Starting phenix.real_space_refine on Fri Sep 27 00:34:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/09_2024/6jd1_9801_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/09_2024/6jd1_9801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/09_2024/6jd1_9801.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/09_2024/6jd1_9801.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/09_2024/6jd1_9801_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jd1_9801/09_2024/6jd1_9801_trim.cif" } resolution = 3.38 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= -0.001 sd= 0.361 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: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 36 5.21 5 S 120 5.16 5 C 20413 2.51 5 N 5190 2.21 5 O 6175 1.98 5 H 31469 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 63427 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 5225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5225 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "B" Number of atoms: 5237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 5237 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Chain: "C" Number of atoms: 5236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 5236 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Chain: "D" Number of atoms: 5225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5225 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "E" Number of atoms: 5211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5211 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 317} Chain: "F" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5223 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "G" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5223 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "H" Number of atoms: 5211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5211 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 317} Chain: "I" Number of atoms: 5189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5189 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "J" Number of atoms: 5211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5211 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 317} Chain: "K" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5184 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "L" Number of atoms: 5188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5188 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {' MG': 4, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "K" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "L" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 24.62, per 1000 atoms: 0.39 Number of scatterers: 63427 At special positions: 0 Unit cell: (147.03, 147.03, 145.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 120 16.00 P 24 15.00 Mg 36 11.99 O 6175 8.00 N 5190 7.00 C 20413 6.00 H 31469 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.52 Conformation dependent library (CDL) restraints added in 4.2 seconds 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7210 Finding SS restraints... Secondary structure from input PDB file: 215 helices and 23 sheets defined 58.1% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.634A pdb=" N VAL A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.960A pdb=" N GLU A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 54' Processing helix chain 'A' and resid 55 through 58 Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.603A pdb=" N ALA A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 69' Processing helix chain 'A' and resid 82 through 90 removed outlier: 3.549A pdb=" N GLU A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 96 Processing helix chain 'A' and resid 135 through 141 removed outlier: 3.535A pdb=" N LEU A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A 141 " --> pdb=" O MET A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 4.214A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 removed outlier: 4.531A pdb=" N LEU A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 removed outlier: 3.798A pdb=" N ILE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 202 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 210 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 removed outlier: 3.703A pdb=" N LEU A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 removed outlier: 4.509A pdb=" N ALA A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 Processing helix chain 'A' and resid 254 through 268 removed outlier: 3.521A pdb=" N GLN A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.698A pdb=" N ARG A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.874A pdb=" N LEU A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 311 Processing helix chain 'A' and resid 313 through 324 removed outlier: 3.829A pdb=" N LYS A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 36 removed outlier: 3.515A pdb=" N ALA B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.665A pdb=" N ALA B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 55' Processing helix chain 'B' and resid 64 through 69 removed outlier: 4.067A pdb=" N ARG B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 removed outlier: 3.774A pdb=" N GLU B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.967A pdb=" N GLN B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.597A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 194 removed outlier: 4.550A pdb=" N LEU B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 216 removed outlier: 3.705A pdb=" N ILE B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 202 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.528A pdb=" N ALA B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 removed outlier: 3.776A pdb=" N LEU B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE B 241 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.586A pdb=" N MET B 250 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 268 removed outlier: 3.801A pdb=" N GLY B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 285 removed outlier: 3.940A pdb=" N ARG B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 279 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 282 " --> pdb=" O ASN B 278 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.898A pdb=" N LYS B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 299 No H-bonds generated for 'chain 'B' and resid 297 through 299' Processing helix chain 'B' and resid 300 through 311 Processing helix chain 'B' and resid 314 through 324 Processing helix chain 'C' and resid 24 through 37 removed outlier: 3.694A pdb=" N ARG C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE C 33 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 removed outlier: 3.534A pdb=" N GLU C 52 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 69 Processing helix chain 'C' and resid 82 through 90 removed outlier: 3.800A pdb=" N GLU C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 96 Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.795A pdb=" N ALA C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 197 removed outlier: 4.425A pdb=" N LEU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 218 removed outlier: 3.755A pdb=" N ILE C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR C 210 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 218 " --> pdb=" O VAL C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 229 removed outlier: 3.523A pdb=" N ALA C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU C 225 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 244 removed outlier: 3.720A pdb=" N ILE C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU C 240 " --> pdb=" O GLU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 253 Processing helix chain 'C' and resid 254 through 268 removed outlier: 4.175A pdb=" N GLY C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 285 removed outlier: 3.587A pdb=" N ARG C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 297 removed outlier: 4.198A pdb=" N LEU C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 311 Processing helix chain 'C' and resid 313 through 324 removed outlier: 3.862A pdb=" N LYS C 317 " --> pdb=" O SER