Starting phenix.real_space_refine on Fri Mar 6 13:35:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n9i_49170/03_2026/9n9i_49170_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n9i_49170/03_2026/9n9i_49170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n9i_49170/03_2026/9n9i_49170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n9i_49170/03_2026/9n9i_49170.map" model { file = "/net/cci-nas-00/data/ceres_data/9n9i_49170/03_2026/9n9i_49170_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n9i_49170/03_2026/9n9i_49170_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 20 5.49 5 Mg 8 5.21 5 S 212 5.16 5 C 19246 2.51 5 N 5225 2.21 5 O 5903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30614 Number of models: 1 Model: "" Number of chains: 21 Chain: "1" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3365 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "3" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "4" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3366 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3365 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3406 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413} Chain: "C" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "M" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3197 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 9, 'TRANS': 389} Chain: "a" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3366 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "b" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "1" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {' MG': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {' MG': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {' MG': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.69, per 1000 atoms: 0.22 Number of scatterers: 30614 At special positions: 0 Unit cell: (124.114, 120.931, 207.917, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 212 16.00 P 20 15.00 Mg 8 11.99 O 5903 8.00 N 5225 7.00 C 19246 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.4 seconds 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7112 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 25 sheets defined 52.6% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain '1' and resid 10 through 29 removed outlier: 3.678A pdb=" N ALA 1 19 " --> pdb=" O GLN 1 15 " (cutoff:3.500A) Processing helix chain '1' and resid 47 through 51 removed outlier: 4.038A pdb=" N THR 1 51 " --> pdb=" O SER 1 48 " (cutoff:3.500A) Processing helix chain '1' and resid 71 through 81 removed outlier: 4.739A pdb=" N ILE 1 75 " --> pdb=" O GLU 1 71 " (cutoff:3.500A) Processing helix chain '1' and resid 82 through 86 removed outlier: 4.343A pdb=" N GLN 1 85 " --> pdb=" O THR 1 82 " (cutoff:3.500A) Processing helix chain '1' and resid 88 through 90 No H-bonds generated for 'chain '1' and resid 88 through 90' Processing helix chain '1' and resid 102 through 108 Processing helix chain '1' and resid 111 through 127 removed outlier: 4.383A pdb=" N ASP 1 116 " --> pdb=" O LYS 1 112 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU 1 117 " --> pdb=" O GLU 1 113 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS 1 124 " --> pdb=" O ASP 1 120 " (cutoff:3.500A) Processing helix chain '1' and resid 143 through 161 removed outlier: 4.274A pdb=" N THR 1 150 " --> pdb=" O GLY 1 146 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL 1 159 " --> pdb=" O GLU 1 155 " (cutoff:3.500A) Processing helix chain '1' and resid 182 through 190 removed outlier: 3.980A pdb=" N ASN 1 186 " --> pdb=" O VAL 1 182 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 197 Processing helix chain '1' and resid 206 through 216 Processing helix chain '1' and resid 223 through 239 removed outlier: 3.523A pdb=" N LEU 1 227 " --> pdb=" O THR 1 223 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG 1 229 " --> pdb=" O THR 1 225 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE 1 234 " --> pdb=" O LEU 1 230 " (cutoff:3.500A) Processing helix chain '1' and resid 251 through 260 removed outlier: 3.746A pdb=" N ASN 1 258 " --> pdb=" O GLU 1 254 " (cutoff:3.500A) Processing helix chain '1' and resid 277 through 282 removed outlier: 4.286A pdb=" N TYR 1 282 " --> pdb=" O ALA 1 278 " (cutoff:3.500A) Processing helix chain '1' and resid 287 through 296 removed outlier: 3.621A pdb=" N PHE 1 296 " --> pdb=" O THR 1 292 " (cutoff:3.500A) Processing helix chain '1' and resid 297 through 301 removed outlier: 3.878A pdb=" N GLN 1 301 " --> pdb=" O PRO 1 298 " (cutoff:3.500A) Processing helix chain '1' and resid 306 through 310 Processing helix chain '1' and resid 324 through 338 removed outlier: 3.558A pdb=" N THR 1 337 " --> pdb=" O ALA 1 333 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS 1 338 " --> pdb=" O THR 1 334 " (cutoff:3.500A) Processing helix chain '1' and resid 384 through 400 removed outlier: 3.715A pdb=" N ARG 1 390 " --> pdb=" O GLU 1 386 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU 1 391 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) Processing helix chain '1' and resid 405 through 410 Processing helix chain '1' and resid 415 through 435 removed outlier: 4.331A pdb=" N SER 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU 1 433 " --> pdb=" O GLU 1 429 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL 1 435 " --> pdb=" O ASP 1 431 " (cutoff:3.500A) Processing helix chain '3' and resid 10 through 28 Processing helix chain '3' and resid 40 through 48 removed outlier: 4.082A pdb=" N LEU 3 44 " --> pdb=" O SER 3 40 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG 3 48 " --> pdb=" O LEU 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 49 through 51 No H-bonds generated for 'chain '3' and resid 49 through 51' Processing helix chain '3' and resid 71 through 80 removed outlier: 4.436A pdb=" N MET 3 75 " --> pdb=" O GLU 3 71 " (cutoff:3.500A) Processing helix chain '3' and resid 88 through 90 No H-bonds generated for 'chain '3' and resid 88 through 90' Processing helix chain '3' and resid 102 through 108 Processing helix chain '3' and resid 111 through 128 removed outlier: 4.589A pdb=" N ASP 3 116 " --> pdb=" O ALA 3 112 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER 3 117 " --> pdb=" O GLU 3 113 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL 3 121 " --> pdb=" O SER 3 117 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS 3 124 " --> pdb=" O ASP 3 120 " (cutoff:3.500A) Processing helix chain '3' and resid 143 through 161 removed outlier: 3.642A pdb=" N GLU 3 159 " --> pdb=" O SER 3 155 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU 3 160 " --> pdb=" O LYS 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 174 through 178 Processing helix chain '3' and resid 182 through 195 removed outlier: 3.570A pdb=" N ASN 3 186 " --> pdb=" O VAL 3 182 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN 3 193 " --> pdb=" O LEU 3 189 " (cutoff:3.500A) Processing helix chain '3' and resid 206 through 216 Processing helix chain '3' and resid 223 through 239 removed outlier: 3.617A pdb=" N LEU 3 227 " --> pdb=" O THR 3 223 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR 3 239 " --> pdb=" O MET 3 235 " (cutoff:3.500A) Processing helix chain '3' and resid 251 through 260 removed outlier: 3.517A pdb=" N ASN 3 258 " --> pdb=" O LYS 3 254 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 284 removed outlier: 3.535A pdb=" N SER 3 280 " --> pdb=" O SER 3 277 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN 3 281 " --> pdb=" O ARG 3 278 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLN 3 282 " --> pdb=" O GLY 3 279 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR 3 283 " --> pdb=" O SER 3 280 " (cutoff:3.500A) Processing helix chain '3' and resid 287 through 296 Processing helix chain '3' and resid 297 through 301 removed outlier: 3.891A pdb=" N MET 3 301 " --> pdb=" O ALA 3 298 " (cutoff:3.500A) Processing helix chain '3' and resid 306 through 310 Processing helix chain '3' and resid 324 through 339 removed outlier: 3.706A pdb=" N VAL 3 328 " --> pdb=" O SER 3 324 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN 3 336 " --> pdb=" O MET 3 332 " (cutoff:3.500A) Processing helix chain '3' and resid 340 through 343 removed outlier: 3.564A pdb=" N PHE 3 343 " --> pdb=" O SER 3 340 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 340 through 343' Processing helix chain '3' and resid 384 through 402 removed outlier: 3.659A pdb=" N PHE 3 388 " --> pdb=" O ILE 3 384 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG 3 390 " --> pdb=" O GLU 3 386 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE 3 391 " --> pdb=" O LEU 3 387 " (cutoff:3.500A) Processing helix chain '3' and resid 404 through 410 removed outlier: 4.127A pdb=" N TYR 3 408 " --> pdb=" O PHE 3 404 " (cutoff:3.500A) Processing helix chain '3' and resid 414 through 435 removed outlier: 3.765A pdb=" N PHE 3 418 " --> pdb=" O ASP 3 414 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR 3 435 " --> pdb=" O GLU 3 431 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 28 Processing helix chain '4' and resid 47 through 51 removed outlier: 3.773A pdb=" N THR 4 51 " --> pdb=" O SER 4 48 " (cutoff:3.500A) Processing helix chain '4' and resid 71 through 80 removed outlier: 4.653A pdb=" N ILE 4 75 " --> pdb=" O GLU 4 71 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU 4 77 " --> pdb=" O THR 4 73 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL 4 78 " --> pdb=" O VAL 4 74 " (cutoff:3.500A) Processing helix chain '4' and resid 88 through 90 No H-bonds generated for 'chain '4' and resid 88 through 90' Processing helix chain '4' and resid 102 through 108 Processing helix chain '4' and resid 110 through 129 removed outlier: 4.096A pdb=" N ILE 4 114 " --> pdb=" O