Starting phenix.real_space_refine on Fri Sep 27 01:11:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcz_9800/09_2024/6jcz_9800_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcz_9800/09_2024/6jcz_9800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcz_9800/09_2024/6jcz_9800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcz_9800/09_2024/6jcz_9800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcz_9800/09_2024/6jcz_9800_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcz_9800/09_2024/6jcz_9800_trim.cif" } resolution = 3.35 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= -0.005 sd= 0.395 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 36 5.49 5 Mg 24 5.21 5 S 120 5.16 5 C 20444 2.51 5 N 5204 2.21 5 O 6123 1.98 5 H 31525 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 63476 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "B" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} 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: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "E" Number of atoms: 5210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5210 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 317} Chain: "F" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "G" Number of atoms: 5221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5221 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "H" Number of atoms: 5210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5210 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 317} Chain: "I" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "J" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "K" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "L" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5224 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 318} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {' MG': 3, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 2, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 2, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 2, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 2, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {' MG': 3, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 2, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 59 Unusual residues: {' MG': 2, '9TY': 1, 'NDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 68 Unusual residues: {' MG': 2, '9TY': 2, 'NDP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {' MG': 2, 'NDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "K" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" C1B NDP A 403 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP A 403 " occ=0.59 residue: pdb=" C1B NDP B 402 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP B 402 " occ=0.59 residue: pdb=" C1B NDP C 402 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP C 402 " occ=0.59 residue: pdb=" C1B NDP D 403 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP D 403 " occ=0.59 residue: pdb=" C1B NDP E 402 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP E 402 " occ=0.59 residue: pdb=" C1B NDP F 403 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP F 403 " occ=0.59 residue: pdb=" C1B NDP G 402 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP G 402 " occ=0.59 residue: pdb=" C1B NDP H 404 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP H 404 " occ=0.59 residue: pdb=" C1B NDP I 402 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP I 402 " occ=0.59 residue: pdb=" C1B NDP J 403 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP J 403 " occ=0.59 residue: pdb=" C1B NDP K 402 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP K 402 " occ=0.59 residue: pdb=" C1B NDP L 403 " occ=0.59 ... (46 atoms not shown) pdb=" PN NDP L 403 " occ=0.59 Time building chain proxies: 23.53, per 1000 atoms: 0.37 Number of scatterers: 63476 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 36 15.00 Mg 24 11.99 O 6123 8.00 N 5204 7.00 C 20444 6.00 H 31525 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.84 Conformation dependent library (CDL) restraints added in 3.9 seconds 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7222 Finding SS restraints... Secondary structure from input PDB file: 213 helices and 20 sheets defined 56.3% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.93 Creating SS restraints... Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.584A pdb=" N GLN A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.725A pdb=" N ARG A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 removed outlier: 4.034A pdb=" N VAL A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 removed outlier: 3.962A pdb=" N GLN A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 removed outlier: 4.235A pdb=" N ASN A 110 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 removed outlier: 3.793A pdb=" N ASP A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 168 removed outlier: 3.574A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 removed outlier: 3.704A pdb=" N LEU A 189 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.706A pdb=" N ALA A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 removed outlier: 3.641A pdb=" N LEU A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 234 through 244 removed outlier: 4.261A pdb=" N LEU A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.972A pdb=" N GLY A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 285 removed outlier: 4.812A pdb=" N ARG A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 299 removed outlier: 3.736A pdb=" N LEU A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 311 removed outlier: 3.630A pdb=" N TYR A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 325 removed outlier: 3.762A pdb=" N LYS A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 37 removed outlier: 3.632A pdb=" N GLN B 30 " --> pdb=" O GLN B 26 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 57 removed outlier: 3.519A pdb=" N GLU B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 71 removed outlier: 3.723A pdb=" N ARG B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 removed outlier: 4.006A pdb=" N VAL B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.965A pdb=" N GLN B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 removed outlier: 4.263A pdb=" N ASN B 110 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 removed outlier: 3.687A pdb=" N ASP B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 168 removed outlier: 3.573A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 194 removed outlier: 3.698A pdb=" N LEU B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.698A pdb=" N ALA B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.645A pdb=" N LEU B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 234 through 244 removed outlier: 4.199A pdb=" N LEU B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.978A pdb=" N GLY B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 285 removed outlier: 4.812A pdb=" N ARG B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 299 removed outlier: 3.744A pdb=" N LEU B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 311 removed outlier: 3.602A pdb=" N TYR B 304 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP B 307 " --> pdb=" O PHE B 303 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 removed outlier: 3.861A pdb=" N LYS B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 321 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 14 removed outlier: 3.589A pdb=" N LYS C 14 " --> pdb=" O ASP C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.730A pdb=" N THR C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 64 through 69 removed outlier: 3.675A pdb=" N ARG C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 removed outlier: 3.933A pdb=" N VAL C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 removed outlier: 3.999A pdb=" N GLN C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 111 removed outlier: 4.291A pdb=" N ASN C 110 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 141 removed outlier: 4.333A pdb=" N ASP C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 168 removed outlier: 3.905A pdb=" N ALA C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.699A pdb=" N LEU C 189 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C 197 " --> pdb=" O MET C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.684A pdb=" N ALA C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 229 removed outlier: 3.661A pdb=" N LEU C 225 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'C' and resid 254 through 266 removed outlier: 4.023A pdb=" N GLY C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 285 removed outlier: 3.883A pdb=" N ASN C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 299 removed outlier: 3.734A pdb=" N LEU C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN C 296 " --> pdb=" O TRP C 292 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 311 