C 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 35 removed outlier: 3.844A pdb=" N ARG D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE D 33 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 57 removed outlier: 3.804A pdb=" N GLU D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 removed outlier: 4.062A pdb=" N ARG D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 removed outlier: 3.627A pdb=" N GLU D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 96 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.844A pdb=" N TYR D 163 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 194 removed outlier: 4.522A pdb=" N LEU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.714A pdb=" N ILE D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR D 210 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP D 211 " --> pdb=" O LYS D 207 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY D 218 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 229 removed outlier: 3.529A pdb=" N ALA D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 244 removed outlier: 4.881A pdb=" N LEU D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.519A pdb=" N GLN D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY D 260 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR D 261 " --> pdb=" O SER D 257 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 285 removed outlier: 3.945A pdb=" N ARG D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR D 282 " --> pdb=" O ASN D 278 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.563A pdb=" N LYS D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 299 No H-bonds generated for 'chain 'D' and resid 297 through 299' Processing helix chain 'D' and resid 300 through 311 Processing helix chain 'D' and resid 313 through 324 removed outlier: 3.650A pdb=" N LYS D 317 " --> pdb=" O SER D 313 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 35 removed outlier: 3.699A pdb=" N THR E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE E 33 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG E 35 " --> pdb=" O ALA E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 57 removed outlier: 3.565A pdb=" N GLU E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 90 removed outlier: 3.678A pdb=" N GLU E 88 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 160 through 171 removed outlier: 3.586A pdb=" N LYS E 169 " --> pdb=" O LYS E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 194 removed outlier: 4.225A pdb=" N LEU E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 216 removed outlier: 3.724A pdb=" N ILE E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR E 210 " --> pdb=" O ILE E 206 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP E 211 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS E 215 " --> pdb=" O ASP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 229 removed outlier: 3.544A pdb=" N ALA E 224 " --> pdb=" O SER E 220 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU E 225 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU E 226 " --> pdb=" O GLU E 222 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR E 229 " --> pdb=" O LEU E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 245 removed outlier: 4.138A pdb=" N LEU E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE E 241 " --> pdb=" O ILE E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 253 removed outlier: 3.509A pdb=" N VAL E 251 " --> pdb=" O ASN E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 removed outlier: 3.980A pdb=" N GLY E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR E 261 " --> pdb=" O SER E 257 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR E 263 " --> pdb=" O TYR E 259 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG E 264 " --> pdb=" O GLY E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 285 removed outlier: 3.793A pdb=" N ARG E 274 " --> pdb=" O ASP E 270 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE E 275 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU E 279 " --> pdb=" O ILE E 275 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR E 282 " --> pdb=" O ASN E 278 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP E 285 " --> pdb=" O LYS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.820A pdb=" N LYS E 290 " --> pdb=" O GLY E 286 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 311 removed outlier: 3.522A pdb=" N TRP E 307 " --> pdb=" O PHE E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 324 removed outlier: 3.870A pdb=" N LYS E 317 " --> pdb=" O SER E 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 30 Processing helix chain 'F' and resid 30 through 37 removed outlier: 3.550A pdb=" N MET F 34 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 57 removed outlier: 3.557A pdb=" N GLU F 52 " --> pdb=" O ASP F 48 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU F 53 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 69 removed outlier: 3.986A pdb=" N ARG F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 90 removed outlier: 3.609A pdb=" N GLU F 88 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 96 Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 141 through 143 No H-bonds generated for 'chain 'F' and resid 141 through 143' Processing helix chain 'F' and resid 159 through 171 removed outlier: 4.098A pdb=" N TYR F 163 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 194 removed outlier: 4.349A pdb=" N LEU F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 218 removed outlier: 3.767A pdb=" N ILE F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR F 210 " --> pdb=" O ILE F 206 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP F 211 " --> pdb=" O LYS F 207 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY F 218 " --> pdb=" O VAL F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 229 removed outlier: 3.763A pdb=" N LEU F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU F 226 " --> pdb=" O GLU F 222 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 244 removed outlier: 3.510A pdb=" N ALA F 238 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU F 240 " --> pdb=" O GLU F 236 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE F 241 " --> pdb=" O ILE F 237 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU F 243 " --> pdb=" O ARG F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 253 removed outlier: 3.569A pdb=" N VAL F 251 " --> pdb=" O ASN F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 removed outlier: 3.566A pdb=" N GLN F 258 " --> pdb=" O SER F 254 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY F 260 " --> pdb=" O THR F 256 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG F 264 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 285 removed outlier: 3.778A pdb=" N ARG F 274 " --> pdb=" O ASP F 270 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE F 275 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU F 279 " --> pdb=" O ILE F 275 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP F 285 " --> pdb=" O LYS F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.806A pdb=" N LEU F 294 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 299 No H-bonds generated for 'chain 'F' and resid 297 through 299' Processing helix chain 'F' and resid 300 through 311 Processing helix chain 'F' and resid 313 through 324 removed outlier: 3.883A pdb=" N LYS F 317 " --> pdb=" O SER F 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 4.798A pdb=" N THR G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE G 33 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 55 removed outlier: 3.521A pdb=" N GLU G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU G 53 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS G 55 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 69 removed outlier: 4.259A pdb=" N ARG G 69 " --> pdb=" O ASP G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 90 removed outlier: 3.706A pdb=" N GLU G 88 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS G 89 " --> pdb=" O GLU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 96 Processing helix chain 'G' and resid 135 through 141 removed