ILE 4 110 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASP 4 116 " --> pdb=" O LYS 4 112 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU 4 117 " --> pdb=" O GLU 4 113 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP 4 120 " --> pdb=" O ASP 4 116 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN 4 128 " --> pdb=" O LYS 4 124 " (cutoff:3.500A) Processing helix chain '4' and resid 149 through 161 removed outlier: 4.010A pdb=" N GLU 4 155 " --> pdb=" O SER 4 151 " (cutoff:3.500A) Processing helix chain '4' and resid 182 through 190 removed outlier: 3.652A pdb=" N ASN 4 186 " --> pdb=" O VAL 4 182 " (cutoff:3.500A) Processing helix chain '4' and resid 190 through 197 removed outlier: 3.588A pdb=" N HIS 4 197 " --> pdb=" O THR 4 193 " (cutoff:3.500A) Processing helix chain '4' and resid 206 through 216 Processing helix chain '4' and resid 223 through 239 removed outlier: 3.624A pdb=" N LEU 4 227 " --> pdb=" O THR 4 223 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG 4 229 " --> pdb=" O THR 4 225 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE 4 234 " --> pdb=" O LEU 4 230 " (cutoff:3.500A) Processing helix chain '4' and resid 251 through 260 Processing helix chain '4' and resid 280 through 284 Processing helix chain '4' and resid 287 through 295 removed outlier: 3.566A pdb=" N ASN 4 293 " --> pdb=" O ALA 4 289 " (cutoff:3.500A) Processing helix chain '4' and resid 296 through 301 removed outlier: 6.048A pdb=" N ALA 4 299 " --> pdb=" O PHE 4 296 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN 4 301 " --> pdb=" O PRO 4 298 " (cutoff:3.500A) Processing helix chain '4' and resid 306 through 310 Processing helix chain '4' and resid 324 through 338 removed outlier: 3.693A pdb=" N LYS 4 338 " --> pdb=" O THR 4 334 " (cutoff:3.500A) Processing helix chain '4' and resid 383 through 400 removed outlier: 3.986A pdb=" N ALA 4 387 " --> pdb=" O ALA 4 383 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG 4 390 " --> pdb=" O GLU 4 386 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU 4 391 " --> pdb=" O ALA 4 387 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS 4 393 " --> pdb=" O ALA 4 389 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET 4 398 " --> pdb=" O LYS 4 394 " (cutoff:3.500A) Processing helix chain '4' and resid 405 through 410 Processing helix chain '4' and resid 415 through 435 removed outlier: 4.058A pdb=" N SER 4 419 " --> pdb=" O GLU 4 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.777A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.992A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.537A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 4.555A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 111 through 127 removed outlier: 4.521A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.319A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.750A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.660A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.947A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.652A pdb=" N CYS A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.664A pdb=" N LYS A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.876A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.500A pdb=" N GLY A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.069A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.694A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 48 removed outlier: 3.995A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 81 through 85 removed outlier: 4.328A pdb=" N GLN B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 109 through 128 removed outlier: 3.815A pdb=" N GLU B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 159 removed outlier: 4.312A pdb=" N THR B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.545A pdb=" N ASN B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.567A pdb=" N LEU B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 243 Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 287 through 296 removed outlier: 3.693A pdb=" N PHE B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.823A pdb=" N MET B 301 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.706A pdb=" N VAL B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 removed outlier: 3.638A pdb=" N PHE B 343 " --> pdb=" O SER B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 340 through 343' Processing helix chain 'B' and resid 384 through 400 removed outlier: 3.562A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.136A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 438 removed outlier: 3.815A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 removed outlier: 3.694A pdb=" N LYS C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 48 removed outlier: 3.995A pdb=" N LEU C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG C 48 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 81 through 85 removed outlier: 4.329A pdb=" N GLN C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 109 through 128 removed outlier: 3.815A pdb=" N GLU C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASP C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 159 removed outlier: 4.312A pdb=" N THR C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.545A pdb=" N ASN C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU C 196 " --> pdb=" O HIS C 192 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.567A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR C 239 " --> pdb=" O MET C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.693A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 removed outlier: 3.823A pdb=" N MET C 301 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 339 removed outlier: 3.706A pdb=" N VAL C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN C 336 " --> pdb=" O MET C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 343 removed outlier: 3.639A pdb=" N PHE C 343 " --> pdb=" O SER C 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 340 through 343' Processing helix chain 'C' and resid 384 through 400 removed outlier: 3.590A pdb=" N MET C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.135A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 435 removed outlier: 3.815A pdb=" N PHE C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 227 Processing helix chain 'M' and resid 233 through 246 Processing helix chain 'M' and resid 273 through 279 Processing helix chain 'M' and resid 324 through 333 removed outlier: 3.588A pdb=" N VAL M 328 " --> pdb=" O THR M 324 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE M 331 " --> pdb=" O VAL M 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 333 through 341 removed outlier: 3.926A pdb=" N PHE M 341 " --> pdb=" O VAL M 337 " (cutoff:3.500A) Processing helix chain 'M' and resid 355 through 364 Processing helix chain 'M' and resid 380 through 390 removed outlier: 3.769A pdb=" N LEU M 389 " --> pdb=" O VAL M 385 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP M 390 " --> pdb=" O PHE M 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 391 through 396 Processing helix chain 'M' and resid 445 through 461 Processing helix chain 'M' and resid 470 through 474 Processing helix chain 'M' and resid 506 through 537 removed outlier: 3.513A pdb=" N GLY M 535 " --> pdb=" O ILE M 531 " (cutoff:3.500A) Processing helix chain 'M' and resid 546 through 554 removed outlier: 3.883A pdb=" N ASP M 554 " --> pdb=" O GLN M 550 " (cutoff:3.500A) Processing helix chain 'M' and resid 572 through 574 No H-bonds generated for 'chain 'M' and resid 572 through 574' Processing helix chain 'M' and resid 575 through 591 Processing helix chain 'a' and resid 10 through 28 removed outlier: 3.904A pdb=" N ALA a 19 " --> pdb=" O GLN a 15 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 51 removed outlier: 3.652A pdb=" N THR a 51 " --> pdb=" O SER a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 79 removed outlier: 3.933A pdb=" N VAL a 78 " --> pdb=" O VAL a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 90 No H-bonds generated for 'chain 'a' and resid 88 through 90' Processing helix chain 'a' and resid 102 through 108 Processing helix chain 'a' and resid 110 through 127 removed outlier: 4.090A pdb=" N ILE a 114 " --> pdb=" O ILE a 110 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP a 116 " --> pdb=" O LYS a 112 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU a 117 " --> pdb=" O GLU a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 161 removed outlier: 4.187A pdb=" N THR a 150 " --> pdb=" O GLY a 146 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU a 155 " --> pdb=" O SER a 151 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG a 156 " --> pdb=" O LEU a 152 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL a 159 " --> pdb=" O GLU a 155 " (cutoff:3.500A) Processing helix chain 'a' and resid 182 through 190 Processing helix chain 'a' and resid 190 through 197 Processing helix chain 'a' and resid 205 through 216 removed outlier: 3.641A pdb=" N ILE a 209 " --> pdb=" O ASP a 205 " (cutoff:3.500A) Processing helix chain 'a' and resid 223 through 240 removed outlier: 3.600A pdb=" N LEU a 227 " --> pdb=" O THR a 223 " (cutoff:3.500A) Processing helix chain 'a' and resid 241 through 243 No H-bonds generated for 'chain 'a' and resid 241 through 243' Processing helix chain 'a' and resid 251 through 260 removed outlier: 3.739A pdb=" N GLN a 256 " --> pdb=" O LEU a 252 " (cutoff:3.500A) Processing helix chain 'a' and resid 277 through 282 removed outlier: 4.167A pdb=" N TYR a 282 " --> pdb=" O ALA a 278 " (cutoff:3.500A) Processing helix chain 'a' and resid 287 through 295 removed outlier: 3.762A pdb=" N CYS a 295 " --> pdb=" O ILE a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 