removed outlier: 3.522A pdb=" N TYR C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C 305 " --> pdb=" O PRO C 301 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TRP C 307 " --> pdb=" O PHE C 303 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU C 308 " --> pdb=" O TYR C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 327 removed outlier: 3.758A pdb=" N LYS C 317 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.618A pdb=" N GLN D 30 " --> pdb=" O GLN D 26 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET D 34 " --> pdb=" O GLN D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 63 through 71 removed outlier: 3.705A pdb=" N ARG D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 removed outlier: 3.998A pdb=" N VAL D 86 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.953A pdb=" N GLN D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 111 removed outlier: 4.209A pdb=" N ASN D 110 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.692A pdb=" N ASP D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 168 removed outlier: 3.509A pdb=" N TYR D 163 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 194 removed outlier: 3.726A pdb=" N LEU D 189 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 211 removed outlier: 3.733A pdb=" N ALA D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 229 removed outlier: 3.681A pdb=" N LEU D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 233 No H-bonds generated for 'chain 'D' and resid 231 through 233' Processing helix chain 'D' and resid 234 through 244 removed outlier: 4.680A pdb=" N LEU D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 252 removed outlier: 4.053A pdb=" N VAL D 251 " --> pdb=" O ASN D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.987A pdb=" N GLY D 260 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 261 " --> pdb=" O SER D 257 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 285 removed outlier: 4.800A pdb=" N ARG D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 299 removed outlier: 3.737A pdb=" N LEU D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN D 296 " --> pdb=" O TRP D 292 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D 299 " --> pdb=" O GLU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 311 removed outlier: 3.748A pdb=" N ARG D 305 " --> pdb=" O PRO D 301 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP D 307 " --> pdb=" O PHE D 303 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 308 " --> pdb=" O TYR D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 325 removed outlier: 3.916A pdb=" N LYS D 317 " --> pdb=" O SER D 313 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.624A pdb=" N GLN E 30 " --> pdb=" O GLN E 26 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 63 through 71 removed outlier: 3.708A pdb=" N ARG E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 90 removed outlier: 3.798A pdb=" N VAL E 86 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 96 removed outlier: 3.516A pdb=" N LEU E 95 " --> pdb=" O ILE E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 111 removed outlier: 4.407A pdb=" N ASN E 110 " --> pdb=" O SER E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 141 removed outlier: 4.264A pdb=" N ASP E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 168 removed outlier: 3.794A pdb=" N ALA E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 194 removed outlier: 3.828A pdb=" N LEU E 189 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 211 removed outlier: 3.694A pdb=" N ALA E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 229 removed outlier: 3.663A pdb=" N LEU E 225 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU E 226 " --> pdb=" O GLU E 222 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 242 removed outlier: 4.206A pdb=" N ALA E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG E 239 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.924A pdb=" N GLY E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR E 261 " --> pdb=" O SER E 257 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG E 264 " --> pdb=" O GLY E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 285 removed outlier: 4.530A pdb=" N ARG E 274 " --> pdb=" O ASP E 270 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN E 278 " --> pdb=" O ARG E 274 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP E 285 " --> pdb=" O LYS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 299 removed outlier: 3.717A pdb=" N LEU E 294 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN E 296 " --> pdb=" O TRP E 292 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN E 297 " --> pdb=" O SER E 293 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY E 299 " --> pdb=" O GLU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 311 removed outlier: 3.502A pdb=" N TYR E 304 " --> pdb=" O TYR E 300 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG E 305 " --> pdb=" O PRO E 301 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TRP E 307 " --> pdb=" O PHE E 303 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU E 308 " --> pdb=" O TYR E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 325 removed outlier: 3.806A pdb=" N LYS E 317 " --> pdb=" O SER E 313 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU E 321 " --> pdb=" O LYS E 317 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS E 324 " --> pdb=" O LYS E 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 36 removed outlier: 3.511A pdb=" N GLN F 30 " --> pdb=" O GLN F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.684A pdb=" N ARG F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 90 removed outlier: 4.023A pdb=" N VAL F 86 " --> pdb=" O VAL F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 96 removed outlier: 3.958A pdb=" N GLN F 96 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 111 removed outlier: 4.246A pdb=" N ASN F 110 " --> pdb=" O SER F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 141 removed outlier: 3.602A pdb=" N ASP F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 168 removed outlier: 3.514A pdb=" N TYR F 163 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 194 removed outlier: 3.715A pdb=" N LEU F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 211 removed outlier: 3.654A pdb=" N ALA F 208 " --> pdb=" O GLY F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 229 removed outlier: 3.668A pdb=" N LEU F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU F 226 " --> pdb=" O GLU F 222 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 244 removed outlier: 4.202A pdb=" N LEU F 240 " --> pdb=" O GLU F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 4.022A pdb=" N GLY F 260 " --> pdb=" O THR F 256 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR F 261 " --> pdb=" O SER F 257 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG F 264 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 285 removed outlier: 4.815A pdb=" N ARG F 274 " --> pdb=" O ASP F 270 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP F 285 " --> pdb=" O LYS F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 299 removed outlier: 3.750A pdb=" N LEU F 294 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN F 296 " --> pdb=" O TRP F 292 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN F 297 " --> pdb=" O SER F 293 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY F 299 " --> pdb=" O GLU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 311 removed outlier: 3.605A pdb=" N TYR F 304 " --> pdb=" O TYR F 300 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG F 305 " --> pdb=" O PRO F 301 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP F 307 " --> pdb=" O PHE F 303 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU F 308 " --> pdb=" O TYR F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 325 removed outlier: 3.881A pdb=" N LYS F 317 " --> pdb=" O SER F 313 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS F 324 " --> pdb=" O LYS F 320 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.830A pdb=" N THR G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 56 Processing helix chain 'G' and resid 63 through 71 removed outlier: 3.652A pdb=" N ARG G 69 " --> pdb=" O ASP G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 90 removed outlier: 3.883A pdb=" N VAL G 86 " --> pdb=" O VAL G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 96 removed outlier: 3.544A pdb=" N LEU G 95 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN G 96 " --> pdb=" O ALA G 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 91 through 96' Processing helix chain 'G' and resid 107 through 111 removed outlier: 4.264A pdb=" N ASN G 110 " --> pdb=" O SER G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 141 removed outlier: 4.270A pdb=" N LYS G 141 " --> pdb=" O MET G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 168 removed outlier: 3.506A pdb=" N TYR G 163 " --> pdb=" O