outlier: 4.213A pdb=" N LYS G 141 " --> pdb=" O MET G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 171 removed outlier: 3.803A pdb=" N ALA G 164 " --> pdb=" O ALA G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 194 removed outlier: 3.508A pdb=" N ALA G 188 " --> pdb=" O PHE G 184 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 218 removed outlier: 3.713A pdb=" N ILE G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR G 210 " --> pdb=" O ILE G 206 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP G 211 " --> pdb=" O LYS G 207 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY G 218 " --> pdb=" O VAL G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 229 removed outlier: 3.553A pdb=" N ALA G 224 " --> pdb=" O SER G 220 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU G 225 " --> pdb=" O PRO G 221 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 244 removed outlier: 4.542A pdb=" N LEU G 240 " --> pdb=" O GLU G 236 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE G 241 " --> pdb=" O ILE G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 253 Processing helix chain 'G' and resid 254 through 268 removed outlier: 3.900A pdb=" N GLY G 260 " --> pdb=" O THR G 256 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR G 261 " --> pdb=" O SER G 257 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG G 264 " --> pdb=" O GLY G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 285 removed outlier: 3.972A pdb=" N ARG G 274 " --> pdb=" O ASP G 270 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE G 275 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU G 279 " --> pdb=" O ILE G 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR G 282 " --> pdb=" O ASN G 278 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP G 285 " --> pdb=" O LYS G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 296 removed outlier: 4.149A pdb=" N LEU G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 299 No H-bonds generated for 'chain 'G' and resid 297 through 299' Processing helix chain 'G' and resid 300 through 311 Processing helix chain 'G' and resid 313 through 324 removed outlier: 3.876A pdb=" N LYS G 317 " --> pdb=" O SER G 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 36 removed outlier: 3.656A pdb=" N THR H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG H 35 " --> pdb=" O ALA H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 56 removed outlier: 4.508A pdb=" N LEU H 53 " --> pdb=" O LYS H 49 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA H 54 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS H 55 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 70 removed outlier: 3.563A pdb=" N VAL H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 90 removed outlier: 3.622A pdb=" N GLU H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 96 removed outlier: 4.023A pdb=" N GLN H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 140 Processing helix chain 'H' and resid 159 through 171 removed outlier: 4.097A pdb=" N TYR H 163 " --> pdb=" O LYS H 159 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA H 164 " --> pdb=" O ALA H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 194 removed outlier: 4.536A pdb=" N LEU H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 216 removed outlier: 3.729A pdb=" N ILE H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU H 202 " --> pdb=" O TRP H 198 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR H 210 " --> pdb=" O ILE H 206 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP H 211 " --> pdb=" O LYS H 207 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS H 215 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 229 removed outlier: 3.515A pdb=" N ALA H 224 " --> pdb=" O SER H 220 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU H 225 " --> pdb=" O PRO H 221 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU H 226 " --> pdb=" O GLU H 222 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU H 227 " --> pdb=" O ALA H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 245 removed outlier: 3.720A pdb=" N ARG H 239 " --> pdb=" O ALA H 235 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU H 240 " --> pdb=" O GLU H 236 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE H 241 " --> pdb=" O ILE H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 253 removed outlier: 3.652A pdb=" N MET H 250 " --> pdb=" O PHE H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 268 removed outlier: 3.885A pdb=" N GLY H 260 " --> pdb=" O THR H 256 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG H 264 " --> pdb=" O GLY H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 285 removed outlier: 3.992A pdb=" N ILE H 275 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN H 278 " --> pdb=" O ARG H 274 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS H 281 " --> pdb=" O GLU H 277 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 297 removed outlier: 3.952A pdb=" N LYS H 290 " --> pdb=" O GLY H 286 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU H 294 " --> pdb=" O LYS H 290 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU H 295 " --> pdb=" O GLU H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 311 Processing helix chain 'H' and resid 313 through 327 removed outlier: 3.834A pdb=" N LYS H 317 " --> pdb=" O SER H 313 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY H 327 " --> pdb=" O TYR H 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 36 removed outlier: 4.797A pdb=" N THR I 32 " --> pdb=" O ARG I 28 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE I 33 " --> pdb=" O VAL I 29 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET I 34 " --> pdb=" O GLN I 30 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG I 35 " --> pdb=" O ALA I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 4.076A pdb=" N GLU I 52 " --> pdb=" O ASP I 48 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU I 53 " --> pdb=" O LYS I 49 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS I 55 " --> pdb=" O TYR I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 90 removed outlier: 3.602A pdb=" N GLU I 88 " --> pdb=" O LYS I 84 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 96 Processing helix chain 'I' and resid 135 through 140 Processing helix chain 'I' and resid 141 through 143 No H-bonds generated for 'chain 'I' and resid 141 through 143' Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.616A pdb=" N TYR I 163 " --> pdb=" O LYS I 159 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA I 164 " --> pdb=" O ALA I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 194 removed outlier: 4.316A pdb=" N LEU I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 216 removed outlier: 3.721A pdb=" N ILE I 201 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU I 202 " --> pdb=" O TRP I 198 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR I 210 " --> pdb=" O ILE I 206 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP I 211 " --> pdb=" O LYS I 207 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS I 215 " --> pdb=" O ASP I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 229 removed outlier: 3.800A pdb=" N LEU I 225 " --> pdb=" O PRO I 221 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU I 226 " --> pdb=" O GLU I 222 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU I 227 " --> pdb=" O ALA I 223 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR I 229 " --> pdb=" O LEU I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 244 removed outlier: 3.741A pdb=" N ARG I 239 " --> pdb=" O ALA I 235 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU I 240 " --> pdb=" O GLU I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 253 Processing helix chain 'I' and resid 254 through 268 removed outlier: 3.956A pdb=" N GLY I 260 " --> pdb=" O THR I 256 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 285 removed outlier: 3.996A pdb=" N ARG I 274 " --> pdb=" O ASP I 270 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE I 275 " --> pdb=" O VAL I 271 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU I 279 " --> pdb=" O ILE I 275 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR I 282 " --> pdb=" O ASN I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 296 removed outlier: 4.037A pdb=" N LYS I 290 " --> pdb=" O GLY I 286 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU I 294 " --> pdb=" O LYS I 290 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU I 295 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 311 Processing helix chain 'I' and resid 313 through 324 removed outlier: 3.785A pdb=" N LYS I 317 " --> pdb=" O SER I 313 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU I 321 " --> pdb=" O LYS I 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 28 Processing helix chain 'J' and resid 29 through 35 Processing helix chain 'J' and resid 48 through 54 Processing helix chain 'J' and resid 55 through 58 Processing helix chain 'J' and resid 64 through 69 removed outlier: 4.140A pdb=" N ARG J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 90 removed outlier: 3.729A pdb=" N GLU J 88 " --> pdb=" O LYS J 84 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 96 Processing helix chain 'J' and resid 133 through 142 removed outlier: 4.351A pdb=" N MET J 137 " --> pdb=" O GLY J 133 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS J 141 " --> pdb=" O MET J 137 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN J 142 " --> pdb=" O ASP J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 171 removed outlier: 3.787A pdb=" N ALA J 164 " --> pdb=" O ALA J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 194 removed outlier: 3.542A pdb=" N ALA J 188 " --> pdb=" O PHE J 184 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 216 removed outlier: 3.648A pdb=" N ILE J 201 " --> pdb=" O THR J 197 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR J 210 " --> pdb=" O ILE J 206 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP J 211 " --> pdb=" O LYS J 207 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 229 removed outlier: 3.812A pdb=" N LEU J 225 " --> pdb=" O PRO J 221 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU J 226 " --> pdb=" O GLU J 222 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU J 227 " --> pdb=" O ALA J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 244 removed outlier: 3.533A pdb=" N GLU J 236 " --> pdb=" O GLY J 232 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU J 240 " --> pdb=" O GLU J 236 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE J 241 " --> pdb=" O ILE J 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 253 Processing helix chain 'J' and resid 254 through 268 removed outlier: 3.931A pdb=" N GLY J 260 " --> pdb=" O THR J 256 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR J 261 " --> pdb=" O SER J 257 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG J 264 " --> pdb=" O GLY J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 285 removed outlier: 3.943A pdb=" N ARG J 274 " --> pdb=" O ASP J 270 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE J 275 " --> pdb=" O VAL J 271 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU J 279 " --> pdb=" O ILE J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 296 removed outlier: 3.998A pdb=" N LYS J 290 " --> pdb=" O GLY J 286 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU J 295 " --> pdb=" O GLU J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 311 Processing helix chain 'J' and resid 318 through 324 Processing helix chain 'K' and resid 28 through 37 removed outlier: 4.711A pdb=" N MET K 34 " --> pdb=" O GLN K 30 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU K 36 " --> pdb=" O THR K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 53 Processing helix chain 'K' and resid 66 through 71 Processing helix chain 'K' and resid 83 through 88 removed outlier: 4.219A pdb=" N GLU K 88 " --> pdb=" O LYS K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 96 removed outlier: 3.856A pdb=" N GLN K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 141 Processing helix chain 'K' and resid 159 through 171 removed outlier: 3.621A pdb=" N ALA K 164 " --> pdb=" O ALA K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 194 removed outlier: 4.356A pdb=" N LEU K 190 " --> pdb=" O GLU K 186 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU K 192 " --> pdb=" O ALA K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 216 removed outlier: 3.567A pdb=" N ILE K 201 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR K 210 " --> pdb=" O ILE K 206 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS K 215 " --> pdb=" O ASP K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 229 removed outlier: 3.522A pdb=" N ALA K 224 " --> pdb=" O SER K 220 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU K 225 " --> pdb=" O PRO K 221 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU K 226 " --> pdb=" O GLU K 222 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU K 227 " --> pdb=" O ALA K 223 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR K 229 " --> pdb=" O LEU K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 237 Processing helix chain 'K' and resid 238 through 244 removed outlier: 3.919A pdb=" N ALA K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 253 Processing helix chain 'K' and resid 254 through 268 removed outlier: 3.907A pdb=" N GLY K 260 " --> pdb=" O THR K 256 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR K 263 " --> pdb=" O TYR K 259 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG K 264 " --> pdb=" O GLY K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 285 removed outlier: 3.932A pdb=" N ARG K 274 " --> pdb=" O ASP K 270 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE K 275 " --> pdb=" O VAL K 271 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU K 279 " --> pdb=" O ILE K 275 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP K 285 " --> pdb=" O LYS K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 296 removed outlier: 3.969A pdb=" N LYS K 290 " --> pdb=" O GLY K 286 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU K 294 " --> pdb=" O LYS K 290 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU K 295 " --> pdb=" O GLU K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 302 through 311 removed outlier: 3.805A pdb=" N GLU K 308 " --> pdb=" O TYR K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 318 through 327 removed outlier: 3.550A pdb=" N LEU K 322 " --> pdb=" O ALA K 318 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY K 327 " --> pdb=" O TYR K 323 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 27 No H-bonds generated for 'chain 'L' and resid 25 through 27' Processing helix chain 'L' and resid 28 through 37 removed outlier: 4.171A pdb=" N THR L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N MET L 34 " --> pdb=" O GLN L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 56 removed outlier: 4.106A pdb=" N GLU L 52 " --> pdb=" O ASP L 48 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU L 53 " --> pdb=" O LYS L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 71 Processing helix chain 'L' and resid 82 through 90 removed outlier: 3.704A pdb=" N LYS L 90 " --> pdb=" O VAL L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 96 Processing helix chain 'L' and resid 135 through 140 Processing helix chain 'L' and resid 159 through 171 removed outlier: 4.165A pdb=" N TYR L 163 " --> pdb=" O LYS L 159 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA L 164 " --> pdb=" O ALA L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 194 removed outlier: 4.314A pdb=" N LEU L 190 " --> pdb=" O GLU L 186 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU L 192 " --> pdb=" O ALA L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 218 removed outlier: 3.648A pdb=" N ILE L 201 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR L 210 " --> pdb=" O ILE L 206 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP L 211 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY L 218 " --> pdb=" O VAL L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 229 removed outlier: 3.734A pdb=" N ALA L 224 " --> pdb=" O SER L 220 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU L 225 " --> pdb=" O PRO L 221 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU L 226 " --> pdb=" O