 326 optimal weight: 10.0000 chunk 632 optimal weight: 6.9990 chunk 244 optimal weight: 0.0470 chunk 384 optimal weight: 6.9990 chunk 470 optimal weight: 8.9990 chunk 732 optimal weight: 8.9990 overall best weight: 4.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 405 ASN C 129 GLN C 156 GLN D 72 GLN D 199 GLN D 324 ASN D 365 GLN D 405 ASN E 81 ASN F 5 GLN F 81 ASN H 55 ASN H 364 ASN I 378 ASN J 315 ASN J 383 HIS J 394 ASN K 154 ASN M 556 GLN M 560 GLN O 383 GLN O 440 ASN O 539 ASN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 66824 Z= 0.330 Angle : 0.674 16.256 90393 Z= 0.341 Chirality : 0.047 0.212 9837 Planarity : 0.005 0.084 11590 Dihedral : 9.476 164.797 9502 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.99 % Allowed : 9.08 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -1.31 (0.09), residues: 8032 helix: -0.27 (0.09), residues: 3236 sheet: 0.33 (0.16), residues: 967 loop : -1.71 (0.09), residues: 3829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 409 HIS 0.012 0.002 HIS B 313 PHE 0.022 0.002 PHE A 130 TYR 0.024 0.002 TYR C 376 ARG 0.009 0.001 ARG R 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 531 time to evaluate : 5.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 PHE cc_start: 0.7279 (m-80) cc_final: 0.7027 (m-80) REVERT: A 374 LYS cc_start: 0.8455 (mttt) cc_final: 0.8193 (mtmm) REVERT: B 121 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8340 (mtmm) REVERT: B 342 LYS cc_start: 0.7941 (mttm) cc_final: 0.7573 (mtpm) REVERT: B 378 ASN cc_start: 0.7482 (m-40) cc_final: 0.7227 (m110) REVERT: C 24 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7364 (mt0) REVERT: C 90 THR cc_start: 0.8759 (m) cc_final: 0.8391 (p) REVERT: C 102 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7918 (mm-30) REVERT: C 361 MET cc_start: 0.6771 (mtp) cc_final: 0.6404 (mtp) REVERT: D 100 ARG cc_start: 0.8433 (mtt90) cc_final: 0.8071 (mtt90) REVERT: D 242 GLU cc_start: 0.9415 (OUTLIER) cc_final: 0.9007 (tt0) REVERT: D 378 ASN cc_start: 0.8378 (m-40) cc_final: 0.8049 (m-40) REVERT: E 323 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8597 (pp) REVERT: F 54 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7677 (mp10) REVERT: F 206 ARG cc_start: 0.6775 (tmm-80) cc_final: 0.6535 (ttm170) REVERT: G 146 GLU cc_start: 0.7568 (tp30) cc_final: 0.7294 (tp30) REVERT: G 262 PHE cc_start: 0.7229 (OUTLIER) cc_final: 0.5789 (p90) REVERT: H 207 ASN cc_start: 0.7249 (m-40) cc_final: 0.6994 (m-40) REVERT: H 270 TYR cc_start: 0.6904 (m-80) cc_final: 0.6410 (m-80) REVERT: I 79 LEU cc_start: 0.8910 (mt) cc_final: 0.8658 (mt) REVERT: I 107 GLU cc_start: 0.8335 (tp30) cc_final: 0.8026 (tp30) REVERT: I 337 LYS cc_start: 0.7422 (mmtt) cc_final: 0.7129 (mmtt) REVERT: J 24 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8061 (mt0) REVERT: J 74 ASP cc_start: 0.7876 (m-30) cc_final: 0.7444 (m-30) REVERT: J 103 ASP cc_start: 0.8274 (m-30) cc_final: 0.8018 (m-30) REVERT: J 263 TYR cc_start: 0.7116 (t80) cc_final: 0.6787 (t80) REVERT: K 24 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.6949 (mp-120) REVERT: K 342 LYS cc_start: 0.7846 (mttm) cc_final: 0.7519 (ttmt) REVERT: L 46 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7917 (ttmt) REVERT: L 121 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8446 (ttmt) REVERT: M 21 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6824 (tp30) REVERT: M 294 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8143 (ptpt) REVERT: M 470 TYR cc_start: 0.7580 (t80) cc_final: 0.7223 (t80) REVERT: M 601 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: N 141 LYS cc_start: 0.7086 (ptmm) cc_final: 0.6799 (ptpt) REVERT: N 443 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8102 (mm-40) REVERT: N 540 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7250 (mm-30) REVERT: N 592 LYS cc_start: 0.8020 (ttpt) cc_final: 0.7472 (tppp) REVERT: O 34 ARG cc_start: 0.7202 (ttp-170) cc_final: 0.6887 (ttm-80) REVERT: O 141 LYS cc_start: 0.7626 (pmtt) cc_final: 0.7195 (tptp) REVERT: O 308 PHE cc_start: 0.7206 (t80) cc_final: 0.7002 (t80) REVERT: O 396 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8085 (pt) REVERT: O 413 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7795 (ptt) REVERT: O 555 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: P 281 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7811 (tt) REVERT: P 300 LEU cc_start: 0.7223 (mp) cc_final: 0.6806 (mt) REVERT: P 338 ASN cc_start: 0.6857 (m110) cc_final: 0.6657 (t0) REVERT: P 550 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.5659 (tmt) REVERT: Q 1 MET cc_start: 0.3152 (OUTLIER) cc_final: 0.2450 (mmt) REVERT: Q 8 GLU cc_start: 0.5990 (mm-30) cc_final: 0.4968 (pm20) REVERT: Q 270 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7639 (pp) REVERT: Q 592 LYS cc_start: 0.7205 (mtmt) cc_final: 0.7005 (tttp) REVERT: R 542 ASP cc_start: 0.7368 (m-30) cc_final: 0.7095 (m-30) outliers start: 138 outliers final: 54 residues processed: 634 average time/residue: 1.5291 time to fit residues: 1231.6959 Evaluate side-chains 549 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 477 time to evaluate : 5.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 235 ASN Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 262 PHE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 24 GLN Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain M residue 294 LYS Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 601 GLU Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 364 SER Chi-restraints excluded: chain N residue 443 GLN Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 555 GLU Chi-restraints excluded: chain P residue 166 ASP Chi-restraints excluded: chain P residue 251 TYR Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain P residue 525 VAL Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 144 LEU Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 538 THR Chi-restraints excluded: chain Q residue 582 ILE Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 115 ASP Chi-restraints excluded: chain R residue 315 ARG Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 407 optimal weight: 1.9990 chunk 227 optimal weight: 7.9990 chunk 609 optimal weight: 20.0000 chunk 499 optimal weight: 8.9990 chunk 202 optimal weight: 1.9990 chunk 734 optimal weight: 20.0000 chunk 793 optimal weight: 20.0000 chunk 653 optimal weight: 5.9990 chunk 728 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 588 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS C 156 GLN D 199 GLN D 247 GLN D 324 ASN G 135 GLN G 154 ASN G 218 HIS G 227 HIS G 315 ASN I 227 HIS M 187 ASN M 297 ASN N 554 ASN O 383 GLN O 440 ASN O 539 ASN P 224 HIS Q 292 HIS Q 338 ASN R 107 ASN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 66824 Z= 0.366 Angle : 0.696 15.459 90393 Z= 0.353 Chirality : 0.047 0.200 9837 Planarity : 0.005 0.051 11590 Dihedral : 9.437 165.857 9498 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.90 % Allowed : 11.43 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -1.52 (0.09), residues: 8032 helix: -0.47 (0.09), residues: 3246 sheet: 0.19 (0.16), residues: 981 loop : -1.81 (0.09), residues: 3805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Q 325 HIS 0.012 0.002 HIS H 313 PHE 0.024 0.002 PHE A 262 TYR 0.035 0.002 TYR R 497 ARG 0.009 0.001 ARG F 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 504 time to evaluate : 5.