LYS G 159 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA G 166 " --> pdb=" O ASP G 162 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA G 168 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 194 removed outlier: 3.728A pdb=" N LEU G 189 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 211 removed outlier: 3.631A pdb=" N ALA G 208 " --> pdb=" O GLY G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 229 removed outlier: 3.658A pdb=" N LEU G 225 " --> pdb=" O PRO G 221 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE G 228 " --> pdb=" O ALA G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 244 removed outlier: 3.619A pdb=" N ALA G 238 " --> pdb=" O LEU G 234 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG G 239 " --> pdb=" O ALA G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 266 removed outlier: 4.014A pdb=" N GLY G 260 " --> pdb=" O THR G 256 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR G 261 " --> pdb=" O SER G 257 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG G 264 " --> pdb=" O GLY G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 285 removed outlier: 4.391A pdb=" N ARG G 274 " --> pdb=" O ASP G 270 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE G 275 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN G 278 " --> pdb=" O ARG G 274 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE G 283 " --> pdb=" O GLU G 279 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP G 285 " --> pdb=" O LYS G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 299 removed outlier: 3.750A pdb=" N LEU G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN G 296 " --> pdb=" O TRP G 292 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN G 297 " --> pdb=" O SER G 293 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY G 299 " --> pdb=" O GLU G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 311 removed outlier: 3.509A pdb=" N TYR G 304 " --> pdb=" O TYR G 300 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG G 305 " --> pdb=" O PRO G 301 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TRP G 307 " --> pdb=" O PHE G 303 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU G 308 " --> pdb=" O TYR G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 325 removed outlier: 3.731A pdb=" N LYS G 317 " --> pdb=" O SER G 313 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU G 321 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU G 322 " --> pdb=" O ALA G 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 14 removed outlier: 3.623A pdb=" N LYS H 14 " --> pdb=" O ASP H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 36 removed outlier: 3.785A pdb=" N MET H 34 " --> pdb=" O GLN H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 56 removed outlier: 3.932A pdb=" N LEU H 53 " --> pdb=" O LYS H 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA H 54 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 71 Processing helix chain 'H' and resid 82 through 90 removed outlier: 3.836A pdb=" N VAL H 86 " --> pdb=" O VAL H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 96 removed outlier: 3.661A pdb=" N LEU H 95 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 91 through 96' Processing helix chain 'H' and resid 107 through 111 removed outlier: 4.461A pdb=" N ASN H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL H 111 " --> pdb=" O GLY H 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 107 through 111' Processing helix chain 'H' and resid 134 through 142 removed outlier: 4.039A pdb=" N ASP H 138 " --> pdb=" O GLU H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 169 removed outlier: 3.613A pdb=" N TYR H 163 " --> pdb=" O LYS H 159 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA H 166 " --> pdb=" O ASP H 162 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS H 169 " --> pdb=" O LYS H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 194 removed outlier: 3.732A pdb=" N LEU H 189 " --> pdb=" O GLU H 185 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU H 192 " --> pdb=" O ALA H 188 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER H 194 " --> pdb=" O LEU H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 211 removed outlier: 3.824A pdb=" N ALA H 208 " --> pdb=" O GLY H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 229 removed outlier: 3.610A pdb=" N LEU H 225 " --> pdb=" O PRO H 221 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU H 226 " --> pdb=" O GLU H 222 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE H 228 " --> pdb=" O ALA H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 244 Processing helix chain 'H' and resid 254 through 266 removed outlier: 4.001A pdb=" N GLY H 260 " --> pdb=" O THR H 256 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR H 261 " --> pdb=" O SER H 257 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG H 264 " --> pdb=" O GLY H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 285 removed outlier: 4.478A pdb=" N ARG H 274 " --> pdb=" O ASP H 270 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN H 278 " --> pdb=" O ARG H 274 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE H 283 " --> pdb=" O GLU H 279 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 299 removed outlier: 3.730A pdb=" N LEU H 294 " --> pdb=" O LYS H 290 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU H 295 " --> pdb=" O GLU H 291 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN H 296 " --> pdb=" O TRP H 292 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN H 297 " --> pdb=" O SER H 293 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY H 299 " --> pdb=" O GLU H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 311 removed outlier: 3.747A pdb=" N ARG H 305 " --> pdb=" O PRO H 301 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP H 307 " --> pdb=" O PHE H 303 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU H 308 " --> pdb=" O TYR H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 323 removed outlier: 3.824A pdb=" N LYS H 317 " --> pdb=" O SER H 313 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA H 318 " --> pdb=" O GLU H 314 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU H 322 " --> pdb=" O ALA H 318 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 37 removed outlier: 3.636A pdb=" N GLN I 30 " --> pdb=" O GLN I 26 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET I 34 " --> pdb=" O GLN I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 63 through 71 removed outlier: 3.646A pdb=" N ARG I 69 " --> pdb=" O ASP I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 90 removed outlier: 4.007A pdb=" N VAL I 86 " --> pdb=" O VAL I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 3.959A pdb=" N GLN I 96 " --> pdb=" O ALA I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 111 removed outlier: 4.291A pdb=" N ASN I 110 " --> pdb=" O SER I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 141 removed outlier: 3.731A pdb=" N ASP I 138 " --> pdb=" O GLU I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 168 removed outlier: 3.520A pdb=" N TYR I 163 " --> pdb=" O LYS I 159 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA I 164 " --> pdb=" O ALA I 160 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA I 166 " --> pdb=" O ASP I 162 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA I 168 " --> pdb=" O ALA I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 195 removed outlier: 3.704A pdb=" N LEU I 189 " --> pdb=" O GLU I 185 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER I 194 " --> pdb=" O LEU I 190 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 211 removed outlier: 3.699A pdb=" N ALA I 208 " --> pdb=" O GLY I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 229 removed outlier: 3.659A pdb=" N LEU I 225 " --> pdb=" O PRO I 221 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU I 226 " --> pdb=" O GLU I 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE I 228 " --> pdb=" O ALA I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 244 removed outlier: 3.927A pdb=" N LEU I 240 " --> pdb=" O GLU I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 266 removed outlier: 3.954A pdb=" N GLY I 260 " --> pdb=" O THR I 256 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR I 261 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 285 removed outlier: 4.815A pdb=" N ARG I 274 " --> pdb=" O ASP I 270 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE I 283 " --> pdb=" O GLU I 279 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP I 285 " --> pdb=" O LYS I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 299 removed outlier: 3.788A pdb=" N LEU I 294 " --> pdb=" O LYS I 290 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU I 295 " --> pdb=" O GLU I 291 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN I 296 " --> pdb=" O TRP I 292 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN I 297 " --> pdb=" O SER I 293 