GLU L 222 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU L 227 " --> pdb=" O ALA L 223 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR L 229 " --> pdb=" O LEU L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 237 Processing helix chain 'L' and resid 237 through 244 removed outlier: 3.821A pdb=" N ILE L 241 " --> pdb=" O ILE L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 252 removed outlier: 3.626A pdb=" N MET L 250 " --> pdb=" O PHE L 247 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL L 251 " --> pdb=" O ASN L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 268 removed outlier: 3.799A pdb=" N GLY L 260 " --> pdb=" O THR L 256 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG L 264 " --> pdb=" O GLY L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 269 through 285 removed outlier: 3.926A pdb=" N ARG L 274 " --> pdb=" O ASP L 270 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE L 275 " --> pdb=" O VAL L 271 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU L 279 " --> pdb=" O ILE L 275 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR L 282 " --> pdb=" O ASN L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 296 removed outlier: 3.706A pdb=" N GLU L 295 " --> pdb=" O GLU L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 311 Processing helix chain 'L' and resid 313 through 327 removed outlier: 3.852A pdb=" N LYS L 317 " --> pdb=" O SER L 313 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA L 318 " --> pdb=" O GLU L 314 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY L 327 " --> pdb=" O TYR L 323 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 6.077A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 75 removed outlier: 6.403A pdb=" N ALA A 74 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE A 101 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE A 125 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A 103 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL A 127 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N PHE A 105 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 126 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY A 151 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 148 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 5 removed outlier: 6.846A pdb=" N VAL B 148 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY B 151 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE B 101 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE B 125 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 103 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL B 127 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N PHE B 105 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 104 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 21 removed outlier: 7.317A pdb=" N VAL B 41 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N TYR B 62 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL B 43 " --> pdb=" O TYR B 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 62 removed outlier: 7.690A pdb=" N VAL C 41 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N TYR C 62 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL C 43 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE C 18 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLY C 44 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL C 20 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY C 19 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 75 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE C 101 " --> pdb=" O ASP C 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.863A pdb=" N VAL C 148 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 41 through 44 removed outlier: 5.673A pdb=" N ILE D 18 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLY D 44 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL D 20 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY D 19 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE D 101 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE D 125 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU D 103 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL D 127 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N PHE D 105 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY D 151 " --> pdb=" O MET D 126 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL D 148 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.528A pdb=" N ALA E 179 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL E 148 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY E 151 " --> pdb=" O MET E 126 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET E 126 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR E 124 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE E 105 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP E 104 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 18 through 21 Processing sheet with id=AB1, first strand: chain 'F' and resid 18 through 21 removed outlier: 7.531A pdb=" N VAL F 41 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N TYR F 62 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL F 43 " --> pdb=" O TYR F 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 73 through 76 removed outlier: 3.755A pdb=" N ASP F 104 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE F 105 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY F 151 " --> pdb=" O MET F 126 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL F 148 " --> pdb=" O VAL F 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 4 through 5 removed outlier: 6.554A pdb=" N VAL G 148 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY G 151 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE G 101 " --> pdb=" O ASP G 123 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE G 125 " --> pdb=" O PHE G 101 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU G 103 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL G 127 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N PHE G 105 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA G 74 " --> pdb=" O ASP G 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 18 through 21 removed outlier: 4.564A pdb=" N GLU G 60 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 18 through 21 removed outlier: 7.806A pdb=" N VAL H 41 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N TYR H 62 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL H 43 " --> pdb=" O TYR H 62 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 101 through 105 removed outlier: 6.627A pdb=" N PHE H 101 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ILE H 125 " --> pdb=" O PHE H 101 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU H 103 " --> pdb=" O ILE H 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'H' and resid 128 through 129 removed outlier: 6.762A pdb=" N VAL H 148 " --> pdb=" O VAL H 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.722A pdb=" N ALA I 179 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL I 148 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY I 151 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE I 105 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA I 74 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP I 104 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 18 through 21 removed outlier: 4.722A pdb=" N GLU I 60 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL I 43 " --> pdb=" O GLU I 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 4 through 5 removed outlier: 7.123A pdb=" N VAL J 148 " --> pdb=" O VAL J 180 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 18 through 21 removed outlier: 6.199A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'J' and resid 73 through 75 removed outlier: 6.341A pdb=" N ALA J 74 " --> pdb=" O ASP J 104 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N PHE J 101 " --> pdb=" O ASP J 123 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ILE J 125 " --> pdb=" O PHE J 101 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU J 103 " --> pdb=" O ILE J 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.774A pdb=" N ALA K 179 " --> pdb=" O VAL K 5 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL K 148 " --> pdb=" O VAL K 180 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY K 151 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE K 105 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL K 41 " --> pdb=" O GLU K 60 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 5 removed outlier: 6.582A pdb=" N VAL L 148 " --> pdb=" O VAL L 180 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY L 151 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE L 101 " --> pdb=" O ASP L 123 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE L 125 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU L 103 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL L 127 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N PHE L 105 " --> pdb=" O VAL L 127 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU L 75 " --> pdb=" O GLY L 19 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) 1143 hydrogen bonds defined for protein. 