296 through 301 removed outlier: 6.149A pdb=" N ALA a 299 " --> pdb=" O PHE a 296 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN a 301 " --> pdb=" O PRO a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 306 through 310 Processing helix chain 'a' and resid 324 through 336 Processing helix chain 'a' and resid 384 through 401 removed outlier: 3.506A pdb=" N ARG a 390 " --> pdb=" O GLU a 386 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU a 391 " --> pdb=" O ALA a 387 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS a 394 " --> pdb=" O ARG a 390 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET a 398 " --> pdb=" O LYS a 394 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS a 401 " --> pdb=" O LEU a 397 " (cutoff:3.500A) Processing helix chain 'a' and resid 404 through 411 removed outlier: 4.081A pdb=" N TYR a 408 " --> pdb=" O PHE a 404 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU a 411 " --> pdb=" O TRP a 407 " (cutoff:3.500A) Processing helix chain 'a' and resid 415 through 435 removed outlier: 4.031A pdb=" N SER a 419 " --> pdb=" O GLU a 415 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG a 422 " --> pdb=" O PHE a 418 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET a 425 " --> pdb=" O ALA a 421 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU a 433 " --> pdb=" O GLU a 429 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 29 removed outlier: 3.559A pdb=" N LYS b 19 " --> pdb=" O GLN b 15 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU b 22 " --> pdb=" O ALA b 18 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 48 removed outlier: 4.125A pdb=" N LEU b 44 " --> pdb=" O SER b 40 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG b 48 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 51 No H-bonds generated for 'chain 'b' and resid 49 through 51' Processing helix chain 'b' and resid 71 through 80 removed outlier: 4.460A pdb=" N MET b 75 " --> pdb=" O GLU b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 108 removed outlier: 3.569A pdb=" N GLY b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) Processing helix chain 'b' and resid 110 through 127 removed outlier: 3.788A pdb=" N LEU b 114 " --> pdb=" O GLU b 110 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASP b 116 " --> pdb=" O ALA b 112 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER b 117 " --> pdb=" O GLU b 113 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL b 121 " --> pdb=" O SER b 117 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS b 124 " --> pdb=" O ASP b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 161 removed outlier: 4.107A pdb=" N THR b 151 " --> pdb=" O SER b 147 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU b 159 " --> pdb=" O SER b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 182 through 195 removed outlier: 3.584A pdb=" N ASN b 186 " --> pdb=" O VAL b 182 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN b 193 " --> pdb=" O LEU b 189 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 216 Processing helix chain 'b' and resid 223 through 239 removed outlier: 3.672A pdb=" N LEU b 227 " --> pdb=" O THR b 223 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR b 239 " --> pdb=" O MET b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 251 through 260 Processing helix chain 'b' and resid 280 through 284 removed outlier: 3.612A pdb=" N ARG b 284 " --> pdb=" O GLN b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 287 through 296 removed outlier: 3.532A pdb=" N PHE b 296 " --> pdb=" O THR b 292 " (cutoff:3.500A) Processing helix chain 'b' and resid 306 through 310 Processing helix chain 'b' and resid 324 through 339 removed outlier: 3.502A pdb=" N VAL b 328 " --> pdb=" O SER b 324 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN b 336 " --> pdb=" O MET b 332 " (cutoff:3.500A) Processing helix chain 'b' and resid 340 through 343 removed outlier: 3.662A pdb=" N PHE b 343 " --> pdb=" O SER b 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 340 through 343' Processing helix chain 'b' and resid 384 through 400 removed outlier: 3.733A pdb=" N PHE b 388 " --> pdb=" O ILE b 384 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG b 390 " --> pdb=" O GLU b 386 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA b 397 " --> pdb=" O GLU b 393 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 410 Processing helix chain 'b' and resid 414 through 435 removed outlier: 3.846A pdb=" N PHE b 418 " --> pdb=" O ASP b 414 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR b 435 " --> pdb=" O GLU b 431 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 92 through 94 removed outlier: 8.231A pdb=" N ILE 1 93 " --> pdb=" O ALA 1 65 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE 1 67 " --> pdb=" O ILE 1 93 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER 1 6 " --> pdb=" O VAL 1 66 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL 1 68 " --> pdb=" O SER 1 6 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N HIS 1 8 " --> pdb=" O VAL 1 68 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE 1 5 " --> pdb=" O LEU 1 136 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE 1 138 " --> pdb=" O ILE 1 5 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE 1 7 " --> pdb=" O PHE 1 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain '1' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain '1' and resid 269 through 273 removed outlier: 6.652A pdb=" N ALA 1 374 " --> pdb=" O TYR 1 319 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TYR 1 319 " --> pdb=" O ALA 1 374 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS 1 376 " --> pdb=" O LEU 1 317 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU 1 317 " --> pdb=" O CYS 1 376 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU 1 378 " --> pdb=" O CYS 1 315 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N CYS 1 315 " --> pdb=" O LEU 1 378 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASN 1 380 " --> pdb=" O MET 1 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 92 through 94 removed outlier: 7.815A pdb=" N VAL 3 93 " --> pdb=" O ALA 3 65 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU 3 67 " --> pdb=" O VAL 3 93 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU 3 3 " --> pdb=" O GLY 3 134 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N GLN 3 136 " --> pdb=" O GLU 3 3 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL 3 5 " --> pdb=" O GLN 3 136 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N THR 3 138 " --> pdb=" O VAL 3 5 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE 3 7 " --> pdb=" O THR 3 138 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N SER 3 140 " --> pdb=" O ILE 3 7 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N ALA 3 9 " --> pdb=" O SER 3 140 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N ILE 3 165 " --> pdb=" O CYS 3 131 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLN 3 133 " --> pdb=" O ILE 3 165 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ASN 3 167 " --> pdb=" O GLN 3 133 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE 3 135 " --> pdb=" O ASN 3 167 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE 3 169 " --> pdb=" O PHE 3 135 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU 3 137 " --> pdb=" O PHE 3 169 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL 3 171 " --> pdb=" O LEU 3 137 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N HIS 3 139 " --> pdb=" O VAL 3 171 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR 3 201 " --> pdb=" O PHE 3 268 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N CYS 3 203 " --> pdb=" O PRO 3 270 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N PHE 3 272 " --> pdb=" O CYS 3 203 " (cutoff:3.500A) removed outlier: 14.024A pdb=" N ASP 3 205 " --> pdb=" O PHE 3 272 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE 3 267 " --> pdb=" O SER 3 381 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER 3 381 " --> pdb=" O PHE 3 267 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER 3 374 " --> pdb=" O PHE 3 319 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE 3 319 " --> pdb=" O SER 3 374 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR 3 376 " --> pdb=" O ALA 3 317 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA 3 317 " --> pdb=" O THR 3 376 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE 3 378 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL 3 315 " --> pdb=" O ILE 3 378 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN 3 380 " --> pdb=" O LEU 3 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain '4' and resid 92 through 94 removed outlier: 8.055A pdb=" N ILE 4 93 " --> pdb=" O ALA 4 65 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE 4 67 " --> pdb=" O ILE 4 93 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N VAL 4 66 " --> pdb=" O CYS 4 4 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER 4 6 " --> pdb=" O VAL 4 66 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL 4 68 " --> pdb=" O SER 4 6 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N HIS 4 8 " --> pdb=" O VAL 4 68 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLU 4 3 " --> pdb=" O LEU 4 132 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY 4 134 " --> pdb=" O GLU 4 3 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER 4 140 " --> pdb=" O VAL 4 9 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU 4 167 " --> pdb=" O GLN 4 133 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE 4 135 " --> pdb=" O LEU 4 167 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N PHE 4 169 " --> pdb=" O PHE 4 135 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL 4 137 " --> pdb=" O PHE 4 169 