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY I 299 " --> pdb=" O GLU I 295 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 311 removed outlier: 3.605A pdb=" N TYR I 304 " --> pdb=" O TYR I 300 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG I 305 " --> pdb=" O PRO I 301 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP I 307 " --> pdb=" O PHE I 303 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU I 308 " --> pdb=" O TYR I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 325 removed outlier: 3.887A pdb=" N LYS I 317 " --> pdb=" O SER I 313 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA I 318 " --> pdb=" O GLU I 314 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU I 321 " --> pdb=" O LYS I 317 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU I 322 " --> pdb=" O ALA I 318 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS I 324 " --> pdb=" O LYS I 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 37 removed outlier: 3.605A pdb=" N GLN J 30 " --> pdb=" O GLN J 26 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET J 34 " --> pdb=" O GLN J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 57 Processing helix chain 'J' and resid 63 through 71 removed outlier: 3.933A pdb=" N ARG J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 90 removed outlier: 4.021A pdb=" N VAL J 86 " --> pdb=" O VAL J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 96 removed outlier: 3.961A pdb=" N GLN J 96 " --> pdb=" O ALA J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 111 removed outlier: 4.209A pdb=" N ASN J 110 " --> pdb=" O SER J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 141 removed outlier: 3.705A pdb=" N ASP J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS J 141 " --> pdb=" O MET J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 168 removed outlier: 3.592A pdb=" N TYR J 163 " --> pdb=" O LYS J 159 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA J 166 " --> pdb=" O ASP J 162 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA J 168 " --> pdb=" O ALA J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 194 removed outlier: 3.713A pdb=" N LEU J 189 " --> pdb=" O GLU J 185 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 211 removed outlier: 3.703A pdb=" N ALA J 208 " --> pdb=" O GLY J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 229 removed outlier: 3.646A pdb=" N LEU J 225 " --> pdb=" O PRO J 221 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU J 226 " --> pdb=" O GLU J 222 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE J 228 " --> pdb=" O ALA J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 231 through 233 No H-bonds generated for 'chain 'J' and resid 231 through 233' Processing helix chain 'J' and resid 234 through 244 removed outlier: 4.209A pdb=" N LEU J 240 " --> pdb=" O GLU J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 266 removed outlier: 4.038A pdb=" N GLY J 260 " --> pdb=" O THR J 256 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR J 261 " --> pdb=" O SER J 257 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG J 264 " --> pdb=" O GLY J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 285 removed outlier: 4.793A pdb=" N ARG J 274 " --> pdb=" O ASP J 270 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP J 285 " --> pdb=" O LYS J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 299 removed outlier: 3.817A pdb=" N LEU J 294 " --> pdb=" O LYS J 290 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU J 295 " --> pdb=" O GLU J 291 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN J 296 " --> pdb=" O TRP J 292 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN J 297 " --> pdb=" O SER J 293 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY J 299 " --> pdb=" O GLU J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 311 removed outlier: 3.578A pdb=" N TYR J 304 " --> pdb=" O TYR J 300 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG J 305 " --> pdb=" O PRO J 301 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TRP J 307 " --> pdb=" O PHE J 303 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU J 308 " --> pdb=" O TYR J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 325 removed outlier: 3.850A pdb=" N LYS J 317 " --> pdb=" O SER J 313 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA J 318 " --> pdb=" O GLU J 314 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU J 321 " --> pdb=" O LYS J 317 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU J 322 " --> pdb=" O ALA J 318 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS J 324 " --> pdb=" O LYS J 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 37 removed outlier: 3.652A pdb=" N GLN K 30 " --> pdb=" O GLN K 26 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET K 34 " --> pdb=" O GLN K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 57 Processing helix chain 'K' and resid 63 through 71 removed outlier: 3.641A pdb=" N ARG K 69 " --> pdb=" O ASP K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 90 removed outlier: 4.017A pdb=" N VAL K 86 " --> pdb=" O VAL K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 96 removed outlier: 3.964A pdb=" N GLN K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 111 removed outlier: 4.281A pdb=" N ASN K 110 " --> pdb=" O SER K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 removed outlier: 3.730A pdb=" N ASP K 138 " --> pdb=" O GLU K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 168 removed outlier: 3.523A pdb=" N ALA K 164 " --> pdb=" O ALA K 160 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA K 166 " --> pdb=" O ASP K 162 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA K 168 " --> pdb=" O ALA K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 194 removed outlier: 3.689A pdb=" N LEU K 189 " --> pdb=" O GLU K 185 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER K 194 " --> pdb=" O LEU K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 211 removed outlier: 3.696A pdb=" N ALA K 208 " --> pdb=" O GLY K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 229 removed outlier: 3.652A pdb=" N LEU K 225 " --> pdb=" O PRO K 221 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU K 226 " --> pdb=" O GLU K 222 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE K 228 " --> pdb=" O ALA K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 244 removed outlier: 4.187A pdb=" N LEU K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 253 Processing helix chain 'K' and resid 254 through 266 removed outlier: 4.005A pdb=" N GLY K 260 " --> pdb=" O THR K 256 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR K 261 " --> pdb=" O SER K 257 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG K 264 " --> pdb=" O GLY K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 268 through 285 removed outlier: 4.823A pdb=" N ARG K 274 " --> pdb=" O ASP K 270 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP K 285 " --> pdb=" O LYS K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 299 removed outlier: 3.732A pdb=" N LEU K 294 " --> pdb=" O LYS K 290 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU K 295 " --> pdb=" O GLU K 291 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN K 296 " --> pdb=" O TRP K 292 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN K 297 " --> pdb=" O SER K 293 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY K 299 " --> pdb=" O GLU K 295 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 311 removed outlier: 3.606A pdb=" N TYR K 304 " --> pdb=" O TYR K 300 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG K 305 " --> pdb=" O PRO K 301 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP K 307 " --> pdb=" O PHE K 303 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU K 308 " --> pdb=" O TYR K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 325 removed outlier: 3.764A pdb=" N LYS K 317 " --> pdb=" O SER K 313 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA K 318 " --> pdb=" O GLU K 314 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU K 321 " --> pdb=" O LYS K 317 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU K 322 " --> pdb=" O ALA K 318 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS K 324 " --> pdb=" O LYS K 320 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 37 removed outlier: 3.613A pdb=" N GLN L 30 " --> pdb=" O GLN L 26 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET L 34 " --> pdb=" O GLN L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 57 Processing helix chain 'L' and resid 63 through 71 removed outlier: 3.937A pdb=" N ARG L 69 " --> pdb=" O ASP L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 90 removed outlier: 4.027A pdb=" N VAL L 86 " --> pdb=" O VAL L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 96 removed outlier: 3.962A pdb=" N GLN L 96 " --> pdb=" O ALA L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 111 removed outlier: 4.219A pdb=" N ASN L 110 " --> pdb=" O SER L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 141 removed outlier: 3.723A pdb=" N ASP L 138 " --> pdb=" O GLU L 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS L 141 " --> pdb=" O MET L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 170 removed outlier: 3.562A pdb=" N TYR L 163 " --> pdb=" O LYS L 159 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA L 166 " --> pdb=" O ASP L 162 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA L 168 " --> pdb=" O ALA L 164 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS L 169 " --> pdb=" O LYS L 165 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY L 170 " --> pdb=" O ALA L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 194 removed outlier: 3.710A pdb=" N LEU L 189 " --> pdb=" O GLU L 185 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER L 194 " --> pdb=" O LEU L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 211 removed outlier: 3.675A pdb=" N ALA L 208 " --> pdb=" O GLY L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 229 removed outlier: 3.652A pdb=" N LEU L 225 " --> pdb=" O PRO L 221 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU L 226 " --> pdb=" O GLU L 222 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE L 228 " --> pdb=" O ALA L 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 231 through 233 No H-bonds generated for 'chain 'L' and resid 231 through 233' Processing helix chain 'L' and resid 234 through 244 removed outlier: 4.144A pdb=" N LEU L 240 " --> pdb=" O GLU L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 266 removed outlier: 4.066A pdb=" N GLY L 260 " --> pdb=" O THR L 256 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR L 261 " --> pdb=" O SER L 257 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG L 264 " --> pdb=" O GLY L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 285 removed outlier: 4.804A pdb=" N ARG L 274 " --> pdb=" O ASP L 270 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP L 285 " --> pdb=" O LYS L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 299 removed outlier: 3.741A pdb=" N LEU L 294 " --> pdb=" O LYS L 290 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU L 295 " --> pdb=" O GLU L 291 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN L 296 " --> pdb=" O TRP L 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN L 297 " --> pdb=" O SER L 293 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY L 299 " --> pdb=" O GLU L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 311 removed outlier: 3.504A pdb=" N TYR L 304 " --> pdb=" O TYR L 300 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG L 305 " --> pdb=" O PRO L 301 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TRP L 307 " --> pdb=" O PHE L 303 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU L 308 " --> pdb=" O TYR L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 325 removed outlier: 3.850A pdb=" N LYS L 317 " --> pdb=" O SER L 313 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA L 318 " --> pdb=" O GLU L 314 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU L 321 " --> pdb=" O LYS L 317 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU L 322 " --> pdb=" O ALA L 318 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS L 324 " --> pdb=" O LYS L 320 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.437A pdb=" N VAL A 152 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N MET A 126 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN A 154 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 103 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL A 127 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE A 105 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.733A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.719A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.470A pdb=" N LEU B 103 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL B 127 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE B 105 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN B 154 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N MET B 126 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B 152 " --> pdb=" O MET B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 44 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 105 removed outlier: 3.676A pdb=" N ILE C 125 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN C 154 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET C 126 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL C 152 " --> pdb=" O MET C 126 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C 148 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 5 removed outlier: 6.440A pdb=" N VAL D 152 " --> pdb=" O MET D 126 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N MET D 126 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN D 154 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE D 125 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA D 74 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 18 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLY D 44 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL D 20 " --> pdb=" O GLY D 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 61 through 62 removed outlier: 9.123A pdb=" N TYR E 62 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL E 43 " --> pdb=" O TYR E 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 102 through 105 removed outlier: 6.472A pdb=" N LEU E 103 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL E 127 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE E 105 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN E 154 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N MET E 126 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL E 152 " --> pdb=" O MET E 126 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ALA E 128 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU E 150 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL E 148 " --> pdb=" O VAL E 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 61 through 62 removed outlier: 8.766A pdb=" N TYR F 62 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL F 43 " --> pdb=" O TYR F 62 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE F 18 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLY F 44 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL F 20 " --> pdb=" O GLY F 44 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 102 through 105 removed outlier: 6.464A pdb=" N LEU F 103 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL F 127 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE F 105 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN F 154 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N MET F 126 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL F 152 " --> pdb=" O MET F 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 61 through 62 removed outlier: 9.057A pdb=" N TYR G 62 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL G 43 " --> pdb=" O TYR G 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 102 through 105 removed outlier: 6.673A pdb=" N LEU G 103 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL G 127 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE G 105 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY G 151 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 180 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 61 through 62 removed outlier: 9.205A pdb=" N TYR H 62 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL H 43 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA H 74 " --> pdb=" O ASP H 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET H 126 " --> pdb=" O GLY H 151 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY H 151 " --> pdb=" O MET H 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 61 through 62 removed outlier: 8.808A pdb=" N TYR I 62 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL I 43 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA I 74 " --> pdb=" O ASP I 104 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU I 103 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL I 127 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE I 105 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN I 154 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N MET I 126 " --> pdb=" O VAL I 152 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL I 152 " --> pdb=" O MET I 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 4 through 5 removed outlier: 6.439A pdb=" N VAL J 152 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N MET J 126 " --> pdb=" O VAL J 152 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN J 154 " --> pdb=" O THR J 124 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU J 103 " --> pdb=" O ILE J 125 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL J 127 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE J 105 " --> pdb=" O