3246 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: 23.92 Time building geometry restraints manager: 16.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 31457 1.03 - 1.23: 48 1.23 - 1.42: 13360 1.42 - 1.62: 18726 1.62 - 1.81: 292 Bond restraints: 63883 Sorted by residual: bond pdb=" C1B NAI I 404 " pdb=" C2B NAI I 404 " ideal model delta sigma weight residual 1.528 1.282 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C1B NAI B 404 " pdb=" C2B NAI B 404 " ideal model delta sigma weight residual 1.528 1.284 0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C1B NAI K 404 " pdb=" C2B NAI K 404 " ideal model delta sigma weight residual 1.528 1.285 0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C1B NAI A 404 " pdb=" C2B NAI A 404 " ideal model delta sigma weight residual 1.528 1.286 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1B NAI L 404 " pdb=" C2B NAI L 404 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.45e+02 ... (remaining 63878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 114963 2.95 - 5.90: 643 5.90 - 8.86: 98 8.86 - 11.81: 40 11.81 - 14.76: 23 Bond angle restraints: 115767 Sorted by residual: angle pdb=" O1N NAI H 404 " pdb=" PN NAI H 404 " pdb=" O2N NAI H 404 " ideal model delta sigma weight residual 123.22 108.46 14.76 3.00e+00 1.11e-01 2.42e+01 angle pdb=" O1N NAI B 404 " pdb=" PN NAI B 404 " pdb=" O2N NAI B 404 " ideal model delta sigma weight residual 123.22 108.47 14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" O1N NAI F 405 " pdb=" PN NAI F 405 " pdb=" O2N NAI F 405 " ideal model delta sigma weight residual 123.22 108.53 14.69 3.00e+00 1.11e-01 2.40e+01 angle pdb=" O1N NAI K 404 " pdb=" PN NAI K 404 " pdb=" O2N NAI K 404 " ideal model delta sigma weight residual 123.22 108.63 14.59 3.00e+00 1.11e-01 2.36e+01 angle pdb=" O1N NAI L 404 " pdb=" PN NAI L 404 " pdb=" O2N NAI L 404 " ideal model delta sigma weight residual 123.22 108.64 14.58 3.00e+00 1.11e-01 2.36e+01 ... (remaining 115762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 26176 17.02 - 34.03: 2926 34.03 - 51.05: 761 51.05 - 68.06: 256 68.06 - 85.08: 22 Dihedral angle restraints: 30141 sinusoidal: 16737 harmonic: 13404 Sorted by residual: dihedral pdb=" CA VAL H 41 " pdb=" C VAL H 41 " pdb=" N ILE H 42 " pdb=" CA ILE H 42 " ideal model delta harmonic sigma weight residual 180.00 153.06 26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA VAL D 41 " pdb=" C VAL D 41 " pdb=" N ILE D 42 " pdb=" CA ILE D 42 " ideal model delta harmonic sigma weight residual 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA VAL L 41 " pdb=" C VAL L 41 " pdb=" N ILE L 42 " pdb=" CA ILE L 42 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 30138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3444 0.046 - 0.092: 1020 0.092 - 0.138: 286 0.138 - 0.185: 32 0.185 - 0.231: 10 Chirality restraints: 4792 Sorted by residual: chirality pdb=" C2B NAI J 404 " pdb=" C1B NAI J 404 " pdb=" C3B NAI J 404 " pdb=" O2B NAI J 404 " both_signs ideal model delta sigma weight residual False -2.55 -2.32 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C2B NAI H 404 " pdb=" C1B NAI H 404 " pdb=" C3B NAI H 404 " pdb=" O2B NAI H 404 " both_signs ideal model delta sigma weight residual False -2.55 -2.33 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C2B NAI G 404 " pdb=" C1B NAI G 404 " pdb=" C3B NAI G 404 " pdb=" O2B NAI G 404 " both_signs ideal model delta sigma weight residual False -2.55 -2.33 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 4789 not shown) Planarity restraints: 9307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 128 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO L 129 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO L 129 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 129 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG J 130 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C ARG J 130 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG J 130 " 0.013 2.00e-02 2.50e+03 pdb=" N MET J 131 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 118 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO D 119 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " -0.026 5.00e-02 4.00e+02 ... (remaining 9304 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 3595 2.20 - 2.80: 132217 2.80 - 3.40: 163236 3.40 - 4.00: 215142 4.00 - 4.60: 343451 Nonbonded interactions: 857641 Sorted by model distance: nonbonded pdb=" HH TYR C 268 " pdb=" OE2 GLU D 279 " model vdw 1.596 2.450 nonbonded pdb=" HH TYR A 268 " pdb=" OE2 GLU B 279 " model vdw 1.601 2.450 nonbonded pdb=" HH TYR K 268 " pdb=" OE2 GLU L 279 " model vdw 1.607 2.450 nonbonded pdb=" HH TYR I 229 " pdb=" OE1 GLU I 319 " model vdw 1.611 2.450 nonbonded pdb=" HH TYR E 229 " pdb=" OE1 GLU E 319 " model vdw 1.616 2.450 ... (remaining 857636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 402 through 405)) selection = (chain 'B' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ \ 1 or name HZ2 or name HZ3)) or resid 4 through 195 or (resid 196 and (name N or \ name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or nam \ e CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or na \ me HE1 or name HE2)) or resid 197 through 329 or resid 402 through 405)) selection = (chain 'C' and (resid 3 through 329 or resid 402 through 405)) selection = (chain 'D' and (resid 3 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 402 through 405)) selection = (chain 'E' and (resid 3 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401 through 404)) selection = (chain 'F' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ \ 1 or name HZ2 or name HZ3)) or resid 4 through 195 or (resid 196 and (name N or \ name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or nam \ e CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or na \ me HE1 or name HE2)) or resid 197 through 329 or resid 403 through 406)) selection = (chain 'G' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ \ 1 or name HZ2 or name HZ3)) or resid 4 through 195 or (resid 196 and (name N or \ name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or nam \ e CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or na \ me HE1 or name HE2)) or resid 197 through 329 or resid 402 through 405)) selection = (chain 'H' and (resid 3 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 402 through 405)) selection = (chain 'I' and (resid 3 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 402 through 405)) selection = (chain 'J' and (resid 3 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 402 through 405)) selection = (chain 'K' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ \ 1 or name HZ2 or name HZ3)) or resid 4 through 329 or resid 402 through 405)) selection = (chain 'L' and (resid 3 through 329 or resid 402 through 405)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.880 Extract box with map and model: 2.010 Check model and map are aligned: 0.370 Set scattering table: 0.490 Process input model: 108.650 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.170 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 : 0.013 0.246 32414 Z= 0.846 Angle : 1.003 14.761 43880 Z= 0.458 Chirality : 0.047 