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE 4 171 " --> pdb=" O VAL 4 137 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N HIS 4 139 " --> pdb=" O ILE 4 171 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS 4 200 " --> pdb=" O LYS 4 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '4' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain '4' and resid 269 through 273 removed outlier: 3.537A pdb=" N ALA 4 314 " --> pdb=" O ASN 4 380 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.995A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLU A 3 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N LEU A 136 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N SER A 140 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N VAL A 9 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.674A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.128A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLU B 3 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY B 134 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N SER B 140 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N CYS B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.496A pdb=" N PHE B 272 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 13.942A pdb=" N ASP B 205 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 314 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AB6, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.128A pdb=" N VAL C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU C 67 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER C 140 " --> pdb=" O ALA C 9 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR C 201 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N CYS C 203 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 10.497A pdb=" N PHE C 272 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 13.942A pdb=" N ASP C 205 " --> pdb=" O PHE C 272 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE C 267 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER C 381 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB8, first strand: chain 'M' and resid 265 through 269 removed outlier: 3.609A pdb=" N ALA M 567 " --> pdb=" O CYS M 266 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS M 345 " --> pdb=" O ARG M 562 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N CYS M 564 " --> pdb=" O LYS M 345 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR M 347 " --> pdb=" O CYS M 564 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ILE M 566 " --> pdb=" O THR M 347 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE M 349 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N MET M 568 " --> pdb=" O PHE M 349 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR M 351 " --> pdb=" O MET M 568 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA M 346 " --> pdb=" O SER M 493 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL M 495 " --> pdb=" O ALA M 346 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS M 348 " --> pdb=" O VAL M 495 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU M 497 " --> pdb=" O CYS M 348 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA M 350 " --> pdb=" O LEU M 497 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU M 488 " --> pdb=" O ARG M 484 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG M 484 " --> pdb=" O LEU M 488 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP M 496 " --> pdb=" O ALA M 476 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA M 476 " --> pdb=" O ASP M 496 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 265 through 269 removed outlier: 3.609A pdb=" N ALA M 567 " --> pdb=" O CYS M 266 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS M 345 " --> pdb=" O ARG M 562 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N CYS M 564 " --> pdb=" O LYS M 345 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR M 347 " --> pdb=" O CYS M 564 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ILE M 566 " --> pdb=" O THR M 347 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE M 349 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N MET M 568 " --> pdb=" O PHE M 349 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR M 351 " --> pdb=" O MET M 568 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA M 346 " --> pdb=" O SER M 493 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL M 495 " --> pdb=" O ALA M 346 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS M 348 " --> pdb=" O VAL M 495 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU M 497 " --> pdb=" O CYS M 348 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA M 350 " --> pdb=" O LEU M 497 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU M 488 " --> pdb=" O ARG M 484 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG M 484 " --> pdb=" O LEU M 488 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP M 496 " --> pdb=" O ALA M 476 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA M 476 " --> pdb=" O ASP M 496 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL M 401 " --> pdb=" O VAL M 443 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS M 441 " --> pdb=" O VAL M 403 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 285 through 286 Processing sheet with id=AC2, first strand: chain 'M' and resid 424 through 427 Processing sheet with id=AC3, first strand: chain 'a' and resid 92 through 94 removed outlier: 8.177A pdb=" N ILE a 93 " --> pdb=" O ALA a 65 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE a 67 " --> pdb=" O ILE a 93 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N VAL a 66 " --> pdb=" O CYS a 4 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER a 6 " --> pdb=" O VAL a 66 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL a 68 " --> pdb=" O SER a 6 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N HIS a 8 " --> pdb=" O VAL a 68 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU a 3 " --> pdb=" O LEU a 132 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLY a 134 " --> pdb=" O GLU a 3 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER a 140 " --> pdb=" O VAL a 9 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N LEU a 167 " --> pdb=" O GLN a 133 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N PHE a 135 " --> pdb=" O LEU a 167 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE a 169 " --> pdb=" O PHE a 135 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL a 137 " --> pdb=" O PHE a 169 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE a 171 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N HIS a 139 " --> pdb=" O ILE a 171 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS a 166 " --> pdb=" O CYS a 200 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N PHE a 202 " --> pdb=" O LYS a 166 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU a 168 " --> pdb=" O PHE a 202 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL a 204 " --> pdb=" O GLU a 168 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER a 170 " --> pdb=" O VAL a 204 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 53 through 55 Processing sheet with id=AC5, first strand: chain 'a' and resid 272 through 273 removed outlier: 6.686A pdb=" N ALA a 374 " --> pdb=" O TYR a 319 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR a 319 " --> pdb=" O ALA a 374 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS a 376 " --> pdb=" O LEU a 317 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU a 317 " --> pdb=" O CYS a 376 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU a 378 " --> pdb=" O CYS a 315 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N CYS a 315 " --> pdb=" O LEU a 378 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN a 380 " --> pdb=" O MET a 313 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b' and resid 92 through 94 removed outlier: 8.175A pdb=" N VAL b 93 " --> pdb=" O ALA b 65 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU b 67 " --> pdb=" O VAL b 93 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU b 3 " --> pdb=" O GLY b 134 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN b 136 " --> pdb=" O GLU b 3 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL b 5 " --> pdb=" O GLN b 136 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N THR b 138 " --> pdb=" O VAL b 5 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE b 7 " --> pdb=" O THR b 138 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N SER b 140 " --> pdb=" O ILE b 7 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ALA b 9 " --> pdb=" O SER b 140 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ILE b 165 " --> pdb=" O CYS b 131 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN b 133 " --> pdb=" O ILE b 165 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASN b 167 " --> pdb=" O GLN b 133 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE b 135 " --> pdb=" O ASN b 167 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE b 169 " --> pdb=" O PHE b 135 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU b 137 " --> pdb=" O PHE b 169 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL b 171 " --> pdb=" O LEU b 137 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N HIS b 139 " --> pdb=" O VAL b 171 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU b 200 " --> pdb=" O MET b 166 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER b 170 " --> pdb=" O TYR b 202 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASP b 205 " --> pdb=" O PRO b 270 " (cutoff:3.500A) removed outlier: 11.946A pdb=" N PHE b 272 " --> pdb=" O ASP b 205 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N PHE b 267 " --> pdb=" O SER b 381 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER b 381 " --> pdb=" O PHE b 267 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR b 314 " --> pdb=" O ASN b 380 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b' and resid 53 through 56 removed outlier: 3.719A pdb=" N LYS b 60 " --> pdb=" O ALA b 56 " (cutoff:3.500A) 1403 hydrogen bonds defined for protein. 