VAL J 127 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 61 through 62 removed outlier: 8.812A pdb=" N TYR J 62 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL J 43 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 41 through 44 removed outlier: 6.732A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA K 74 " --> pdb=" O ASP K 104 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE K 125 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN K 154 " --> pdb=" O THR K 124 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N MET K 126 " --> pdb=" O VAL K 152 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL K 152 " --> pdb=" O MET K 126 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 4 through 5 removed outlier: 6.438A pdb=" N VAL L 152 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N MET L 126 " --> pdb=" O VAL L 152 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN L 154 " --> pdb=" O THR L 124 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE L 125 " --> pdb=" O LEU L 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 61 through 62 removed outlier: 8.894A pdb=" N TYR L 62 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL L 43 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 3054 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: 23.06 Time building geometry restraints manager: 14.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 31513 1.05 - 1.26: 5292 1.26 - 1.47: 12514 1.47 - 1.68: 14466 1.68 - 1.89: 252 Bond restraints: 64037 Sorted by residual: bond pdb=" C GLY A 44 " pdb=" N ASN A 45 " ideal model delta sigma weight residual 1.330 1.259 0.071 1.22e-02 6.72e+03 3.38e+01 bond pdb=" CB GLN G 26 " pdb=" CG GLN G 26 " ideal model delta sigma weight residual 1.520 1.636 -0.116 3.00e-02 1.11e+03 1.49e+01 bond pdb=" C4D NDP G 402 " pdb=" O4D NDP G 402 " ideal model delta sigma weight residual 1.419 1.512 -0.093 3.50e-02 8.16e+02 7.00e+00 bond pdb=" C4D NDP G 402 " pdb=" C5D NDP G 402 " ideal model delta sigma weight residual 1.511 1.581 -0.070 3.40e-02 8.65e+02 4.23e+00 bond pdb=" CG GLN G 26 " pdb=" HG3 GLN G 26 " ideal model delta sigma weight residual 0.970 1.010 -0.040 2.00e-02 2.50e+03 3.97e+00 ... (remaining 64032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.53: 115891 4.53 - 9.05: 141 9.05 - 13.58: 9 13.58 - 18.10: 0 18.10 - 22.63: 3 Bond angle restraints: 116044 Sorted by residual: angle pdb=" HG2 GLN G 26 " pdb=" CG GLN G 26 " pdb=" HG3 GLN G 26 " ideal model delta sigma weight residual 110.00 132.63 -22.63 3.00e+00 1.11e-01 5.69e+01 angle pdb=" CD GLN G 26 " pdb=" CG GLN G 26 " pdb=" HG3 GLN G 26 " ideal model delta sigma weight residual 108.00 85.50 22.50 3.00e+00 1.11e-01 5.63e+01 angle pdb=" CD GLN G 26 " pdb=" CG GLN G 26 " pdb=" HG2 GLN G 26 " ideal model delta sigma weight residual 108.00 86.69 21.31 3.00e+00 1.11e-01 5.04e+01 angle pdb=" C2B NDP G 402 " pdb=" O2B NDP G 402 " pdb=" P2B NDP G 402 " ideal model delta sigma weight residual 111.34 124.02 -12.68 2.68e+00 1.40e-01 2.24e+01 angle pdb=" C2B NDP I 402 " pdb=" O2B NDP I 402 " pdb=" P2B NDP I 402 " ideal model delta sigma weight residual 111.34 124.01 -12.67 2.68e+00 1.40e-01 2.24e+01 ... (remaining 116039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.52: 28221 30.52 - 61.04: 1303 61.04 - 91.55: 34 91.55 - 122.07: 11 122.07 - 152.59: 1 Dihedral angle restraints: 29570 sinusoidal: 16157 harmonic: 13413 Sorted by residual: dihedral pdb=" CA ASN A 45 " pdb=" C ASN A 45 " pdb=" N VAL A 46 " pdb=" CA VAL A 46 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ASN B 45 " pdb=" C ASN B 45 " pdb=" N VAL B 46 " pdb=" CA VAL B 46 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ARG C 70 " pdb=" C ARG C 70 " pdb=" N SER C 71 " pdb=" CA SER C 71 " ideal model delta harmonic sigma weight residual -180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 29567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4496 0.093 - 0.186: 301 0.186 - 0.278: 1 0.278 - 0.371: 0 0.371 - 0.464: 1 Chirality restraints: 4799 Sorted by residual: chirality pdb=" C4D NDP G 402 " pdb=" C3D NDP G 402 " pdb=" C5D NDP G 402 " pdb=" O4D NDP G 402 " both_signs ideal model delta sigma weight residual False -2.71 -3.18 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA ASP H 11 " pdb=" N ASP H 11 " pdb=" C ASP H 11 " pdb=" CB ASP H 11 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C2B NDP I 402 " pdb=" C1B NDP I 402 " pdb=" C3B NDP I 402 " pdb=" O2B NDP I 402 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 4796 not shown) Planarity restraints: 9344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 44 " 0.022 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" N ASN A 45 " -0.068 2.00e-02 2.50e+03 pdb=" CA ASN A 45 " 0.018 2.00e-02 2.50e+03 pdb=" H ASN A 45 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 44 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C GLY A 44 " 0.062 2.00e-02 2.50e+03 pdb=" O GLY A 44 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A 45 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 220 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO H 221 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO H 221 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 221 " 0.028 5.00e-02 4.00e+02 ... (remaining 9341 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 666 2.07 - 2.70: 103541 2.70 - 3.34: 174306 3.34 - 3.97: 218058 3.97 - 4.60: 361172 Nonbonded interactions: 857743 Sorted by model distance: nonbonded pdb=" HA2 GLY G 22 " pdb="HD22 ASN G 45 " model vdw 1.441 2.270 nonbonded pdb=" HA2 GLY E 22 " pdb="HD22 ASN E 45 " model vdw 1.463 2.270 nonbonded pdb=" HA2 GLY H 22 " pdb="HD22 ASN H 45 " model vdw 1.633 2.270 nonbonded pdb=" HA2 GLY C 22 " pdb="HD22 ASN C 45 " model vdw 1.667 2.270 nonbonded pdb=" CD GLU E 195 " pdb="MG MG E 401 " model vdw 1.670 2.350 ... (remaining 857738 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 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'B' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'C' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'D' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'E' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'F' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) 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 331)) selection = (chain 'H' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'I' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'J' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'K' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) selection = (chain 'L' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 26 through 331)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.59 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: 5.170 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: 0.850 Extract box with map and model: 1.760 Check model and map are aligned: 0.350 Set scattering table: 0.440 Process input model: 102.530 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.180 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 : 0.006 0.116 32512 Z= 0.365 Angle : 0.809 12.677 44029 Z= 0.420 Chirality : 0.045 0.464 4799 Planarity : 0.005 0.049 5530 Dihedral : 15.493 152.588 11973 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: -5.41 (0.11), residues: 3935 helix: -4.33 (0.06), residues: 2048 sheet: -3.03 (0.23), residues: 462 loop : -2.15 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 198 HIS 0.013 0.003 HIS I 196 PHE 0.012 0.002 PHE E 184 TYR 0.023 0.002 TYR H 51 ARG 0.003 0.000 ARG H 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 726 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: C 291 GLU cc_start: 0.6652 (tt0) cc_final: 0.6234 (tt0) REVERT: D 291 GLU cc_start: 0.6735 (tt0) cc_final: 0.6285 (tt0) REVERT: I 104 ASP cc_start: 0.6946 (t70) cc_final: 0.6579 (t0) REVERT: K 104 ASP cc_start: 0.6900 (t70) cc_final: 0.6515 (t0) outliers start: 0 outliers final: 0 residues processed: 726 average time/residue: 0.9307 time to fit residues: 1024.5791 Evaluate side-chains 469 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 332 optimal weight: 0.9980 chunk 298 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 308 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 357 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 297 GLN C 26 GLN C 332 ASN E 297 GLN F 154 GLN G 140 HIS G 278 ASN H 25 ASN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 GLN K 154 GLN L 154 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32512 Z= 0.248 Angle : 0.666 10.146 44029 Z= 0.357 Chirality : 0.043 0.170 4799 Planarity : 0.005 0.042 5530 Dihedral : 9.255 154.455 4463 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.49 % Allowed : 8.83 % Favored : 89.68 % 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: -4.67 (0.11), residues: 3935 helix: -3.42 (0.08), residues: 2171 sheet: -2.68 (0.23), residues: 490 loop : -2.12 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 198 HIS 0.005 0.001 HIS J 196 PHE 0.010 0.001 PHE G 303 TYR 0.019 0.001 TYR G 51 ARG 0.004 0.000 ARG J 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 511 time to evaluate : 3.705 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: C 75 LEU cc_start: 0.8743 (mp) cc_final: 0.8468 (mp) REVERT: C 249 GLN cc_start: 0.7924 (pm20) cc_final: 0.7502 (pm20) REVERT: C 281 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8189 (ttpp) REVERT: E 80 ASP cc_start: 0.6895 (p0) cc_final: 0.6692 (p0) REVERT: E 281 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8217 (ttpp) REVERT: G 75 LEU cc_start: 0.8694 (mp) cc_final: 0.8379 (mp) REVERT: H 281 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8230 (ttpp) REVERT: I 75 LEU cc_start: 0.8621 (mp) cc_final: 0.8312 (mp) REVERT: K 250 MET cc_start: 0.7683 (mmm) cc_final: 0.7269 (mmm) outliers start: 48 outliers final: 39 residues processed: 544 average time/residue: 0.8673 time to fit residues: 738.8597 Evaluate side-chains 472 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 430 time to evaluate : 3.