0.231 4792 Planarity : 0.004 0.048 5498 Dihedral : 16.006 85.078 12562 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -4.95 (0.11), residues: 3929 helix: -3.93 (0.07), residues: 1896 sheet: -2.74 (0.29), residues: 269 loop : -2.43 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 198 HIS 0.004 0.001 HIS B 252 PHE 0.017 0.001 PHE C 101 TYR 0.014 0.002 TYR I 217 ARG 0.006 0.001 ARG H 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 802 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 LEU cc_start: 0.8072 (tp) cc_final: 0.7635 (tt) REVERT: H 189 LEU cc_start: 0.7987 (tp) cc_final: 0.7526 (tt) REVERT: J 189 LEU cc_start: 0.8054 (tp) cc_final: 0.7663 (tt) outliers start: 0 outliers final: 0 residues processed: 802 average time/residue: 0.9628 time to fit residues: 1169.5129 Evaluate side-chains 512 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 8.9990 chunk 295 optimal weight: 0.0070 chunk 164 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 305 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 354 optimal weight: 0.9980 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 96 GLN B 154 GLN B 296 GLN C 297 GLN C 332 ASN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN E 154 GLN E 296 GLN F 154 GLN G 278 ASN H 154 GLN I 154 GLN I 278 ASN J 154 GLN K 154 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN L 296 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32414 Z= 0.243 Angle : 0.706 9.136 43880 Z= 0.377 Chirality : 0.043 0.139 4792 Planarity : 0.005 0.086 5498 Dihedral : 11.535 89.949 5069 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.15 % Allowed : 11.11 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -4.04 (0.12), residues: 3929 helix: -2.74 (0.09), residues: 2076 sheet: -2.20 (0.31), residues: 265 loop : -2.47 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 198 HIS 0.005 0.002 HIS G 252 PHE 0.016 0.001 PHE F 228 TYR 0.017 0.001 TYR I 259 ARG 0.007 0.001 ARG I 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 561 time to evaluate : 3.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 291 GLU cc_start: 0.6706 (tt0) cc_final: 0.6457 (mt-10) outliers start: 37 outliers final: 27 residues processed: 575 average time/residue: 0.9026 time to fit residues: 808.8758 Evaluate side-chains 514 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 487 time to evaluate : 3.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 278 ASN Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 278 ASN Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 315 MET Chi-restraints excluded: chain K residue 125 ILE Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 315 MET Chi-restraints excluded: chain L residue 190 LEU Chi-restraints excluded: chain L residue 279 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 294 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 354 optimal weight: 4.9990 chunk 383 optimal weight: 10.0000 chunk 315 optimal weight: 1.9990 chunk 351 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 284 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN I 154 GLN I 297 GLN J 297 GLN K 297 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32414 Z= 0.332 Angle : 0.667 8.599 43880 Z= 0.364 Chirality : 0.043 0.159 4792 Planarity : 0.005 0.045 5498 Dihedral : 10.116 88.835 5069 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.27 % Allowed : 14.16 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.12), residues: 3929 helix: -2.22 (0.09), residues: 2121 sheet: -2.15 (0.29), residues: 294 loop : -2.31 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 307 HIS 0.005 0.001 HIS E 252 PHE 0.017 0.001 PHE F 288 TYR 0.029 0.002 TYR F 282 ARG 0.004 0.000 ARG E 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 480 time to evaluate : 4.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 282 TYR cc_start: 0.7280 (t80) cc_final: 0.6093 (t80) outliers start: 41 outliers final: 32 residues processed: 497 average time/residue: 0.8959 time to fit residues: 701.1710 Evaluate side-chains 447 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 415 time to evaluate : 3.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 278 ASN Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain G residue 250 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 278 ASN Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 273 ARG Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 315 MET Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 315 MET Chi-restraints excluded: chain L residue 154 GLN Chi-restraints excluded: chain L residue 279 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 238 optimal weight: 0.0870 chunk 356 optimal weight: 5.9990 chunk 376 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 337 optimal weight: 0.3980 chunk 101 optimal weight: 9.9990 overall best weight: 3.6964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 ASN B 278 ASN C 296 GLN C 297 GLN C 332 ASN I 154 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 32414 Z= 0.244 Angle : 0.612 8.428 43880 Z= 0.329 Chirality : 0.041 0.144 4792 Planarity : 0.004 0.049 5498 Dihedral : 9.605 89.716 5069 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.52 % Allowed : 15.99 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.12), residues: 3929 helix: -1.82 (0.10), residues: 2126 sheet: -1.76 (0.32), residues: 274 loop : -2.12 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 198 HIS 0.006 0.001 HIS I 140 PHE 0.014 0.001 PHE F 228 TYR 0.019 0.001 TYR L 282 ARG 0.004 0.000 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 457 time to evaluate : 3.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 285 ASP cc_start: 0.8010 (p0) cc_final: 0.7751 (p0) REVERT: E 287 SER cc_start: 0.7520 (m) cc_final: 0.7308 (m) outliers start: 49 outliers final: 34 residues processed: 478 average time/residue: 0.8291 time to fit residues: 628.3685 Evaluate side-chains 454 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 420 time to evaluate : 3.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 278 ASN Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 278 ASN Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 273 ARG Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 297 GLN Chi-restraints excluded: chain J residue 315 MET Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 315 MET Chi-restraints excluded: chain L residue 189 LEU Chi-restraints excluded: chain L residue 279 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 1.9990 chunk 213 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 280 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 321 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 338 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32414 Z= 0.263 Angle : 0.600 7.661 43880 Z= 0.325 Chirality : 0.042 0.180 4792 Planarity : 0.004 0.051 5498 Dihedral : 9.221 88.875 5069 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.40 % Allowed : 17.39 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.12), residues: 3929 helix: -1.57 (0.10), residues: 2136 sheet: -1.73 (0.30), residues: 314 loop : -2.18 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 198 HIS 0.004 0.001 HIS B 252 PHE 0.016 0.001 PHE F 228 TYR 0.019 0.001 TYR J 282 ARG 0.006 0.000 ARG L 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 436 time to evaluate : 3.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 38 residues processed: 453 average time/residue: 0.9495 time to fit residues: 697.7736 Evaluate side-chains 441 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 403 time to evaluate : 4.