4005 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: 6.50 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5160 1.31 - 1.43: 8425 1.43 - 1.56: 17334 1.56 - 1.69: 46 1.69 - 1.81: 335 Bond restraints: 31300 Sorted by residual: bond pdb=" C3' GTP a 501 " pdb=" C4' GTP a 501 " ideal model delta sigma weight residual 1.524 1.303 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C4' GTP a 501 " pdb=" O4' GTP a 501 " ideal model delta sigma weight residual 1.410 1.618 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C5 GTP a 501 " pdb=" C6 GTP a 501 " ideal model delta sigma weight residual 1.390 1.531 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C4 GTP a 501 " pdb=" N3 GTP a 501 " ideal model delta sigma weight residual 1.355 1.491 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C2 GTP a 501 " pdb=" N2 GTP a 501 " ideal model delta sigma weight residual 1.330 1.451 -0.121 2.00e-02 2.50e+03 3.63e+01 ... (remaining 31295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 41949 2.82 - 5.64: 448 5.64 - 8.45: 52 8.45 - 11.27: 42 11.27 - 14.09: 12 Bond angle restraints: 42503 Sorted by residual: angle pdb=" N SER A 340 " pdb=" CA SER A 340 " pdb=" C SER A 340 " ideal model delta sigma weight residual 112.54 106.63 5.91 1.22e+00 6.72e-01 2.35e+01 angle pdb=" PA GTP 1 501 " pdb=" O3A GTP 1 501 " pdb=" PB GTP 1 501 " ideal model delta sigma weight residual 120.50 134.59 -14.09 3.00e+00 1.11e-01 2.21e+01 angle pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sigma weight residual 120.50 134.23 -13.73 3.00e+00 1.11e-01 2.09e+01 angle pdb=" C14 TA1 B 503 " pdb=" C11 TA1 B 503 " pdb=" O04 TA1 B 503 " ideal model delta sigma weight residual 119.42 106.39 13.03 3.00e+00 1.11e-01 1.89e+01 angle pdb=" C THR b 287 " pdb=" N VAL b 288 " pdb=" CA VAL b 288 " ideal model delta sigma weight residual 120.24 122.90 -2.66 6.30e-01 2.52e+00 1.78e+01 ... (remaining 42498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 18497 35.21 - 70.42: 392 70.42 - 105.63: 58 105.63 - 140.84: 19 140.84 - 176.05: 5 Dihedral angle restraints: 18971 sinusoidal: 7897 harmonic: 11074 Sorted by residual: dihedral pdb=" C8 GTP a 501 " pdb=" C1' GTP a 501 " pdb=" N9 GTP a 501 " pdb=" O4' GTP a 501 " ideal model delta sinusoidal sigma weight residual 104.59 -71.46 176.05 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C8 GTP 4 502 " pdb=" C1' GTP 4 502 " pdb=" N9 GTP 4 502 " pdb=" O4' GTP 4 502 " ideal model delta sinusoidal sigma weight residual 104.59 -80.89 -174.52 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -46.03 150.62 1 2.00e+01 2.50e-03 4.49e+01 ... (remaining 18968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4317 0.096 - 0.192: 315 0.192 - 0.288: 10 0.288 - 0.384: 0 0.384 - 0.480: 4 Chirality restraints: 4646 Sorted by residual: chirality pdb=" C18 TA1 B 503 " pdb=" C10 TA1 B 503 " pdb=" C17 TA1 B 503 " pdb=" C20 TA1 B 503 " both_signs ideal model delta sigma weight residual False -3.16 -2.68 -0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" C18 TA1 C 502 " pdb=" C10 TA1 C 502 " pdb=" C17 TA1 C 502 " pdb=" C20 TA1 C 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.71 -0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" C18 TA1 b 503 " pdb=" C10 TA1 b 503 " pdb=" C17 TA1 b 503 " pdb=" C20 TA1 b 503 " both_signs ideal model delta sigma weight residual False -3.16 -2.72 -0.44 2.00e-01 2.50e+01 4.94e+00 ... (remaining 4643 not shown) Planarity restraints: 5517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 TA1 C 502 " 0.199 2.00e-02 2.50e+03 1.64e-01 3.37e+02 pdb=" C30 TA1 C 502 " -0.055 2.00e-02 2.50e+03 pdb=" C31 TA1 C 502 " 0.145 2.00e-02 2.50e+03 pdb=" N01 TA1 C 502 " -0.266 2.00e-02 2.50e+03 pdb=" O14 TA1 C 502 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C29 TA1 3 503 " -0.050 2.00e-02 2.50e+03 4.14e-02 2.14e+01 pdb=" C30 TA1 3 503 " 0.017 2.00e-02 2.50e+03 pdb=" C31 TA1 3 503 " -0.039 2.00e-02 2.50e+03 pdb=" N01 TA1 3 503 " 0.064 2.00e-02 2.50e+03 pdb=" O14 TA1 3 503 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 532 " 0.282 9.50e-02 1.11e+02 1.26e-01 9.83e+00 pdb=" NE ARG M 532 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG M 532 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG M 532 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG M 532 " 0.010 2.00e-02 2.50e+03 ... (remaining 5514 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 594 2.70 - 3.25: 30544 3.25 - 3.80: 47317 3.80 - 4.35: 65640 4.35 - 4.90: 110367 Nonbonded interactions: 254462 Sorted by model distance: nonbonded pdb=" O1G GTP 4 502 " pdb="MG MG 4 503 " model vdw 2.144 2.170 nonbonded pdb=" OG1 THR b 287 " pdb=" OE1 GLU b 290 " model vdw 2.212 3.040 nonbonded pdb=" O ASN b 300 " pdb=" ND2 ASN b 300 " model vdw 2.269 3.120 nonbonded pdb=" OG1 THR 3 287 " pdb=" OE1 GLU 3 290 " model vdw 2.276 3.040 nonbonded pdb=" OG SER a 151 " pdb=" OG1 THR a 193 " model vdw 2.277 3.040 ... (remaining 254457 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 '1' and (resid 1 through 254 or (resid 255 and (name N or name CA or name \ C or name O or name CB )) or resid 256 through 437)) selection = (chain '4' and (resid 1 through 431 or (resid 432 and (name N or name CA or name \ C or name O or name CB )) or resid 433 through 437)) selection = (chain 'A' and (resid 1 through 254 or (resid 255 and (name N or name CA or name \ C or name O or name CB )) or resid 256 through 437)) selection = (chain 'a' and (resid 1 through 431 or (resid 432 and (name N or name CA or name \ C or name O or name CB )) or resid 433 through 437)) } ncs_group { reference = (chain '3' and resid 1 through 501) selection = (chain 'B' and (resid 1 through 436 or resid 501)) selection = (chain 'C' and resid 1 through 501) selection = (chain 'b' and resid 1 through 501) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.040 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.230 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.221 31300 Z= 0.314 Angle : 0.805 14.090 42503 Z= 0.440 Chirality : 0.050 0.480 4646 Planarity : 0.006 0.164 5517 Dihedral : 15.969 176.055 11859 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.12 % Allowed : 7.57 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 3805 helix: 0.08 (0.13), residues: 1622 sheet: 0.61 (0.21), residues: 607 loop : -0.52 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 1 123 TYR 0.011 0.001 TYR B 312 PHE 0.018 0.001 PHE M 236 TRP 0.016 0.002 TRP 4 21 HIS 0.008 0.001 HIS M 360 Details of bonding type rmsd covalent geometry : bond 0.00530 (31300) covalent geometry : angle 0.80452 (42503) hydrogen bonds : bond 0.18638 ( 1384) hydrogen bonds : angle 7.11780 ( 4005) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 350 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 163 LYS cc_start: 0.7175 (mppt) cc_final: 0.6965 (ptpp) REVERT: 3 323 MET cc_start: 0.8659 (ptp) cc_final: 0.8266 (ptp) REVERT: A 377 MET cc_start: 0.7147 (tmm) cc_final: 0.6779 (tmm) REVERT: C 301 MET cc_start: 0.8363 (mmp) cc_final: 0.7908 (mmp) REVERT: M 565 MET cc_start: 0.8235 (tpt) cc_final: 0.7946 (tpt) REVERT: a 1 MET cc_start: 0.8412 (mmt) cc_final: 0.8175 (mmt) REVERT: b 59 ASN cc_start: 0.8667 (t0) cc_final: 0.8152 (t0) REVERT: b 281 GLN cc_start: 0.8515 (pp30) cc_final: 0.8291 (pp30) REVERT: b 323 MET cc_start: 0.7997 (mtm) cc_final: 0.7644 (mtt) outliers start: 4 outliers final: 2 residues processed: 353 average time/residue: 0.2084 time to fit residues: 114.3523 Evaluate side-chains 217 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 215 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 193 THR Chi-restraints excluded: chain M residue 543 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.0470 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 197 HIS 1 300 ASN ** 3 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN A 192 HIS B 8 GLN B 11 GLN B 37 HIS B 101 ASN B 334 ASN C 8 GLN C 11 GLN C 101 ASN M 371 GLN b 300 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.079919 restraints weight = 50077.403| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.02 r_work: 0.3200 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31300 Z= 0.139 Angle : 0.581 10.288 42503 Z= 0.291 Chirality : 0.045 0.224 4646 Planarity : 0.004 0.049 5517 Dihedral : 10.682 171.930 4697 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.50 % Allowed : 9.19 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.14), residues: 3805 helix: 0.66 (0.13), residues: 1678 sheet: 0.44 (0.20), residues: 632 loop : -0.48 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 502 TYR 0.012 0.001 TYR 4 172 PHE 0.030 0.001 PHE 1 255 TRP 0.017 0.002 TRP a 21 HIS 0.009 0.001 HIS M 360 Details of bonding type rmsd covalent geometry : bond 0.00313 (31300) covalent geometry : angle 0.58090 (42503) hydrogen bonds : bond 0.04236 ( 1384) hydrogen bonds : angle 4.64792 ( 4005) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 1 MET cc_start: 0.6516 (tpt) cc_final: 0.6248 (tpt) REVERT: 1 279 GLU cc_start: 0.8395 (pt0) cc_final: 0.8106 (pm20) REVERT: 1 384 ILE cc_start: 0.7751 (tp) cc_final: 0.7539 (tt) REVERT: 3 323 MET cc_start: 0.8801 (ptp) cc_final: 0.8397 (ptp) REVERT: A 377 MET cc_start: 0.7313 (tmm) cc_final: 0.6818 (tmm) REVERT: C 166 MET cc_start: 0.8324 (tpp) cc_final: 0.7880 (mmt) REVERT: C 301 MET cc_start: 0.8570 (mmp) cc_final: 0.8049 (mmp) REVERT: a 117 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8338 (tt) REVERT: a 154 MET cc_start: 0.8363 (mmt) cc_final: 0.8085 (mmm) REVERT: b 59 ASN cc_start: 0.8803 (t0) cc_final: 0.8379 (t0) REVERT: b 323 MET cc_start: 0.8322 (mtm) cc_final: 0.7960 (mtt) REVERT: b 390 ARG cc_start: 0.8021 (mtm180) cc_final: 0.7773 (mtm-85) outliers start: 49 outliers final: 24 residues processed: 267 average time/residue: 0.1731 time to fit residues: 77.1264 Evaluate side-chains 223 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 1 residue 193 THR Chi-restraints excluded: chain 1 residue 413 MET Chi-restraints excluded: chain 1 residue 428 LEU Chi-restraints excluded: chain 3 residue 335 VAL Chi-restraints excluded: chain 4 residue 9 VAL Chi-restraints excluded: chain 4 residue 82 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 506 THR Chi-restraints excluded: chain M residue 589 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 323 VAL Chi-restraints excluded: chain a residue 361 THR Chi-restraints excluded: chain b residue 37 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 253 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 332 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 295 optimal weight: 7.9990 chunk 201 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 205 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 chunk 257 optimal weight: 20.