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7517 (mmp) cc_final: 0.6996 (mmp) REVERT: A 156 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7589 (mp10) REVERT: A 374 LYS cc_start: 0.8498 (mttt) cc_final: 0.8197 (mtmm) REVERT: B 128 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7523 (mm-30) REVERT: B 342 LYS cc_start: 0.7924 (mttm) cc_final: 0.7533 (mtpm) REVERT: B 378 ASN cc_start: 0.7532 (m-40) cc_final: 0.7249 (m110) REVERT: C 24 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7373 (mt0) REVERT: C 102 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7909 (mm-30) REVERT: C 352 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6864 (mm-30) REVERT: C 361 MET cc_start: 0.6850 (mtp) cc_final: 0.6188 (mtp) REVERT: D 100 ARG cc_start: 0.8480 (mtt90) cc_final: 0.8205 (mtp85) REVERT: D 242 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.8924 (tt0) REVERT: D 378 ASN cc_start: 0.8394 (m-40) cc_final: 0.8084 (m-40) REVERT: E 361 MET cc_start: 0.8162 (mmt) cc_final: 0.7741 (mmt) REVERT: F 206 ARG cc_start: 0.6730 (tmm-80) cc_final: 0.6250 (ttm170) REVERT: F 374 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8329 (mtpt) REVERT: G 262 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.6088 (p90) REVERT: G 361 MET cc_start: 0.7114 (tpp) cc_final: 0.6783 (tpp) REVERT: H 207 ASN cc_start: 0.7266 (m-40) cc_final: 0.7006 (m-40) REVERT: H 270 TYR cc_start: 0.6907 (m-80) cc_final: 0.6436 (m-80) REVERT: I 259 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7433 (mtmt) REVERT: I 337 LYS cc_start: 0.7257 (mmtt) cc_final: 0.7039 (mmtt) REVERT: J 24 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8134 (mt0) REVERT: J 171 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8031 (mt) REVERT: J 287 MET cc_start: 0.8660 (mmt) cc_final: 0.7902 (mmt) REVERT: K 156 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8460 (tp40) REVERT: K 342 LYS cc_start: 0.7882 (mttm) cc_final: 0.7542 (ttmt) REVERT: K 345 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7313 (mmtp) REVERT: L 46 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7910 (ttmt) REVERT: L 342 LYS cc_start: 0.8288 (ttmt) cc_final: 0.8052 (ttmm) REVERT: M 21 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6846 (tp30) REVERT: M 34 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6529 (ptm160) REVERT: M 95 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8857 (mm) REVERT: M 294 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8131 (ptpt) REVERT: M 466 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6632 (pp30) REVERT: M 470 TYR cc_start: 0.7736 (t80) cc_final: 0.7447 (t80) REVERT: M 498 GLU cc_start: 0.5260 (OUTLIER) cc_final: 0.4448 (pt0) REVERT: M 601 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: N 5 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7340 (mttm) REVERT: N 55 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7490 (p0) REVERT: N 540 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7269 (mm-30) REVERT: N 592 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7754 (tppt) REVERT: O 34 ARG cc_start: 0.7281 (ttp-170) cc_final: 0.6839 (ttm-80) REVERT: O 141 LYS cc_start: 0.7631 (pmtt) cc_final: 0.7276 (tptp) REVERT: O 237 GLU cc_start: 0.6061 (mp0) cc_final: 0.5193 (pm20) REVERT: O 555 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: P 141 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7356 (ptmt) REVERT: P 281 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7828 (tt) REVERT: P 520 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8398 (mt-10) REVERT: P 550 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.5692 (tmt) REVERT: Q 1 MET cc_start: 0.3449 (OUTLIER) cc_final: 0.2453 (mmt) REVERT: Q 8 GLU cc_start: 0.6019 (mm-30) cc_final: 0.4945 (pm20) REVERT: Q 270 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7727 (pp) REVERT: Q 484 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6455 (mtt90) REVERT: Q 520 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: R 144 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6030 (tm) REVERT: R 300 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.6039 (mp) REVERT: R 551 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6787 (tp30) outliers start: 201 outliers final: 96 residues processed: 660 average time/residue: 1.4823 time to fit residues: 1250.7741 Evaluate side-chains 580 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 452 time to evaluate : 5.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 374 LYS Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 235 ASN Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 374 LYS Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 262 PHE Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain I residue 259 LYS Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 156 GLN Chi-restraints excluded: chain K residue 345 LYS Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 139 ILE Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 294 LYS Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 498 GLU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain M residue 601 GLU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 364 SER Chi-restraints excluded: chain N residue 443 GLN Chi-restraints excluded: chain N residue 559 LYS Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 252 CYS Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 555 GLU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 166 ASP Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 394 VAL Chi-restraints excluded: chain P residue 520 GLU Chi-restraints excluded: chain P residue 525 VAL Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 276 THR Chi-restraints excluded: chain Q residue 309 LEU Chi-restraints excluded: chain Q residue 346 LEU Chi-restraints excluded: chain Q residue 484 ARG Chi-restraints excluded: chain Q residue 520 GLU Chi-restraints excluded: chain Q residue 538 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 155 ARG Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 551 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 725 optimal weight: 10.0000 chunk 551 optimal weight: 4.9990 chunk 381 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 350 optimal weight: 8.9990 chunk 492 optimal weight: 10.0000 chunk 736 optimal weight: 30.0000 chunk 780 optimal weight: 8.9990 chunk 384 optimal weight: 3.9990 chunk 698 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN D 199 GLN D 324 ASN E 266 GLN G 315 ASN H 209 ASN I 227 HIS J 227 HIS K 254 ASN N 297 ASN O 383 GLN O 440 ASN O 539 ASN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 66824 Z= 0.270 Angle : 0.616 13.936 90393 Z= 0.313 Chirality : 0.044 0.176 9837 Planarity : 0.004 0.053 11590 Dihedral : 9.196 165.917 9498 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.85 % Allowed : 13.29 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -1.44 (0.09), residues: 8032 helix: -0.36 (0.09), residues: 3219 sheet: 0.18 (0.16), residues: 982 loop : -1.79 (0.09), residues: 3831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 409 HIS 0.008 0.001 HIS I 267 PHE 0.024 0.002 PHE A 262 TYR 0.024 0.002 TYR R 497 ARG 0.008 0.000 ARG F 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 484 time to evaluate : 5.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7537 (mmp) cc_final: 0.6997 (mmp) REVERT: A 156 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7568 (mp10) REVERT: A 374 LYS cc_start: 0.8479 (mttt) cc_final: 0.8185 (mtmm) REVERT: B 342 LYS cc_start: 0.7910 (mttm) cc_final: 0.7503 (mtpm) REVERT: B 378 ASN cc_start: 0.7478 (m-40) cc_final: 0.7191 (m110) REVERT: C 24 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7357 (mt0) REVERT: C 102 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7901 (mm-30) REVERT: C 335 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6467 (mm-30) REVERT: C 361 MET cc_start: 0.6844 (mtp) cc_final: 0.6108 (mtp) REVERT: D 83 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.6719 (mm-30) REVERT: D 100 ARG cc_start: 0.8479 (mtt90) cc_final: 0.8221 (mtp85) REVERT: D 242 GLU cc_start: 0.9361 (OUTLIER) cc_final: 0.8918 (tt0) REVERT: D 378 ASN cc_start: 0.8385 (m-40) cc_final: 0.8065 (m-40) REVERT: E 361 MET cc_start: 0.8143 (mmt) cc_final: 0.7723 (mmt) REVERT: F 206 ARG cc_start: 0.6715 (tmm-80) cc_final: 0.6498 (ttm170) REVERT: G 146 GLU cc_start: 0.7615 (tp30) cc_final: 0.7354 (tp30) REVERT: G 219 TYR cc_start: 0.7086 (m-80) cc_final: 0.6649 (m-80) REVERT: H 128 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7203 (pp20) REVERT: H 207 ASN cc_start: 0.7255 (m-40) cc_final: 0.6994 (m-40) REVERT: H 270 TYR cc_start: 0.6900 (m-80) cc_final: 0.6521 (m-80) REVERT: J 24 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: J 129 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8360 (mt0) REVERT: J 171 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7957 (mt) REVERT: J 199 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: K 156 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8381 (tp40) REVERT: K 206 ARG cc_start: 0.8403 (ptt90) cc_final: 0.8076 (ptt90) REVERT: K 342 LYS cc_start: 0.7877 (mttm) cc_final: 0.7522 (ttmt) REVERT: L 46 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7917 (ttmt) REVERT: L 342 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7927 (ttmm) REVERT: M 21 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6659 (tp30) REVERT: M 294 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8059 (ptpt) REVERT: M 386 