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 278 ASN Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 278 ASN Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 273 ARG Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 315 MET Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 315 MET Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 126 optimal weight: 5.9990 chunk 339 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 221 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 377 optimal weight: 0.6980 chunk 313 optimal weight: 0.9990 chunk 174 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN J 296 GLN L 312 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32414 Z= 0.173 Angle : 0.561 8.008 43880 Z= 0.296 Chirality : 0.041 0.128 4792 Planarity : 0.003 0.050 5498 Dihedral : 8.930 89.015 5069 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.30 % Allowed : 17.67 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.13), residues: 3929 helix: -1.19 (0.10), residues: 2140 sheet: -1.54 (0.31), residues: 292 loop : -1.89 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 198 HIS 0.003 0.001 HIS I 140 PHE 0.018 0.001 PHE C 288 TYR 0.012 0.001 TYR J 282 ARG 0.004 0.000 ARG L 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 458 time to evaluate : 3.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 332 ASN cc_start: 0.3676 (OUTLIER) cc_final: 0.2347 (p0) outliers start: 42 outliers final: 32 residues processed: 472 average time/residue: 0.8281 time to fit residues: 622.9630 Evaluate side-chains 451 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 418 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 278 ASN Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 315 MET Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 chunk 214 optimal weight: 10.0000 chunk 275 optimal weight: 0.0670 chunk 213 optimal weight: 0.7980 chunk 317 optimal weight: 9.9990 chunk 210 optimal weight: 8.9990 chunk 375 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 chunk 229 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 overall best weight: 2.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32414 Z= 0.194 Angle : 0.558 7.706 43880 Z= 0.296 Chirality : 0.041 0.130 4792 Planarity : 0.003 0.049 5498 Dihedral : 8.784 89.819 5069 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.30 % Allowed : 18.41 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.13), residues: 3929 helix: -1.08 (0.10), residues: 2170 sheet: -1.41 (0.31), residues: 298 loop : -1.80 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 198 HIS 0.003 0.001 HIS A 252 PHE 0.017 0.001 PHE F 228 TYR 0.010 0.001 TYR H 62 ARG 0.004 0.000 ARG L 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 424 time to evaluate : 3.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 295 GLU cc_start: 0.6499 (tp30) cc_final: 0.5844 (tp30) outliers start: 42 outliers final: 38 residues processed: 438 average time/residue: 0.8790 time to fit residues: 622.9743 Evaluate side-chains 453 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 415 time to evaluate : 3.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 278 ASN Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 315 MET Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 7.9990 chunk 150 optimal weight: 0.0980 chunk 224 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 295 optimal weight: 2.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 296 GLN L 312 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32414 Z= 0.211 Angle : 0.567 7.236 43880 Z= 0.302 Chirality : 0.041 0.143 4792 Planarity : 0.003 0.049 5498 Dihedral : 8.614 89.795 5069 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.24 % Allowed : 18.72 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.96 (0.13), residues: 3929 helix: -0.90 (0.11), residues: 2163 sheet: -1.34 (0.31), residues: 298 loop : -1.71 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 161 HIS 0.003 0.001 HIS B 252 PHE 0.015 0.001 PHE F 228 TYR 0.012 0.001 TYR F 217 ARG 0.005 0.000 ARG G 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 427 time to evaluate : 3.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 295 GLU cc_start: 0.6529 (tp30) cc_final: 0.5924 (tp30) outliers start: 40 outliers final: 39 residues processed: 440 average time/residue: 0.8251 time to fit residues: 584.3399 Evaluate side-chains 456 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 417 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 278 ASN Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 315 MET Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 294 LEU Chi-restraints excluded: chain K residue 306 LEU Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 341 optimal weight: 0.8980 chunk 360 optimal weight: 10.0000 chunk 328 optimal weight: 1.9990 chunk 350 optimal weight: 5.9990 chunk 210 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 275 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 316 optimal weight: 7.9990 chunk 331 optimal weight: 10.0000 chunk 349 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32414 Z= 0.183 Angle : 0.554 7.382 43880 Z= 0.291 Chirality : 0.041 0.128 4792 Planarity : 0.003 0.048 5498 Dihedral : 8.427 89.964 5069 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.24 % Allowed : 18.97 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.73 (0.13), residues: 3929 helix: -0.76 (0.11), residues: 2171 sheet: -1.25 (0.31), residues: 298 loop : -1.53 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.003 0.001 HIS B 252 PHE 0.013 0.001 PHE F 228 TYR 0.012 0.001 TYR C 217 ARG 0.004 0.000 ARG L 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 435 time to evaluate : 3.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 295 GLU cc_start: 0.6516 (tp30) cc_final: 0.5952 (tp30) outliers start: 40 outliers final: 35 residues processed: 450 average time/residue: 0.8439 time to fit residues: 617.0012 Evaluate side-chains 457 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 422 time to evaluate : 3.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 315 MET Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 306 LEU Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 230 optimal weight: 20.0000 chunk 370 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 257 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 357 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32414 Z= 0.242 Angle : 0.573 7.100 43880 Z= 0.305 Chirality : 0.041 0.132 4792 Planarity : 0.003 0.049 5498 Dihedral : 8.339 89.787 5069 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.18 % Allowed : 19.22 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.77 (0.13), residues: 3929 helix: -0.81 (0.11), residues: 2179 sheet: -1.17 (0.31), residues: 298 loop : -1.53 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 161 HIS 0.004 0.001 HIS C 252 PHE 0.013 0.001 PHE F 228 TYR 0.014 0.001 TYR F 217 ARG 0.003 0.000 ARG L 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7858 Ramachandran restraints generated. 3929 Oldfield, 0 Emsley, 3929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 419 time to evaluate : 3.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 295 GLU cc_start: 0.6596 (tp30) cc_final: 0.6017 (tp30) outliers start: 38 outliers final: 35 residues processed: 434 average time/residue: 0.8272 time to fit residues: 579.0264 Evaluate side-chains 446 residues out of total 3221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 411 time to evaluate : 3.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 237 ILE Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 306 LEU Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 245 optimal weight: 10.0000 chunk 329 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 285 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 309 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 318 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.059817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046254 restraints weight = 410857.115| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 6.01 r_work: 0.2822 rms_B_bonded: 5.97 restraints_weight: 2.0000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32414 Z= 0.168 Angle : 0.553 7.320 43880 Z= 0.287 Chirality : 0.041 0.127 4792 Planarity : 0.003 0.048 5498 Dihedral : 8.203 89.493 5069 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.06 % Allowed : 19.47 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.13), residues: 3929 helix: -0.56 (0.11), residues: 2155 sheet: -1.09 (0.31), residues: 321 loop : -1.41 (0.17), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.002 0.001 HIS C 252 PHE 0.012 0.001 PHE F 228 TYR 0.010 0.001 TYR C 217 ARG 0.003 0.000 ARG L 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13277.75 seconds wall clock time: 227 minutes 29.06 seconds (13649.06 seconds total)