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 50 ASN 3 6 HIS 3 133 GLN 3 350 ASN A 380 ASN B 37 HIS B 281 GLN C 101 ASN M 233 ASN M 560 ASN b 300 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.119312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.089489 restraints weight = 53229.397| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.79 r_work: 0.3169 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31300 Z= 0.154 Angle : 0.557 9.058 42503 Z= 0.279 Chirality : 0.044 0.189 4646 Planarity : 0.004 0.051 5517 Dihedral : 10.081 170.298 4695 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.74 % Allowed : 10.04 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3805 helix: 0.76 (0.13), residues: 1687 sheet: 0.34 (0.20), residues: 639 loop : -0.51 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 322 TYR 0.014 0.001 TYR B 312 PHE 0.018 0.002 PHE 1 255 TRP 0.013 0.002 TRP 4 21 HIS 0.008 0.001 HIS M 360 Details of bonding type rmsd covalent geometry : bond 0.00359 (31300) covalent geometry : angle 0.55683 (42503) hydrogen bonds : bond 0.04671 ( 1384) hydrogen bonds : angle 4.49231 ( 4005) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 205 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 1 MET cc_start: 0.7322 (tpt) cc_final: 0.7046 (mmt) REVERT: 1 279 GLU cc_start: 0.8309 (pt0) cc_final: 0.7905 (pm20) REVERT: 1 384 ILE cc_start: 0.8025 (tp) cc_final: 0.7737 (tt) REVERT: 3 79 ARG cc_start: 0.8474 (ttp-170) cc_final: 0.8090 (ttp80) REVERT: 3 323 MET cc_start: 0.8754 (ptp) cc_final: 0.8326 (ptp) REVERT: 4 413 MET cc_start: 0.8804 (ttm) cc_final: 0.8445 (mmm) REVERT: 4 432 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.7918 (t80) REVERT: A 31 GLN cc_start: 0.8626 (mt0) cc_final: 0.8382 (pm20) REVERT: A 35 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8909 (mm-40) REVERT: A 255 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7011 (p90) REVERT: C 166 MET cc_start: 0.8298 (tpp) cc_final: 0.7901 (mmt) REVERT: C 301 MET cc_start: 0.8658 (mmp) cc_final: 0.8354 (mmp) REVERT: a 26 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8783 (tp) REVERT: a 117 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8470 (tt) REVERT: a 432 TYR cc_start: 0.9237 (OUTLIER) cc_final: 0.7864 (t80) REVERT: b 59 ASN cc_start: 0.8867 (t0) cc_final: 0.8387 (t0) REVERT: b 259 MET cc_start: 0.8698 (mmm) cc_final: 0.8350 (mmm) outliers start: 57 outliers final: 38 residues processed: 254 average time/residue: 0.1749 time to fit residues: 74.0629 Evaluate side-chains 226 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 1 residue 193 THR Chi-restraints excluded: chain 1 residue 327 ASP Chi-restraints excluded: chain 1 residue 379 SER Chi-restraints excluded: chain 1 residue 413 MET Chi-restraints excluded: chain 1 residue 428 LEU Chi-restraints excluded: chain 3 residue 120 ASP Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 328 VAL Chi-restraints excluded: chain 4 residue 9 VAL Chi-restraints excluded: chain 4 residue 82 THR Chi-restraints excluded: chain 4 residue 101 ASN Chi-restraints excluded: chain 4 residue 130 THR Chi-restraints excluded: chain 4 residue 391 LEU Chi-restraints excluded: chain 4 residue 432 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 589 VAL Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 323 VAL Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain a residue 361 THR Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain a residue 432 TYR Chi-restraints excluded: chain b residue 37 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 207 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 235 optimal weight: 7.9990 chunk 181 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 356 optimal weight: 4.9990 chunk 308 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 266 HIS B 37 HIS C 101 ASN b 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.119552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.089455 restraints weight = 52539.232| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.72 r_work: 0.3187 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31300 Z= 0.123 Angle : 0.515 7.666 42503 Z= 0.255 Chirality : 0.043 0.206 4646 Planarity : 0.004 0.052 5517 Dihedral : 9.818 172.333 4695 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.74 % Allowed : 10.83 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3805 helix: 0.92 (0.13), residues: 1685 sheet: 0.32 (0.20), residues: 639 loop : -0.47 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 322 TYR 0.016 0.001 TYR C 36 PHE 0.017 0.001 PHE 1 255 TRP 0.013 0.001 TRP 1 21 HIS 0.008 0.001 HIS M 360 Details of bonding type rmsd covalent geometry : bond 0.00282 (31300) covalent geometry : angle 0.51467 (42503) hydrogen bonds : bond 0.03781 ( 1384) hydrogen bonds : angle 4.29264 ( 4005) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: 1 1 MET cc_start: 0.7227 (tpt) cc_final: 0.6477 (mmt) REVERT: 1 384 ILE cc_start: 0.7916 (tp) cc_final: 0.7705 (tt) REVERT: 1 413 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7769 (ttt) REVERT: 3 79 ARG cc_start: 0.8390 (ttp-170) cc_final: 0.8010 (ttp80) REVERT: 3 323 MET cc_start: 0.8710 (ptp) cc_final: 0.8266 (ptp) REVERT: 4 432 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.7962 (t80) REVERT: A 31 GLN cc_start: 0.8610 (mt0) cc_final: 0.8104 (mp-120) REVERT: A 255 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.6775 (p90) REVERT: C 166 MET cc_start: 0.8295 (tpp) cc_final: 0.7957 (mmt) REVERT: C 301 MET cc_start: 0.8615 (mmp) cc_final: 0.8304 (mmp) REVERT: M 263 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7413 (mp) REVERT: a 26 LEU cc_start: 0.8968 (tp) cc_final: 0.8651 (tp) REVERT: a 117 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8422 (tt) REVERT: a 432 TYR cc_start: 0.9200 (OUTLIER) cc_final: 0.7947 (t80) REVERT: b 59 ASN cc_start: 0.8852 (t0) cc_final: 0.8358 (t0) REVERT: b 259 MET cc_start: 0.8681 (mmm) cc_final: 0.8440 (mmm) REVERT: b 390 ARG cc_start: 0.7945 (mtm180) cc_final: 0.7456 (mtm180) outliers start: 57 outliers final: 32 residues processed: 241 average time/residue: 0.1719 time to fit residues: 69.9091 Evaluate side-chains 221 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 1 residue 193 THR Chi-restraints excluded: chain 1 residue 379 SER Chi-restraints excluded: chain 1 residue 413 MET Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 335 VAL Chi-restraints excluded: chain 4 residue 9 VAL Chi-restraints excluded: chain 4 residue 82 THR Chi-restraints excluded: chain 4 residue 101 ASN Chi-restraints excluded: chain 4 residue 130 THR Chi-restraints excluded: chain 4 residue 152 LEU Chi-restraints excluded: chain 4 residue 391 LEU Chi-restraints excluded: chain 4 residue 432 TYR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 589 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 73 THR Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 323 VAL Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain a residue 367 ASP Chi-restraints excluded: chain a residue 432 TYR Chi-restraints excluded: chain b residue 37 HIS Chi-restraints excluded: chain b residue 323 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 45 optimal weight: 7.9990 chunk 214 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 377 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 235 optimal weight: 0.8980 chunk 371 optimal weight: 0.9990 chunk 375 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 GLN b 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.118284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.088094 restraints weight = 53011.236| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.72 r_work: 0.3168 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31300 Z= 0.143 Angle : 0.524 7.338 42503 Z= 0.260 Chirality : 0.044 0.207 4646 Planarity : 0.004 0.064 5517 Dihedral : 9.695 174.576 4695 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.23 % Allowed : 10.77 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3805 helix: 0.94 (0.13), residues: 1686 sheet: 0.38 (0.20), residues: 623 loop : -0.51 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 339 TYR 0.013 0.001 TYR a 357 PHE 0.016 0.001 PHE M 236 TRP 0.012 0.001 TRP 1 21 HIS 0.008 0.001 HIS M 360 Details of bonding type rmsd covalent geometry : bond 0.00336 (31300) covalent geometry : angle 0.52383 (42503) hydrogen bonds : bond 0.04015 ( 1384) hydrogen bonds : angle 4.30880 ( 4005) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 188 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: 1 1 MET cc_start: 