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6658 (mm-30) REVERT: M 454 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6915 (mt) REVERT: M 466 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6707 (pp30) REVERT: M 478 GLU cc_start: 0.8659 (mp0) cc_final: 0.8353 (mp0) REVERT: M 498 GLU cc_start: 0.5461 (OUTLIER) cc_final: 0.4687 (pt0) REVERT: M 601 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: N 5 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7337 (mttm) REVERT: N 55 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7430 (p0) REVERT: N 443 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8242 (mm-40) REVERT: N 540 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7250 (mm-30) REVERT: N 592 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7584 (tppp) REVERT: O 34 ARG cc_start: 0.7385 (ttp-170) cc_final: 0.6871 (ttm-80) REVERT: O 238 LYS cc_start: 0.7147 (tptp) cc_final: 0.6687 (tppt) REVERT: O 413 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7880 (ptt) REVERT: O 555 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: P 3 LEU cc_start: 0.5640 (OUTLIER) cc_final: 0.4534 (tt) REVERT: P 141 LYS cc_start: 0.7904 (mmtm) cc_final: 0.7340 (ptmt) REVERT: P 281 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7868 (tt) REVERT: P 478 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: P 550 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.5818 (tmt) REVERT: Q 1 MET cc_start: 0.3735 (OUTLIER) cc_final: 0.2773 (mmt) REVERT: Q 270 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7728 (pp) REVERT: Q 520 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: R 144 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6042 (tm) REVERT: R 300 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6173 (mp) REVERT: R 476 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7452 (mp) REVERT: R 551 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6676 (tp30) outliers start: 198 outliers final: 81 residues processed: 637 average time/residue: 1.4694 time to fit residues: 1209.7947 Evaluate side-chains 576 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 461 time to evaluate : 5.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 374 LYS Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 235 ASN Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 129 GLN Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 199 GLN Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 156 GLN Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 294 LYS Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 386 GLU Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain M residue 454 LEU Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 498 GLU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain M residue 601 GLU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 259 GLN Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 443 GLN Chi-restraints excluded: chain N residue 444 ASP Chi-restraints excluded: chain N residue 601 GLU Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 252 CYS Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 413 MET Chi-restraints excluded: chain O residue 555 GLU Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 478 GLU Chi-restraints excluded: chain P residue 524 THR Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 144 LEU Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 346 LEU Chi-restraints excluded: chain Q residue 520 GLU Chi-restraints excluded: chain Q residue 538 THR Chi-restraints excluded: chain Q residue 582 ILE Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 551 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 649 optimal weight: 9.9990 chunk 442 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 580 optimal weight: 6.9990 chunk 321 optimal weight: 0.5980 chunk 665 optimal weight: 5.9990 chunk 539 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 chunk 398 optimal weight: 7.9990 chunk 700 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 135 GLN D 199 GLN D 324 ASN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN N 297 ASN O 383 GLN O 440 ASN ** P 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 66824 Z= 0.201 Angle : 0.560 13.023 90393 Z= 0.285 Chirality : 0.042 0.179 9837 Planarity : 0.004 0.048 11590 Dihedral : 9.005 166.602 9498 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.93 % Allowed : 14.37 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -1.29 (0.09), residues: 8032 helix: -0.23 (0.09), residues: 3225 sheet: 0.30 (0.16), residues: 971 loop : -1.71 (0.09), residues: 3836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 116 HIS 0.007 0.001 HIS I 267 PHE 0.025 0.001 PHE A 262 TYR 0.027 0.001 TYR R 497 ARG 0.009 0.000 ARG F 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 479 time to evaluate : 5.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7544 (mmp) cc_final: 0.6989 (mmp) REVERT: A 156 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7567 (mp10) REVERT: A 374 LYS cc_start: 0.8456 (mttt) cc_final: 0.8176 (mtmm) REVERT: B 342 LYS cc_start: 0.7875 (mttm) cc_final: 0.7482 (mtpm) REVERT: B 378 ASN cc_start: 0.7391 (m-40) cc_final: 0.7142 (m110) REVERT: C 24 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7280 (mt0) REVERT: C 102 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7874 (mm-30) REVERT: C 335 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6424 (mm-30) REVERT: C 352 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7184 (mt-10) REVERT: C 361 MET cc_start: 0.6818 (mtp) cc_final: 0.6198 (mtp) REVERT: D 83 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.6688 (mm-30) REVERT: D 100 ARG cc_start: 0.8421 (mtt90) cc_final: 0.7984 (mtt90) REVERT: D 242 GLU cc_start: 0.9342 (OUTLIER) cc_final: 0.8860 (tt0) REVERT: D 378 ASN cc_start: 0.8379 (m-40) cc_final: 0.8046 (m-40) REVERT: E 361 MET cc_start: 0.7999 (mmt) cc_final: 0.7541 (mmt) REVERT: F 206 ARG cc_start: 0.6714 (tmm-80) cc_final: 0.6429 (ttm170) REVERT: G 146 GLU cc_start: 0.7504 (tp30) cc_final: 0.7252 (tp30) REVERT: G 219 TYR cc_start: 0.7029 (m-80) cc_final: 0.6611 (m-80) REVERT: G 287 MET cc_start: 0.8646 (mmt) cc_final: 0.8152 (mmt) REVERT: H 128 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7235 (pp20) REVERT: H 207 ASN cc_start: 0.7250 (m-40) cc_final: 0.6994 (m-40) REVERT: H 270 TYR cc_start: 0.6898 (m-80) cc_final: 0.6540 (m-80) REVERT: I 337 LYS cc_start: 0.7424 (mmtt) cc_final: 0.7062 (pttp) REVERT: J 24 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8026 (mt0) REVERT: J 74 ASP cc_start: 0.7795 (m-30) cc_final: 0.7365 (m-30) REVERT: J 129 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8331 (mt0) REVERT: K 156 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8350 (tp40) REVERT: K 206 ARG cc_start: 0.8402 (ptt90) cc_final: 0.8019 (ptt90) REVERT: K 345 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7037 (mmtp) REVERT: L 46 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7865 (ttmt) REVERT: L 68 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8450 (mt) REVERT: L 342 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7887 (ttmm) REVERT: M 21 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6517 (tp30) REVERT: M 34 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6588 (ptm160) REVERT: M 95 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8779 (mm) REVERT: M 294 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8050 (ptpt) REVERT: M 313 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7208 (m-30) REVERT: M 454 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6931 (mt) REVERT: M 466 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6707 (pp30) REVERT: M 478 GLU cc_start: 0.8622 (mp0) cc_final: 0.8289 (mp0) REVERT: M 498 GLU cc_start: 0.5562 (OUTLIER) cc_final: 0.4874 (pt0) REVERT: M 601 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: N 5 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7333 (mttm) REVERT: N 55 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7435 (p0) REVERT: N 326 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7777 (mp) REVERT: N 443 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8232 (mm-40) REVERT: N 540 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7219 (mm-30) REVERT: N 592 LYS cc_start: 0.8193 (ttpt) cc_final: 0.7633 (tppp) REVERT: O 21 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7353 (tp30) REVERT: O 34 ARG cc_start: 0.7385 (ttp-170) cc_final: 0.6881 (ttm-80) REVERT: O 238 LYS cc_start: 0.7094 (tptp) cc_final: 0.6639 (ttpt) REVERT: O 505 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7526 (tpp-160) REVERT: O 555 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: P 3 LEU cc_start: 0.5524 (OUTLIER) cc_final: 0.4435 (tt) REVERT: P 281 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7815 (tt) REVERT: P 325 TRP cc_start: 0.6291 (t60) cc_final: 0.6049 (m100) REVERT: P 456 MET cc_start: 0.8123 (mtp) cc_final: 0.7843 (mtp) REVERT: P 478 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: P 550 MET cc_start: 0.6455 (OUTLIER) cc_final: 0.5768 (tmt) REVERT: Q 1 MET cc_start: 0.3834 (OUTLIER) cc_final: 0.2818 (mmt) REVERT: Q 270 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7732 (pp) REVERT: Q 520 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: R 144 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6210 (tm) REVERT: R 196 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5641 (mp0) REVERT: R 300 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6158 (mp) REVERT: R 476 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7558 (mp) REVERT: R 517 ARG cc_start: 0.7461 (ttm110) cc_final: 0.7250 (ptm-80) REVERT: R 536 ARG cc_start: 0.6559 (tpp80) cc_final: 0.6317 (tpp80) outliers start: 203 outliers final: 104 residues processed: 638 average time/residue: 1.4846 time to fit residues: 1223.9898 Evaluate side-chains 588 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 447 time to evaluate : 5.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 235 ASN Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain I residue 386 TYR Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 129 GLN Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 156 GLN Chi-restraints excluded: chain K residue 345 LYS Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 46 LYS Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 34 ARG Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 139 ILE Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 294 LYS Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain M residue 454 LEU Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 498 GLU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain M residue 601 GLU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 259 GLN Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 364 SER Chi-restraints excluded: chain N residue 443 GLN Chi-restraints excluded: chain N residue 444 ASP Chi-restraints excluded: chain N residue 601 GLU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 252 CYS Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 440 ASN Chi-restraints excluded: chain O residue 505 ARG Chi-restraints excluded: chain O residue 555 GLU Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 478 GLU Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 144 LEU Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 346 LEU Chi-restraints excluded: chain Q residue 520 GLU Chi-restraints excluded: chain Q residue 538 THR Chi-restraints excluded: chain Q residue 582 ILE Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 155 ARG Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 321 LYS Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 475 LEU Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 582 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 262 optimal weight: 8.9990 chunk 702 optimal weight: 0.9980 chunk 154 optimal weight: 0.0060 chunk 457 optimal weight: 0.9980 chunk 192 optimal weight: 9.9990 chunk 780 optimal weight: 6.9990 chunk 648 optimal weight: 3.9990 chunk 361 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 409 optimal weight: 0.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 GLN D 199 GLN D 218 HIS ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 315 ASN N 297 ASN N 554 ASN O 383 GLN O 440 ASN P 319 GLN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 66824 Z= 0.143 Angle : 0.509 12.676 90393 Z= 0.258 Chirality : 0.041 0.170 9837 Planarity : 0.004 0.047 11590 Dihedral : 8.745 168.677 9498 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.57 % Allowed : 15.35 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -1.09 (0.09), residues: 8032 helix: -0.05 (0.10), residues: 3224 sheet: 0.33 (0.16), residues: 979 loop : -1.59 (0.09), residues: 3829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 116 HIS 0.004 0.001 HIS B 313 PHE 0.025 0.001 PHE A 262 TYR 0.030 0.001 TYR R 497 ARG 0.009 0.000 ARG P 468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 482 time to evaluate : 5.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7474 (mmp) cc_final: 0.6958 (mmp) REVERT: A 156 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7550 (mp10) REVERT: A 374 LYS cc_start: 0.8400 (mttt) cc_final: 0.8124 (mtmm) REVERT: B 338 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: B 342 LYS cc_start: 0.7834 (mttm) cc_final: 0.7454 (mtpm) REVERT: B 378 ASN cc_start: 0.7386 (m-40) cc_final: 0.7096 (m110) REVERT: C 24 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7622 (mt0) REVERT: C 102 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7805 (mm-30) REVERT: C 335 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6947 (mp0) REVERT: C 352 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7135 (mt-10) REVERT: C 361 MET cc_start: 0.6826 (mtp) cc_final: 0.6165 (mtp) REVERT: D 83 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.6603 (mm-30) REVERT: D 100 ARG cc_start: 0.8404 (mtt90) cc_final: 0.7970 (mtt90) REVERT: D 242 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.8841 (tt0) REVERT: D 378 ASN cc_start: 0.8358 (m-40) cc_final: 0.8024 (m-40) REVERT: E 323 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8650 (pp) REVERT: F 206 ARG cc_start: 0.6635 (tmm-80) cc_final: 0.6326 (ttm170) REVERT: G 219 TYR cc_start: 0.7015 (m-80) cc_final: 0.6608 (m-80) REVERT: G 364 ASN cc_start: 0.6700 (p0) cc_final: 0.6338 (m-40) REVERT: H 128 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7221 (pp20) REVERT: H 207 ASN cc_start: 0.7143 (m-40) cc_final: 0.6879 (m-40) REVERT: H 270 TYR cc_start: 0.6887 (m-80) cc_final: 0.6506 (m-80) REVERT: I 337 LYS cc_start: 0.7407 (mmtt) cc_final: 0.7062 (pttp) REVERT: J 24 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7961 (mt0) REVERT: J 74 ASP cc_start: 0.7811 (m-30) cc_final: 0.7483 (m-30) REVERT: J 129 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8316 (mt0) REVERT: K 206 ARG cc_start: 0.8385 (ptt90) cc_final: 0.7962 (ptt90) REVERT: K 312 TYR cc_start: 0.8308 (t80) cc_final: 0.8049 (t80) REVERT: K 342 LYS cc_start: 0.7842 (mttm) cc_final: 0.7503 (ttmm) REVERT: M 21 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6515 (tp30) REVERT: M 294 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8036 (ptpt) REVERT: M 313 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6995 (m-30) REVERT: M 454 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.7007 (mt) REVERT: M 466 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6674 (pp30) REVERT: M 478 GLU cc_start: 0.8594 (mp0) cc_final: 0.8250 (mp0) REVERT: M 498 GLU cc_start: 0.5444 (OUTLIER) cc_final: 0.4792 (pt0) REVERT: N 5 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7330 (mttm) REVERT: N 55 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7362 (p0) REVERT: N 326 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7729 (mp) REVERT: N 540 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7178 (mm-30) REVERT: N 592 LYS cc_start: 0.8189 (ttpt) cc_final: 0.7658 (tppp) REVERT: O 34 ARG cc_start: 0.7364 (ttp-170) cc_final: 0.6882 (ttm-80) REVERT: O 238 LYS cc_start: 0.7067 (tptp) cc_final: 0.6656 (ttpt) REVERT: O 505 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7515 (tpp-160) REVERT: O 555 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: P 3 LEU cc_start: 0.5537 (OUTLIER) cc_final: 0.4438 (tt) REVERT: P 281 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7884 (tt) REVERT: P 325 TRP cc_start: 0.6300 (t60) cc_final: 0.6081 (m100) REVERT: P 456 MET cc_start: 0.8052 (mtp) cc_final: 0.7752 (mtp) REVERT: P 478 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: P 550 MET cc_start: 0.6322 (OUTLIER) cc_final: 0.5656 (tmt) REVERT: Q 1 MET cc_start: 0.3852 (OUTLIER) cc_final: 0.2838 (mmt) REVERT: Q 8 GLU cc_start: 0.5291 (mm-30) cc_final: 0.4411 (pm20) REVERT: Q 270 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7724 (pp) REVERT: Q 389 ARG cc_start: 0.6671 (mmm160) cc_final: 0.6461 (mmm160) REVERT: Q 410 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7571 (p0) REVERT: Q 520 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: R 144 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6207 (tm) REVERT: R 196 GLU cc_start: 0.5901 (OUTLIER) cc_final: 0.5647 (mp0) REVERT: R 248 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5737 (mt-10) REVERT: R 300 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6081 (mp) REVERT: R 508 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6450 (pttt) REVERT: R 536 ARG cc_start: 0.6549 (tpp80) cc_final: 0.6315 (tpp80) outliers start: 178 outliers final: 91 residues processed: 629 average time/residue: 1.4600 time to fit residues: 1182.3998 Evaluate side-chains 578 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 455 time to evaluate : 5.