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 267 LYS Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 267 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 267 LYS Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 314 GLU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 267 LYS Chi-restraints excluded: chain I residue 314 GLU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 314 GLU Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 314 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 198 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 297 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 358 optimal weight: 4.9990 chunk 387 optimal weight: 0.8980 chunk 319 optimal weight: 8.9990 chunk 355 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 GLN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 32512 Z= 0.320 Angle : 0.649 9.986 44029 Z= 0.346 Chirality : 0.043 0.191 4799 Planarity : 0.004 0.037 5530 Dihedral : 9.130 153.308 4463 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.36 % Allowed : 9.20 % Favored : 88.44 % 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: -4.16 (0.12), residues: 3935 helix: -2.88 (0.08), residues: 2241 sheet: -2.51 (0.23), residues: 489 loop : -2.04 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 198 HIS 0.009 0.002 HIS G 253 PHE 0.011 0.001 PHE E 303 TYR 0.016 0.001 TYR G 51 ARG 0.003 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 460 time to evaluate : 3.874 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: A 75 LEU cc_start: 0.8681 (mp) cc_final: 0.8385 (mp) REVERT: G 104 ASP cc_start: 0.6910 (t70) cc_final: 0.6160 (t0) outliers start: 76 outliers final: 51 residues processed: 498 average time/residue: 0.7945 time to fit residues: 646.9795 Evaluate side-chains 469 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 418 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 220 SER Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 297 GLN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 250 MET Chi-restraints excluded: chain G residue 267 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 314 GLU Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 220 SER Chi-restraints excluded: chain I residue 250 MET Chi-restraints excluded: chain I residue 314 GLU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 314 GLU Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 314 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 354 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 chunk 186 optimal weight: 0.0030 chunk 39 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 240 optimal weight: 7.9990 chunk 359 optimal weight: 0.7980 chunk 380 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 340 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 overall best weight: 2.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS G 96 GLN H 25 ASN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32512 Z= 0.236 Angle : 0.597 9.822 44029 Z= 0.313 Chirality : 0.042 0.163 4799 Planarity : 0.004 0.050 5530 Dihedral : 8.883 153.205 4463 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.29 % Allowed : 10.07 % Favored : 87.64 % 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: -3.60 (0.12), residues: 3935 helix: -2.34 (0.09), residues: 2259 sheet: -2.50 (0.23), residues: 477 loop : -1.90 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 198 HIS 0.003 0.001 HIS E 196 PHE 0.012 0.001 PHE E 303 TYR 0.012 0.001 TYR A 282 ARG 0.002 0.000 ARG G 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 475 time to evaluate : 3.836 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: F 75 LEU cc_start: 0.8494 (mm) cc_final: 0.7577 (mm) REVERT: L 75 LEU cc_start: 0.8301 (mm) cc_final: 0.7281 (mm) outliers start: 74 outliers final: 49 residues processed: 506 average time/residue: 0.7802 time to fit residues: 648.9044 Evaluate side-chains 468 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 419 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain G residue 26 GLN Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 267 LYS Chi-restraints excluded: chain G residue 314 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 314 GLU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 314 GLU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 314 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 317 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 283 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 324 optimal weight: 4.9990 chunk 263 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 341 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32512 Z= 0.229 Angle : 0.581 9.681 44029 Z= 0.302 Chirality : 0.042 0.164 4799 Planarity : 0.003 0.038 5530 Dihedral : 8.732 153.081 4463 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.23 % Allowed : 10.97 % Favored : 86.80 % 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: -3.11 (0.12), residues: 3935 helix: -1.84 (0.10), residues: 2229 sheet: -2.44 (0.23), residues: 477 loop : -1.87 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 161 HIS 0.004 0.001 HIS C 253 PHE 0.010 0.001 PHE E 303 TYR 0.016 0.001 TYR C 62 ARG 0.004 0.000 ARG G 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 425 time to evaluate : 3.836 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 outliers start: 72 outliers final: 50 residues processed: 453 average time/residue: 0.7988 time to fit residues: 601.6310 Evaluate side-chains 438 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 388 time to evaluate : 3.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 297 GLN Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain G residue 26 GLN Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 314 GLU Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 314 GLU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 314 GLU Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 314 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 128 optimal weight: 4.9990 chunk 342 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 381 optimal weight: 6.9990 chunk 316 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 252 HIS H 312 GLN I 252 HIS ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 32512 Z= 0.361 Angle : 0.644 9.266 44029 Z= 0.340 Chirality : 0.043 0.196 4799 Planarity : 0.004 0.036 5530 Dihedral : 8.894 153.541 4463 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.51 % Allowed : 12.02 % Favored : 85.47 % 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: 3935 helix: -1.48 (0.10), residues: 2237 sheet: -2.37 (0.22), residues: 484 loop : -2.06 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 161 HIS 0.005 0.002 HIS E 196 PHE 0.008 0.001 PHE I 184 TYR 0.011 0.001 TYR G 282 ARG 0.003 0.000 ARG G 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 411 time to evaluate : 3.750 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: E 30 GLN cc_start: 0.7907 (mt0) cc_final: 0.7541 (mt0) REVERT: F 104 ASP cc_start: 0.6577 (t0) cc_final: 0.6284 (t0) outliers start: 81 outliers final: 57 residues processed: 446 average time/residue: 0.7808 time to fit residues: 574.6400 Evaluate side-chains 446 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 389 time to evaluate : 3.