0.7414 (tpt) cc_final: 0.6698 (mmt) REVERT: 1 384 ILE cc_start: 0.7922 (tp) cc_final: 0.7693 (tt) REVERT: 3 79 ARG cc_start: 0.8408 (ttp-170) cc_final: 0.8003 (ttp80) REVERT: 3 323 MET cc_start: 0.8757 (ptp) cc_final: 0.8307 (ptp) REVERT: 4 432 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.7783 (t80) REVERT: A 31 GLN cc_start: 0.8497 (mt0) cc_final: 0.8034 (mp10) REVERT: A 117 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8345 (tt) REVERT: A 255 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.6806 (p90) REVERT: A 339 ARG cc_start: 0.8464 (mmp-170) cc_final: 0.8261 (mmm160) REVERT: A 398 MET cc_start: 0.9097 (ttm) cc_final: 0.8762 (mtp) REVERT: B 42 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8944 (mm) REVERT: B 259 MET cc_start: 0.8597 (mmm) cc_final: 0.8281 (mtp) REVERT: C 166 MET cc_start: 0.8254 (tpp) cc_final: 0.7940 (mmt) REVERT: C 269 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8125 (mtp) REVERT: C 301 MET cc_start: 0.8635 (mmp) cc_final: 0.8304 (mmp) REVERT: a 26 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8661 (tp) REVERT: a 117 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8443 (tt) REVERT: a 432 TYR cc_start: 0.9219 (OUTLIER) cc_final: 0.7922 (t80) REVERT: b 59 ASN cc_start: 0.8835 (t0) cc_final: 0.8333 (t0) outliers start: 73 outliers final: 47 residues processed: 253 average time/residue: 0.1744 time to fit residues: 74.3500 Evaluate side-chains 238 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 1 residue 193 THR Chi-restraints excluded: chain 1 residue 379 SER Chi-restraints excluded: chain 1 residue 413 MET Chi-restraints excluded: chain 1 residue 428 LEU Chi-restraints excluded: chain 3 residue 120 ASP Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 291 LEU Chi-restraints excluded: chain 3 residue 328 VAL Chi-restraints excluded: chain 4 residue 3 GLU Chi-restraints excluded: chain 4 residue 9 VAL Chi-restraints excluded: chain 4 residue 82 THR Chi-restraints excluded: chain 4 residue 130 THR Chi-restraints excluded: chain 4 residue 152 LEU Chi-restraints excluded: chain 4 residue 391 LEU Chi-restraints excluded: chain 4 residue 432 TYR Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 395 LYS Chi-restraints excluded: chain M residue 413 VAL Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 501 GLU Chi-restraints excluded: chain M residue 589 VAL Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 73 THR Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 323 VAL Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain a residue 432 TYR Chi-restraints excluded: chain b residue 37 HIS Chi-restraints excluded: chain b residue 133 GLN Chi-restraints excluded: chain b residue 323 MET Chi-restraints excluded: chain b residue 328 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 160 optimal weight: 20.0000 chunk 375 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 323 optimal weight: 5.9990 chunk 223 optimal weight: 8.9990 chunk 166 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 271 optimal weight: 6.9990 chunk 352 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 18 ASN 1 139 HIS 4 50 ASN 4 266 HIS A 380 ASN C 336 GLN C 350 ASN a 406 HIS b 300 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.107879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.079775 restraints weight = 53469.470| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.84 r_work: 0.3132 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 31300 Z= 0.284 Angle : 0.648 7.819 42503 Z= 0.328 Chirality : 0.048 0.237 4646 Planarity : 0.005 0.055 5517 Dihedral : 10.072 177.543 4695 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.69 % Allowed : 11.26 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3805 helix: 0.60 (0.13), residues: 1663 sheet: 0.16 (0.20), residues: 648 loop : -0.71 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 322 TYR 0.019 0.002 TYR A 312 PHE 0.023 0.002 PHE a 135 TRP 0.013 0.002 TRP 1 21 HIS 0.009 0.001 HIS M 360 Details of bonding type rmsd covalent geometry : bond 0.00680 (31300) covalent geometry : angle 0.64753 (42503) hydrogen bonds : bond 0.05383 ( 1384) hydrogen bonds : angle 4.77419 ( 4005) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 178 time to evaluate : 1.247 Fit side-chains REVERT: 1 313 MET cc_start: 0.9075 (mtt) cc_final: 0.8799 (mtp) REVERT: 3 79 ARG cc_start: 0.8385 (ttp-170) cc_final: 0.8140 (ttp80) REVERT: 3 322 ARG cc_start: 0.8750 (mtp85) cc_final: 0.8511 (mmm160) REVERT: 3 323 MET cc_start: 0.8867 (ptp) cc_final: 0.8307 (ptp) REVERT: 4 378 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8878 (mt) REVERT: A 117 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8470 (tt) REVERT: A 205 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8555 (t0) REVERT: A 255 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7063 (p90) REVERT: A 339 ARG cc_start: 0.8386 (mmp-170) cc_final: 0.8140 (mmm160) REVERT: B 42 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8968 (mm) REVERT: C 166 MET cc_start: 0.8349 (tpp) cc_final: 0.8111 (mmt) REVERT: C 301 MET cc_start: 0.8710 (mmp) cc_final: 0.8214 (mmp) REVERT: M 263 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7466 (mp) REVERT: a 26 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8781 (tp) REVERT: a 117 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8567 (tt) REVERT: a 432 TYR cc_start: 0.9272 (OUTLIER) cc_final: 0.7817 (t80) REVERT: b 59 ASN cc_start: 0.8837 (t0) cc_final: 0.8330 (t0) outliers start: 88 outliers final: 56 residues processed: 253 average time/residue: 0.1789 time to fit residues: 76.9051 Evaluate side-chains 238 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 1 residue 340 SER Chi-restraints excluded: chain 1 residue 379 SER Chi-restraints excluded: chain 1 residue 413 MET Chi-restraints excluded: chain 1 residue 428 LEU Chi-restraints excluded: chain 3 residue 120 ASP Chi-restraints excluded: chain 3 residue 145 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 269 MET Chi-restraints excluded: chain 3 residue 291 LEU Chi-restraints excluded: chain 3 residue 328 VAL Chi-restraints excluded: chain 4 residue 3 GLU Chi-restraints excluded: chain 4 residue 9 VAL Chi-restraints excluded: chain 4 residue 82 THR Chi-restraints excluded: chain 4 residue 101 ASN Chi-restraints excluded: chain 4 residue 130 THR Chi-restraints excluded: chain 4 residue 375 VAL Chi-restraints excluded: chain 4 residue 378 LEU Chi-restraints excluded: chain 4 residue 391 LEU Chi-restraints excluded: chain 4 residue 432 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 395 LYS Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 501 GLU Chi-restraints excluded: chain M residue 589 VAL Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 73 THR Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 182 VAL Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain a residue 361 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 432 TYR Chi-restraints excluded: chain b residue 37 HIS Chi-restraints excluded: chain b residue 133 GLN Chi-restraints excluded: chain b residue 323 MET Chi-restraints excluded: chain b residue 328 VAL Chi-restraints excluded: chain b residue 335 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 319 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 299 optimal weight: 3.9990 chunk 258 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 283 HIS C 6 HIS C 101 ASN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.111227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.081652 restraints weight = 53175.154| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.97 r_work: 0.3172 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31300 Z= 0.151 Angle : 0.537 7.297 42503 Z= 0.268 Chirality : 0.044 0.211 4646 Planarity : 0.004 0.052 5517 Dihedral : 9.799 179.825 4694 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.23 % Allowed : 11.50 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3805 helix: 0.84 (0.13), residues: 1668 sheet: 0.13 (0.20), residues: 620 loop : -0.66 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 322 TYR 0.021 0.001 TYR C 36 PHE 0.017 0.001 PHE M 236 TRP 0.014 0.001 TRP 1 21 HIS 0.007 0.001 HIS M 360 Details of bonding type rmsd covalent geometry : bond 0.00358 (31300) covalent geometry : angle 0.53651 (42503) hydrogen bonds : bond 0.04115 ( 1384) hydrogen bonds : angle 4.43375 ( 4005) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 180 time to evaluate : 1.102 Fit side-chains REVERT: 1 1 MET cc_start: 0.7223 (tpt) cc_final: 0.6903 (mmm) REVERT: 1 313 MET cc_start: 0.9030 (mtt) cc_final: 0.8792 (mtp) REVERT: 3 79 ARG cc_start: 0.8362 (ttp-170) cc_final: 0.8131 (ttp80) REVERT: 3 323 MET cc_start: 0.8799 (ptp) cc_final: 0.8269 (ptp) REVERT: 4 378 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8848 (mt) REVERT: 4 432 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.7727 (t80) REVERT: A 117 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8480 (tt) REVERT: A 205 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8497 (t0) REVERT: A 255 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.6636 (p90) REVERT: A 313 MET cc_start: 0.8987 (mtm) cc_final: 0.8759 (mtt) REVERT: A 339 ARG cc_start: 0.8348 (mmp-170) cc_final: 0.8101 (mmm160) REVERT: B 42 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8876 (mm) REVERT: B 259 MET cc_start: 0.8602 (mmm) cc_final: 0.8352 (mtp) REVERT: C 301 MET cc_start: 0.8672 (mmp) cc_final: 0.8292 (mmp) REVERT: M 263 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7441 (mp) REVERT: a 26 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8755 (tp) REVERT: a 117 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8508 (tt) REVERT: a 432 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.7850 (t80) REVERT: b 59 ASN