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 235 ASN Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 129 GLN Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 386 TYR Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 294 LYS Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain M residue 454 LEU Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 498 GLU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 259 GLN Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 364 SER Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 601 GLU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 252 CYS Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 440 ASN Chi-restraints excluded: chain O residue 505 ARG Chi-restraints excluded: chain O residue 555 GLU Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 478 GLU Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 144 LEU Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 410 ASP Chi-restraints excluded: chain Q residue 520 GLU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 248 GLU Chi-restraints excluded: chain R residue 300 LEU Chi-restraints excluded: chain R residue 321 LYS Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 508 LYS Chi-restraints excluded: chain R residue 582 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 752 optimal weight: 6.9990 chunk 88 optimal weight: 0.0070 chunk 444 optimal weight: 1.9990 chunk 570 optimal weight: 10.0000 chunk 441 optimal weight: 2.9990 chunk 657 optimal weight: 3.9990 chunk 436 optimal weight: 0.9980 chunk 777 optimal weight: 40.0000 chunk 486 optimal weight: 4.9990 chunk 474 optimal weight: 6.9990 chunk 359 optimal weight: 8.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 GLN D 199 GLN D 313 HIS D 324 ASN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 315 ASN N 297 ASN N 554 ASN O 383 GLN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 66824 Z= 0.178 Angle : 0.530 11.720 90393 Z= 0.269 Chirality : 0.041 0.181 9837 Planarity : 0.004 0.048 11590 Dihedral : 8.758 170.101 9498 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.58 % Allowed : 15.63 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -1.05 (0.09), residues: 8032 helix: -0.02 (0.10), residues: 3220 sheet: 0.39 (0.16), residues: 977 loop : -1.58 (0.09), residues: 3835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 116 HIS 0.005 0.001 HIS B 313 PHE 0.028 0.001 PHE G 380 TYR 0.028 0.001 TYR R 497 ARG 0.008 0.000 ARG P 468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 458 time to evaluate : 5.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7524 (mmp) cc_final: 0.7011 (mmp) REVERT: A 156 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7555 (mp10) REVERT: A 374 LYS cc_start: 0.8423 (mttt) cc_final: 0.8145 (mtmm) REVERT: B 338 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: B 342 LYS cc_start: 0.7859 (mttm) cc_final: 0.7467 (mtpm) REVERT: B 378 ASN cc_start: 0.7407 (m-40) cc_final: 0.7116 (m110) REVERT: C 24 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7405 (mt0) REVERT: C 102 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7800 (mm-30) REVERT: C 335 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: C 352 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7148 (mt-10) REVERT: D 83 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.6631 (mm-30) REVERT: D 100 ARG cc_start: 0.8388 (mtt90) cc_final: 0.8154 (mtp85) REVERT: D 242 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.8849 (tt0) REVERT: D 378 ASN cc_start: 0.8367 (m-40) cc_final: 0.8039 (m-40) REVERT: F 206 ARG cc_start: 0.6638 (tmm-80) cc_final: 0.6330 (ttm170) REVERT: G 219 TYR cc_start: 0.7004 (m-80) cc_final: 0.6605 (m-80) REVERT: G 287 MET cc_start: 0.8655 (mmt) cc_final: 0.8203 (mmt) REVERT: G 364 ASN cc_start: 0.6669 (p0) cc_final: 0.6227 (m-40) REVERT: H 128 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7218 (pp20) REVERT: H 207 ASN cc_start: 0.7138 (m-40) cc_final: 0.6860 (m-40) REVERT: H 270 TYR cc_start: 0.6890 (m-80) cc_final: 0.6584 (m-80) REVERT: I 337 LYS cc_start: 0.7442 (mmtt) cc_final: 0.7045 (pttp) REVERT: J 24 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: J 74 ASP cc_start: 0.7757 (m-30) cc_final: 0.7440 (m-30) REVERT: J 129 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8314 (mt0) REVERT: K 206 ARG cc_start: 0.8384 (ptt90) cc_final: 0.8073 (ptt90) REVERT: K 312 TYR cc_start: 0.8321 (t80) cc_final: 0.8096 (t80) REVERT: K 342 LYS cc_start: 0.7853 (mttm) cc_final: 0.7467 (ttmt) REVERT: M 21 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6537 (tp30) REVERT: M 95 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8740 (mm) REVERT: M 281 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7834 (tt) REVERT: M 294 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8012 (ptpt) REVERT: M 313 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.7022 (m-30) REVERT: M 466 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6693 (pp30) REVERT: M 478 GLU cc_start: 0.8606 (mp0) cc_final: 0.8262 (mp0) REVERT: M 498 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.4752 (pt0) REVERT: M 601 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: N 5 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7328 (mttm) REVERT: N 55 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7397 (p0) REVERT: N 326 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7741 (mp) REVERT: N 540 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7202 (mm-30) REVERT: N 592 LYS cc_start: 0.8163 (ttpt) cc_final: 0.7612 (tppp) REVERT: O 21 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7036 (tp30) REVERT: O 34 ARG cc_start: 0.7266 (ttp-170) cc_final: 0.6809 (ttm-80) REVERT: O 238 LYS cc_start: 0.7067 (tptp) cc_final: 0.6656 (ttpt) REVERT: O 389 ARG cc_start: 0.6652 (mtp85) cc_final: 0.6145 (mtp180) REVERT: O 455 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7966 (mt-10) REVERT: O 505 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7481 (tpp-160) REVERT: O 555 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: P 3 LEU cc_start: 0.5501 (OUTLIER) cc_final: 0.4406 (tt) REVERT: P 281 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7885 (tt) REVERT: P 325 TRP cc_start: 0.6301 (t60) cc_final: 0.6086 (m100) REVERT: P 456 MET cc_start: 0.8032 (mtp) cc_final: 0.7736 (mtp) REVERT: P 462 PHE cc_start: 0.7306 (m-10) cc_final: 0.7041 (m-10) REVERT: P 478 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: P 550 MET cc_start: 0.6430 (OUTLIER) cc_final: 0.5712 (tmt) REVERT: Q 1 MET cc_start: 0.3864 (OUTLIER) cc_final: 0.2817 (mmt) REVERT: Q 8 GLU cc_start: 0.5426 (mm-30) cc_final: 0.4447 (pm20) REVERT: Q 270 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7728 (pp) REVERT: Q 389 ARG cc_start: 0.6707 (mmm160) cc_final: 0.6476 (mmm160) REVERT: Q 410 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7579 (p0) REVERT: Q 520 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: R 144 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6261 (tm) REVERT: R 196 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5631 (mp0) REVERT: R 248 GLU cc_start: 0.6006 (OUTLIER) cc_final: 0.5716 (mt-10) REVERT: R 508 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6504 (pttt) REVERT: R 536 ARG cc_start: 0.6557 (tpp80) cc_final: 0.6304 (tpp80) REVERT: R 542 ASP cc_start: 0.7624 (m-30) cc_final: 0.7299 (t0) outliers start: 179 outliers final: 112 residues processed: 605 average time/residue: 1.5119 time to fit residues: 1178.9369 Evaluate side-chains 581 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 436 time to evaluate : 5.