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 297 GLN Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain G residue 26 GLN Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 314 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 220 SER Chi-restraints excluded: chain I residue 306 LEU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 314 GLU Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 104 ASP Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 306 LEU Chi-restraints excluded: chain L residue 314 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 367 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 278 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 320 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 chunk 379 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 175 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 GLN ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 312 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32512 Z= 0.209 Angle : 0.576 9.172 44029 Z= 0.296 Chirality : 0.041 0.167 4799 Planarity : 0.003 0.034 5530 Dihedral : 8.675 153.132 4463 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.92 % Allowed : 13.20 % Favored : 84.88 % 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: -2.57 (0.13), residues: 3935 helix: -1.24 (0.10), residues: 2291 sheet: -2.38 (0.23), residues: 474 loop : -1.92 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 161 HIS 0.003 0.001 HIS C 253 PHE 0.008 0.001 PHE A 247 TYR 0.010 0.001 TYR C 62 ARG 0.003 0.000 ARG G 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 418 time to evaluate : 3.718 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: F 131 MET cc_start: 0.7298 (mmm) cc_final: 0.6928 (mmm) outliers start: 62 outliers final: 47 residues processed: 441 average time/residue: 0.7579 time to fit residues: 563.6727 Evaluate side-chains 439 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 392 time to evaluate : 3.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain G residue 26 GLN Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 314 GLU Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 307 TRP Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 306 LEU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 314 GLU Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 306 LEU Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 306 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 234 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 241 optimal weight: 0.7980 chunk 258 optimal weight: 0.5980 chunk 187 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN B 312 GLN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN H 312 GLN I 312 GLN ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32512 Z= 0.171 Angle : 0.561 8.945 44029 Z= 0.285 Chirality : 0.041 0.164 4799 Planarity : 0.003 0.037 5530 Dihedral : 8.465 152.972 4463 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.95 % Allowed : 13.48 % 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: -2.14 (0.13), residues: 3935 helix: -0.95 (0.10), residues: 2314 sheet: -2.37 (0.22), residues: 470 loop : -1.54 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 161 HIS 0.003 0.001 HIS C 253 PHE 0.008 0.001 PHE H 184 TYR 0.009 0.001 TYR C 62 ARG 0.005 0.000 ARG H 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 418 time to evaluate : 3.730 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: A 104 ASP cc_start: 0.6447 (t70) cc_final: 0.5815 (t0) REVERT: F 131 MET cc_start: 0.7341 (mmm) cc_final: 0.7050 (mmm) outliers start: 63 outliers final: 45 residues processed: 440 average time/residue: 0.7634 time to fit residues: 554.9132 Evaluate side-chains 454 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 409 time to evaluate : 3.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain G residue 26 GLN Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 314 GLU Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 307 TRP Chi-restraints excluded: chain H residue 312 GLN Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 306 LEU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 314 GLU Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 306 LEU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 306 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 345 optimal weight: 3.9990 chunk 363 optimal weight: 6.9990 chunk 331 optimal weight: 6.9990 chunk 353 optimal weight: 6.9990 chunk 212 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 277 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 319 optimal weight: 3.9990 chunk 334 optimal weight: 2.9990 chunk 352 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 GLN H 312 GLN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 32512 Z= 0.239 Angle : 0.584 8.655 44029 Z= 0.301 Chirality : 0.042 0.169 4799 Planarity : 0.003 0.070 5530 Dihedral : 8.435 153.035 4463 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.67 % Allowed : 14.10 % Favored : 84.23 % 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: -2.10 (0.13), residues: 3935 helix: -0.91 (0.10), residues: 2312 sheet: -2.32 (0.22), residues: 474 loop : -1.55 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.003 0.001 HIS C 253 PHE 0.007 0.001 PHE F 247 TYR 0.010 0.001 TYR H 51 ARG 0.009 0.000 ARG L 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 404 time to evaluate : 3.760 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: A 104 ASP cc_start: 0.6499 (t70) cc_final: 0.5888 (t0) REVERT: F 30 GLN cc_start: 0.7676 (mt0) cc_final: 0.7392 (mt0) REVERT: F 131 MET cc_start: 0.7461 (mmm) cc_final: 0.7105 (mmm) outliers start: 54 outliers final: 49 residues processed: 425 average time/residue: 0.7966 time to fit residues: 557.4635 Evaluate side-chains 435 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 386 time to evaluate : 3.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain G residue 26 GLN Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 312 GLN Chi-restraints excluded: chain G residue 314 GLU Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 307 TRP Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 306 LEU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 314 GLU Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 306 LEU Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 306 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 232 optimal weight: 3.9990 chunk 374 optimal weight: 8.9990 chunk 228 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 392 optimal weight: 6.9990 chunk 361 optimal weight: 9.9990 chunk 312 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 241 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 HIS G 312 GLN ** J 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32512 Z= 0.226 Angle : 0.583 9.129 44029 Z= 0.300 Chirality : 0.042 0.163 4799 Planarity : 0.003 0.075 5530 Dihedral : 8.416 153.036 4463 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.52 % Allowed : 14.10 % Favored : 84.38 % 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: -2.09 (0.13), residues: 3935 helix: -0.91 (0.10), residues: 2323 sheet: -2.30 (0.22), residues: 474 loop : -1.54 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.003 0.001 HIS C 253 PHE 0.006 0.001 PHE H 203 TYR 0.010 0.001 TYR K 109 ARG 0.013 0.000 ARG D 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7870 Ramachandran restraints generated. 3935 Oldfield, 0 Emsley, 3935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 397 time to evaluate : 3.762 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: A 104 ASP cc_start: 0.6479 (t70) cc_final: 0.5871 (t0) REVERT: F 30 GLN cc_start: 0.7641 (mt0) cc_final: 0.7364 (mt0) REVERT: F 131 MET cc_start: 0.7444 (mmm) cc_final: 0.7085 (mmm) outliers start: 49 outliers final: 46 residues processed: 417 average time/residue: 0.7657 time to fit residues: 529.2482 Evaluate side-chains 436 residues out of total 3227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 390 time to evaluate : 3.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain G residue 26 GLN Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 306 LEU Chi-restraints excluded: chain H residue 307 TRP Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 306 LEU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 314 GLU Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 306 LEU Chi-restraints excluded: chain K residue 314 GLU Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 306 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 248 optimal weight: 4.9990 chunk 332 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 313 optimal weight: 7.9990 chunk 131 optimal weight: 0.1980 chunk 321 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.076874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.062840 restraints weight = 325613.399| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 5.35 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32512 Z= 0.200 Angle : 0.578 9.352 44029 Z= 0.294 Chirality : 0.042 0.191 4799 Planarity : 0.003 0.038 5530 Dihedral : 8.320 152.980 4463 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.36 % Allowed : 14.47 % Favored : 84.16 % 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: -1.95 (0.13), residues: 3935 helix: -0.76 (0.10), residues: 2323 sheet: -2.26 (0.22), residues: 474 loop : -1.58 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 198 HIS 0.004 0.001 HIS E 252 PHE 0.009 0.001 PHE E 247 TYR 0.009 0.001 TYR H 51 ARG 0.005 0.000 ARG J 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11984.11 seconds wall clock time: 206 minutes 44.36 seconds (12404.36 seconds total)