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 235 ASN Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 129 GLN Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 386 TYR Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 139 ILE Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 294 LYS Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 498 GLU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain M residue 601 GLU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 259 GLN Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 364 SER Chi-restraints excluded: chain N residue 444 ASP Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 601 GLU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 252 CYS Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 505 ARG Chi-restraints excluded: chain O residue 555 GLU Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 478 GLU Chi-restraints excluded: chain P residue 524 THR Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 144 LEU Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 410 ASP Chi-restraints excluded: chain Q residue 520 GLU Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 155 ARG Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain R residue 248 GLU Chi-restraints excluded: chain R residue 321 LYS Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 401 GLU Chi-restraints excluded: chain R residue 508 LYS Chi-restraints excluded: chain R residue 582 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 481 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 464 optimal weight: 2.9990 chunk 234 optimal weight: 0.2980 chunk 152 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 494 optimal weight: 0.9990 chunk 529 optimal weight: 2.9990 chunk 384 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 611 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 GLN D 199 GLN E 81 ASN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN N 297 ASN N 554 ASN O 383 GLN P 319 GLN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 66824 Z= 0.135 Angle : 0.493 12.063 90393 Z= 0.249 Chirality : 0.040 0.181 9837 Planarity : 0.003 0.047 11590 Dihedral : 8.564 172.709 9498 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.29 % Allowed : 16.19 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.91 (0.09), residues: 8032 helix: 0.10 (0.10), residues: 3225 sheet: 0.47 (0.16), residues: 990 loop : -1.51 (0.09), residues: 3817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 116 HIS 0.004 0.001 HIS B 313 PHE 0.026 0.001 PHE A 262 TYR 0.029 0.001 TYR R 497 ARG 0.009 0.000 ARG P 468 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 462 time to evaluate : 5.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7489 (mmp) cc_final: 0.7035 (mmp) REVERT: A 156 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7565 (mp10) REVERT: A 374 LYS cc_start: 0.8357 (mttt) cc_final: 0.8091 (mtmm) REVERT: B 338 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: B 342 LYS cc_start: 0.7830 (mttm) cc_final: 0.7448 (mtpm) REVERT: B 378 ASN cc_start: 0.7386 (m-40) cc_final: 0.7095 (m110) REVERT: C 102 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7769 (mm-30) REVERT: C 335 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: C 352 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7100 (mt-10) REVERT: D 83 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.6738 (mm-30) REVERT: D 100 ARG cc_start: 0.8349 (mtt90) cc_final: 0.7895 (mtt90) REVERT: D 242 GLU cc_start: 0.9307 (OUTLIER) cc_final: 0.8828 (tt0) REVERT: D 378 ASN cc_start: 0.8303 (m-40) cc_final: 0.8031 (m-40) REVERT: F 206 ARG cc_start: 0.6515 (tmm-80) cc_final: 0.6227 (ttm170) REVERT: G 219 TYR cc_start: 0.7084 (m-80) cc_final: 0.6689 (m-80) REVERT: G 287 MET cc_start: 0.8660 (mmt) cc_final: 0.8180 (mmt) REVERT: G 364 ASN cc_start: 0.6558 (p0) cc_final: 0.6106 (t0) REVERT: H 128 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7231 (pp20) REVERT: H 207 ASN cc_start: 0.7125 (m-40) cc_final: 0.6847 (m-40) REVERT: H 270 TYR cc_start: 0.6878 (m-80) cc_final: 0.6450 (m-80) REVERT: I 337 LYS cc_start: 0.7472 (mmtt) cc_final: 0.7092 (pttp) REVERT: J 24 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8001 (mt0) REVERT: J 74 ASP cc_start: 0.7736 (m-30) cc_final: 0.7424 (m-30) REVERT: K 206 ARG cc_start: 0.8375 (ptt90) cc_final: 0.8049 (ptt90) REVERT: K 312 TYR cc_start: 0.8296 (t80) cc_final: 0.8054 (t80) REVERT: K 342 LYS cc_start: 0.7884 (mttm) cc_final: 0.7487 (ttmt) REVERT: M 21 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6602 (tp30) REVERT: M 95 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8713 (mm) REVERT: M 281 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7806 (tt) REVERT: M 294 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8013 (ptpt) REVERT: M 313 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6831 (m-30) REVERT: M 466 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6685 (pp30) REVERT: M 478 GLU cc_start: 0.8609 (mp0) cc_final: 0.8272 (mp0) REVERT: N 5 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7325 (mttm) REVERT: N 55 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7484 (p0) REVERT: N 326 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7743 (mp) REVERT: N 540 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7160 (mm-30) REVERT: N 592 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7620 (tppp) REVERT: O 34 ARG cc_start: 0.7252 (ttp-170) cc_final: 0.6758 (ttm-80) REVERT: O 238 LYS cc_start: 0.7047 (tptp) cc_final: 0.6646 (ttpt) REVERT: O 344 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7024 (tppt) REVERT: O 389 ARG cc_start: 0.6657 (mtp85) cc_final: 0.6173 (mtp180) REVERT: O 505 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7553 (tpp-160) REVERT: O 555 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: P 3 LEU cc_start: 0.5485 (OUTLIER) cc_final: 0.4416 (tt) REVERT: P 456 MET cc_start: 0.7968 (mtp) cc_final: 0.7657 (mtp) REVERT: P 550 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.5674 (tmt) REVERT: Q 1 MET cc_start: 0.3724 (OUTLIER) cc_final: 0.2593 (mmt) REVERT: Q 8 GLU cc_start: 0.5529 (mm-30) cc_final: 0.4594 (pm20) REVERT: Q 270 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7729 (pp) REVERT: Q 389 ARG cc_start: 0.6702 (mmm160) cc_final: 0.6383 (mmm160) REVERT: Q 410 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7612 (p0) REVERT: Q 520 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: R 144 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6309 (tm) REVERT: R 462 PHE cc_start: 0.7850 (t80) cc_final: 0.7450 (t80) REVERT: R 508 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6554 (pttt) REVERT: R 536 ARG cc_start: 0.6530 (tpp80) cc_final: 0.6277 (tpp80) REVERT: R 542 ASP cc_start: 0.7571 (m-30) cc_final: 0.7294 (t0) outliers start: 159 outliers final: 94 residues processed: 586 average time/residue: 1.5050 time to fit residues: 1141.0833 Evaluate side-chains 558 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 437 time to evaluate : 5.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 219 TYR Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 11 ASN Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 235 ASN Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 257 ILE Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 139 ASP Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 386 TYR Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 317 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 294 LYS Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 195 SER Chi-restraints excluded: chain N residue 259 GLN Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 364 SER Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 601 GLU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 252 CYS Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 505 ARG Chi-restraints excluded: chain O residue 555 GLU Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 524 THR Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 144 LEU Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 276 THR Chi-restraints excluded: chain Q residue 410 ASP Chi-restraints excluded: chain Q residue 520 GLU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 321 LYS Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 401 GLU Chi-restraints excluded: chain R residue 508 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 707 optimal weight: 8.9990 chunk 745 optimal weight: 10.0000 chunk 679 optimal weight: 9.9990 chunk 724 optimal weight: 10.0000 chunk 744 optimal weight: 8.9990 chunk 436 optimal weight: 3.9990 chunk 315 optimal weight: 10.0000 chunk 569 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 chunk 654 optimal weight: 3.9990 chunk 685 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN C 24 GLN C 266 GLN D 199 GLN D 324 ASN E 81 ASN E 234 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 HIS I 227 HIS J 247 GLN J 315 ASN N 297 ASN N 554 ASN O 383 GLN O 440 ASN P 319 GLN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 66824 Z= 0.525 Angle : 0.787 14.696 90393 Z= 0.400 Chirality : 0.052 0.269 9837 Planarity : 0.005 0.059 11590 Dihedral : 9.478 169.630 9498 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.84 % Allowed : 16.12 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -1.54 (0.09), residues: 8032 helix: -0.49 (0.09), residues: 3242 sheet: 0.10 (0.16), residues: 986 loop : -1.80 (0.09), residues: 3804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 232 HIS 0.015 0.002 HIS H 313 PHE 0.031 0.003 PHE A 262 TYR 0.027 0.003 TYR R 497 ARG 0.008 0.001 ARG E 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 448 time to evaluate : 5.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7471 (mm-30) REVERT: A 156 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7637 (mp10) REVERT: A 374 LYS cc_start: 0.8639 (mttt) cc_final: 0.8332 (mtmm) REVERT: B 247 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: B 342 LYS cc_start: 0.7862 (mttm) cc_final: 0.7458 (mtpm) REVERT: B 378 ASN cc_start: 0.7514 (m-40) cc_final: 0.7265 (m110) REVERT: C 24 GLN cc_start: 0.7995 (mt0) cc_final: 0.7632 (mt0) REVERT: C 102 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7920 (mm-30) REVERT: C 335 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6583 (mm-30) REVERT: C 352 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7265 (mt-10) REVERT: D 83 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.6718 (mm-30) REVERT: D 100 ARG cc_start: 0.8479 (mtt90) cc_final: 0.8234 (mtp85) REVERT: D 242 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.8973 (tt0) REVERT: D 378 ASN cc_start: 0.8405 (m-40) cc_final: 0.8086 (m-40) REVERT: E 361 MET cc_start: 0.8139 (mmt) cc_final: 0.7698 (mmt) REVERT: F 206 ARG cc_start: 0.6815 (tmm-80) cc_final: 0.6535 (ttm170) REVERT: F 264 ARG cc_start: 0.6341 (mtm110) cc_final: 0.5868 (mtm180) REVERT: G 219 TYR cc_start: 0.7096 (m-80) cc_final: 0.6804 (m-80) REVERT: H 128 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7423 (pp20) REVERT: H 207 ASN cc_start: 0.7228 (m-40) cc_final: 0.6968 (m-40) REVERT: H 270 TYR cc_start: 0.6951 (m-80) cc_final: 0.6603 (m-80) REVERT: I 259 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7443 (mtmt) REVERT: I 337 LYS cc_start: 0.7512 (mmtt) cc_final: 0.7081 (pttp) REVERT: J 24 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8155 (mt0) REVERT: J 287 MET cc_start: 0.8772 (mmt) cc_final: 0.8087 (mmt) REVERT: K 206 ARG cc_start: 0.8381 (ptt90) cc_final: 0.8053 (ptt90) REVERT: K 266 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.6625 (pp30) REVERT: K 342 LYS cc_start: 0.7905 (mttm) cc_final: 0.7528 (ttmt) REVERT: K 345 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7243 (mmtp) REVERT: L 342 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7976 (ttmm) REVERT: M 8 GLU cc_start: 0.4711 (tp30) cc_final: 0.4468 (tm-30) REVERT: M 21 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6467 (tp30) REVERT: M 95 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8825 (mm) REVERT: M 281 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7713 (tt) REVERT: M 294 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8092 (ptpt) REVERT: M 313 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: M 466 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6907 (pp30) REVERT: M 478 GLU cc_start: 0.8676 (mp0) cc_final: 0.8369 (mp0) REVERT: M 498 GLU cc_start: 0.5216 (OUTLIER) cc_final: 0.4441 (pt0) REVERT: M 601 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7447 (mt-10) REVERT: N 5 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7332 (mttm) REVERT: N 55 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7671 (p0) REVERT: N 326 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7800 (mp) REVERT: N 540 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7330 (mm-30) REVERT: N 592 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7769 (tppt) REVERT: O 21 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7087 (tp30) REVERT: O 34 ARG cc_start: 0.7583 (ttp-170) cc_final: 0.6852 (ttm-80) REVERT: O 238 LYS cc_start: 0.6943 (tptp) cc_final: 0.6478 (ttpt) REVERT: O 389 ARG cc_start: 0.6839 (mtp85) cc_final: 0.6261 (mtp180) REVERT: O 505 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7535 (tpp-160) REVERT: O 555 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: P 3 LEU cc_start: 0.5523 (OUTLIER) cc_final: 0.4406 (tt) REVERT: P 438 MET cc_start: 0.8998 (ptp) cc_final: 0.8687 (mtt) REVERT: P 456 MET cc_start: 0.8117 (mtp) cc_final: 0.7854 (mtp) REVERT: P 478 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: P 550 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.5756 (tmt) REVERT: P 601 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: Q 8 GLU cc_start: 0.5465 (mm-30) cc_final: 0.4355 (pm20) REVERT: Q 270 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7841 (pp) REVERT: Q 346 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7139 (tp) REVERT: Q 520 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: R 144 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6146 (tm) REVERT: R 508 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6707 (pttt) REVERT: R 551 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6621 (tp30) outliers start: 197 outliers final: 107 residues processed: 608 average time/residue: 1.4911 time to fit residues: 1175.4511 Evaluate side-chains 566 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 426 time to evaluate : 5.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 235 ASN Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 262 PHE Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 259 LYS Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 257 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 266 GLN Chi-restraints excluded: chain K residue 345 LYS Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 134 ASN Chi-restraints excluded: chain M residue 139 ILE Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 294 LYS Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 498 GLU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain M residue 601 GLU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 259 GLN Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 444 ASP Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 601 GLU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 252 CYS Chi-restraints excluded: chain O residue 300 LEU Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 440 ASN Chi-restraints excluded: chain O residue 505 ARG Chi-restraints excluded: chain O residue 555 GLU Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 478 GLU Chi-restraints excluded: chain P residue 524 THR Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain P residue 601 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 94 ILE Chi-restraints excluded: chain Q residue 144 LEU Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 346 LEU Chi-restraints excluded: chain Q residue 410 ASP Chi-restraints excluded: chain Q residue 520 GLU Chi-restraints excluded: chain Q residue 538 THR Chi-restraints excluded: chain Q residue 582 ILE Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 155 ARG Chi-restraints excluded: chain R residue 321 LYS Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 508 LYS Chi-restraints excluded: chain R residue 551 GLU Chi-restraints excluded: chain R residue 582 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 722 optimal weight: 1.9990 chunk 475 optimal weight: 6.9990 chunk 766 optimal weight: 3.9990 chunk 467 optimal weight: 6.9990 chunk 363 optimal weight: 0.9990 chunk 532 optimal weight: 3.9990 chunk 803 optimal weight: 9.9990 chunk 739 optimal weight: 9.9990 chunk 640 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 494 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 GLN D 199 GLN E 234 GLN E 266 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 HIS I 227 HIS N 107 ASN N 297 ASN O 383 GLN O 440 ASN P 319 GLN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 66824 Z= 0.196 Angle : 0.572 12.816 90393 Z= 0.291 Chirality : 0.042 0.201 9837 Planarity : 0.004 0.048 11590 Dihedral : 9.084 169.130 9498 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.86 % Allowed : 17.18 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -1.27 (0.09), residues: 8032 helix: -0.21 (0.09), residues: 3213 sheet: 0.29 (0.16), residues: 979 loop : -1.70 (0.09), residues: 3840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 116 HIS 0.012 0.001 HIS C 267 PHE 0.028 0.001 PHE A 262 TYR 0.032 0.001 TYR R 497 ARG 0.009 0.000 ARG P 468 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 443 time to evaluate : 5.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.7472 (mmp) cc_final: 0.6951 (mmp) REVERT: A 156 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: A 374 LYS cc_start: 0.8476 (mttt) cc_final: 0.8200 (mtmm) REVERT: B 342 LYS cc_start: 0.7873 (mttm) cc_final: 0.7468 (mtpm) REVERT: B 378 ASN cc_start: 0.7387 (m-40) cc_final: 0.7139 (m110) REVERT: C 24 GLN cc_start: 0.7912 (mt0) cc_final: 0.7541 (mt0) REVERT: C 102 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7820 (mm-30) REVERT: C 335 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6470 (mm-30) REVERT: C 352 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7177 (mt-10) REVERT: D 83 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.6683 (mm-30) REVERT: D 100 ARG cc_start: 0.8387 (mtt90) cc_final: 0.8152 (mtp85) REVERT: D 242 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.8869 (tt0) REVERT: D 378 ASN cc_start: 0.8383 (m-40) cc_final: 0.8059 (m-40) REVERT: E 361 MET cc_start: 0.8119 (mmt) cc_final: 0.7667 (mmt) REVERT: F 206 ARG cc_start: 0.6757 (tmm-80) cc_final: 0.6460 (ttm170) REVERT: G 219 TYR cc_start: 0.7061 (m-80) cc_final: 0.6704 (m-80) REVERT: H 128 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7285 (pp20) REVERT: H 207 ASN cc_start: 0.7158 (m-40) cc_final: 0.6888 (m-40) REVERT: H 270 TYR cc_start: 0.6846 (m-80) cc_final: 0.6444 (m-80) REVERT: I 30 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8868 (t) REVERT: I 337 LYS cc_start: 0.7507 (mmtt) cc_final: 0.7098 (pttp) REVERT: J 24 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8056 (mt0) REVERT: K 206 ARG cc_start: 0.8356 (ptt90) cc_final: 0.8019 (ptt90) REVERT: K 312 TYR cc_start: 0.8399 (t80) cc_final: 0.8139 (t80) REVERT: K 342 LYS cc_start: 0.7923 (mttm) cc_final: 0.7505 (ttmt) REVERT: L 54 GLN cc_start: 0.7705 (tp-100) cc_final: 0.7391 (tt0) REVERT: L 342 LYS cc_start: 0.8212 (ttmt) cc_final: 0.8011 (ttmm) REVERT: M 21 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6597 (tp30) REVERT: M 95 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8779 (mm) REVERT: M 294 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8019 (ptpt) REVERT: M 313 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.7090 (m-30) REVERT: M 466 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6878 (pp30) REVERT: M 478 GLU cc_start: 0.8610 (mp0) cc_final: 0.8298 (mp0) REVERT: M 601 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: N 5 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7325 (mttm) REVERT: N 55 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7633 (p0) REVERT: N 326 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7751 (mp) REVERT: N 540 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7218 (mm-30) REVERT: N 592 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7621 (tppp) REVERT: O 21 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7051 (tp30) REVERT: O 34 ARG cc_start: 0.7318 (ttp-170) cc_final: 0.6745 (ttm-80) REVERT: O 238 LYS cc_start: 0.6935 (tptp) cc_final: 0.6509 (ttpt) REVERT: O 389 ARG cc_start: 0.6802 (mtp85) cc_final: 0.6253 (mtp180) REVERT: O 505 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7478 (tpp-160) REVERT: O 555 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: P 3 LEU cc_start: 0.5432 (OUTLIER) cc_final: 0.4320 (tt) REVERT: P 456 MET cc_start: 0.8014 (mtp) cc_final: 0.7588 (mtp) REVERT: P 550 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.5839 (tmt) REVERT: Q 8 GLU cc_start: 0.5674 (mm-30) cc_final: 0.4547 (pm20) REVERT: Q 270 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7805 (pp) REVERT: Q 346 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7239 (tp) REVERT: Q 520 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: R 144 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6267 (tm) REVERT: R 508 LYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6632 (pttt) outliers start: 129 outliers final: 84 residues processed: 549 average time/residue: 1.5103 time to fit residues: 1071.4734 Evaluate side-chains 538 residues out of total 6937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 429 time to evaluate : 5.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 235 ASN Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 251 GLU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 239 THR Chi-restraints excluded: chain I residue 363 PHE Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 21 GLU Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 94 ILE Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain M residue 294 LYS Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain M residue 332 ARG Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain M residue 444 ASP Chi-restraints excluded: chain M residue 466 GLN Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain M residue 601 GLU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 55 ASP Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 259 GLN Chi-restraints excluded: chain N residue 326 LEU Chi-restraints excluded: chain N residue 339 VAL Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 444 ASP Chi-restraints excluded: chain N residue 474 LEU Chi-restraints excluded: chain N residue 601 GLU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 134 ASN Chi-restraints excluded: chain O residue 152 VAL Chi-restraints excluded: chain O residue 252 CYS Chi-restraints excluded: chain O residue 316 ASP Chi-restraints excluded: chain O residue 344 LYS Chi-restraints excluded: chain O residue 505 ARG Chi-restraints excluded: chain O residue 555 GLU Chi-restraints excluded: chain P residue 3 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 256 ILE Chi-restraints excluded: chain P residue 337 THR Chi-restraints excluded: chain P residue 524 THR Chi-restraints excluded: chain P residue 550 MET Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 144 LEU Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 191 THR Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 346 LEU Chi-restraints excluded: chain Q residue 410 ASP Chi-restraints excluded: chain Q residue 520 GLU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 321 LYS Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 508 LYS Chi-restraints excluded: chain R residue 582 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 392 optimal weight: 2.9990 chunk 508 optimal weight: 0.7980 chunk 681 optimal weight: 9.9990 chunk 196 optimal weight: 6.9990 chunk 590 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 641 optimal weight: 0.9980 chunk 268 optimal weight: 10.0000 chunk 658 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN C 266 GLN D 199 GLN D 324 ASN E 234 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 HIS N 297 ASN O 383 GLN O 440 ASN P 319 GLN ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.156065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107807 restraints weight = 82003.143| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.24 r_work: 0.3006 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 66824 Z= 0.268 Angle : 0.619 13.914 90393 Z= 0.314 Chirality : 0.044 0.204 9837 Planarity : 0.004 0.048 11590 Dihedral : 9.146 169.847 9498 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.10 % Allowed : 17.23 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -1.33 (0.09), residues: 8032 helix: -0.26 (0.09), residues: 3222 sheet: 0.25 (0.16), residues: 979 loop : -1.73 (0.09), residues: 3831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 116 HIS 0.008 0.001 HIS B 313 PHE 0.029 0.002 PHE A 262 TYR 0.032 0.002 TYR R 497 ARG 0.008 0.000 ARG P 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20154.60 seconds wall clock time: 349 minutes 24.07 seconds (20964.07 seconds total)