cc_start: 0.8840 (t0) cc_final: 0.8329 (t0) REVERT: b 390 ARG cc_start: 0.7997 (mtm180) cc_final: 0.7568 (mtm180) outliers start: 73 outliers final: 54 residues processed: 243 average time/residue: 0.1808 time to fit residues: 73.5915 Evaluate side-chains 240 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 176 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 1 residue 200 CYS Chi-restraints excluded: chain 1 residue 375 VAL Chi-restraints excluded: chain 1 residue 379 SER Chi-restraints excluded: chain 1 residue 413 MET Chi-restraints excluded: chain 1 residue 428 LEU Chi-restraints excluded: chain 3 residue 94 PHE Chi-restraints excluded: chain 3 residue 120 ASP Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 291 LEU Chi-restraints excluded: chain 3 residue 328 VAL Chi-restraints excluded: chain 4 residue 3 GLU Chi-restraints excluded: chain 4 residue 9 VAL Chi-restraints excluded: chain 4 residue 73 THR Chi-restraints excluded: chain 4 residue 82 THR Chi-restraints excluded: chain 4 residue 130 THR Chi-restraints excluded: chain 4 residue 375 VAL Chi-restraints excluded: chain 4 residue 378 LEU Chi-restraints excluded: chain 4 residue 391 LEU Chi-restraints excluded: chain 4 residue 432 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 425 MET Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 395 LYS Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 501 GLU Chi-restraints excluded: chain M residue 589 VAL Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 73 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 151 SER Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain a residue 361 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 432 TYR Chi-restraints excluded: chain b residue 37 HIS Chi-restraints excluded: chain b residue 133 GLN Chi-restraints excluded: chain b residue 300 ASN Chi-restraints excluded: chain b residue 323 MET Chi-restraints excluded: chain b residue 335 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 201 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 134 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 367 optimal weight: 0.0000 overall best weight: 2.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 HIS C 101 ASN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.100830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.076597 restraints weight = 52343.621| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.91 r_work: 0.3155 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 31300 Z= 0.189 Angle : 0.565 7.203 42503 Z= 0.282 Chirality : 0.045 0.221 4646 Planarity : 0.004 0.052 5517 Dihedral : 9.766 177.272 4694 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.35 % Allowed : 11.87 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3805 helix: 0.77 (0.13), residues: 1679 sheet: 0.07 (0.20), residues: 620 loop : -0.69 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 322 TYR 0.033 0.001 TYR C 36 PHE 0.018 0.002 PHE M 236 TRP 0.013 0.002 TRP 1 21 HIS 0.008 0.001 HIS M 360 Details of bonding type rmsd covalent geometry : bond 0.00453 (31300) covalent geometry : angle 0.56455 (42503) hydrogen bonds : bond 0.04429 ( 1384) hydrogen bonds : angle 4.48757 ( 4005) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 178 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: 1 1 MET cc_start: 0.7161 (tpt) cc_final: 0.6870 (mmm) REVERT: 1 47 ASP cc_start: 0.7763 (t70) cc_final: 0.7375 (t0) REVERT: 1 313 MET cc_start: 0.9056 (mtt) cc_final: 0.8814 (mtp) REVERT: 1 327 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8118 (m-30) REVERT: 3 79 ARG cc_start: 0.8363 (ttp-170) cc_final: 0.8123 (ttp80) REVERT: 3 323 MET cc_start: 0.8844 (ptp) cc_final: 0.8276 (ptp) REVERT: 4 378 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8874 (mt) REVERT: 4 432 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.7700 (t80) REVERT: A 117 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8542 (tt) REVERT: A 205 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8501 (t0) REVERT: A 255 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.6663 (p90) REVERT: A 339 ARG cc_start: 0.8323 (mmp-170) cc_final: 0.8089 (mmm160) REVERT: B 42 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8861 (mm) REVERT: B 259 MET cc_start: 0.8622 (mmm) cc_final: 0.8382 (mtp) REVERT: C 301 MET cc_start: 0.8690 (mmp) cc_final: 0.8280 (mmp) REVERT: a 26 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8780 (tp) REVERT: a 117 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8515 (tt) REVERT: a 432 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.7899 (t80) REVERT: b 59 ASN cc_start: 0.8848 (t0) cc_final: 0.8329 (t0) outliers start: 77 outliers final: 56 residues processed: 246 average time/residue: 0.1775 time to fit residues: 73.5560 Evaluate side-chains 240 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 174 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 1 residue 200 CYS Chi-restraints excluded: chain 1 residue 327 ASP Chi-restraints excluded: chain 1 residue 340 SER Chi-restraints excluded: chain 1 residue 375 VAL Chi-restraints excluded: chain 1 residue 379 SER Chi-restraints excluded: chain 1 residue 413 MET Chi-restraints excluded: chain 1 residue 428 LEU Chi-restraints excluded: chain 3 residue 94 PHE Chi-restraints excluded: chain 3 residue 120 ASP Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 291 LEU Chi-restraints excluded: chain 3 residue 328 VAL Chi-restraints excluded: chain 4 residue 3 GLU Chi-restraints excluded: chain 4 residue 9 VAL Chi-restraints excluded: chain 4 residue 73 THR Chi-restraints excluded: chain 4 residue 82 THR Chi-restraints excluded: chain 4 residue 130 THR Chi-restraints excluded: chain 4 residue 375 VAL Chi-restraints excluded: chain 4 residue 378 LEU Chi-restraints excluded: chain 4 residue 391 LEU Chi-restraints excluded: chain 4 residue 432 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 294 LEU Chi-restraints excluded: chain M residue 395 LYS Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 501 GLU Chi-restraints excluded: chain M residue 589 VAL Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 73 THR Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 151 SER Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain a residue 361 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 432 TYR Chi-restraints excluded: chain b residue 37 HIS Chi-restraints excluded: chain b residue 133 GLN Chi-restraints excluded: chain b residue 323 MET Chi-restraints excluded: chain b residue 328 VAL Chi-restraints excluded: chain b residue 335 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 102 optimal weight: 1.9990 chunk 365 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 295 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 355 optimal weight: 0.8980 chunk 247 optimal weight: 10.0000 chunk 351 optimal weight: 2.9990 chunk 318 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 160 optimal weight: 0.0770 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 216 ASN C 6 HIS ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.112058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.083591 restraints weight = 52767.434| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.90 r_work: 0.3156 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31300 Z= 0.114 Angle : 0.511 7.016 42503 Z= 0.253 Chirality : 0.043 0.205 4646 Planarity : 0.004 0.054 5517 Dihedral : 9.478 178.852 4694 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.71 % Allowed : 12.51 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3805 helix: 1.03 (0.13), residues: 1667 sheet: 0.14 (0.20), residues: 620 loop : -0.59 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 1 123 TYR 0.020 0.001 TYR C 36 PHE 0.017 0.001 PHE M 236 TRP 0.014 0.001 TRP 1 21 HIS 0.007 0.001 HIS M 360 Details of bonding type rmsd covalent geometry : bond 0.00260 (31300) covalent geometry : angle 0.51071 (42503) hydrogen bonds : bond 0.03595 ( 1384) hydrogen bonds : angle 4.27196 ( 4005) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: 1 1 MET cc_start: 0.7147 (tpt) cc_final: 0.6864 (mmm) REVERT: 1 313 MET cc_start: 0.9033 (mtt) cc_final: 0.8809 (mtp) REVERT: 3 79 ARG cc_start: 0.8299 (ttp-170) cc_final: 0.8059 (ttp80) REVERT: 3 323 MET cc_start: 0.8739 (ptp) cc_final: 0.8131 (ptp) REVERT: 4 432 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.7779 (t80) REVERT: A 31 GLN cc_start: 0.8337 (mt0) cc_final: 0.7762 (mp10) REVERT: A 117 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8478 (tt) REVERT: A 255 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.6525 (p90) REVERT: A 339 ARG cc_start: 0.8346 (mmp-170) cc_final: 0.8127 (mmm160) REVERT: B 259 MET cc_start: 0.8558 (mmm) cc_final: 0.8350 (mtp) REVERT: C 48 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7379 (ttm170) REVERT: C 75 MET cc_start: 0.8242 (mtp) cc_final: 0.7796 (mtp) REVERT: C 301 MET cc_start: 0.8716 (mmp) cc_final: 0.8476 (mmp) REVERT: a 26 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8743 (tp) REVERT: a 117 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8448 (tt) REVERT: a 432 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.7985 (t80) REVERT: b 59 ASN cc_start: 0.8835 (t0) cc_final: 0.8347 (t0) outliers start: 56 outliers final: 41 residues processed: 238 average time/residue: 0.1808 time to fit residues: 71.5824 Evaluate side-chains 227 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 1 residue 200 CYS Chi-restraints excluded: chain 1 residue 375 VAL Chi-restraints excluded: chain 1 residue 379 SER Chi-restraints excluded: chain 1 residue 428 LEU Chi-restraints excluded: chain 3 residue 120 ASP Chi-restraints excluded: chain 3 residue 291 LEU Chi-restraints excluded: chain 4 residue 9 VAL Chi-restraints excluded: chain 4 residue 73 THR Chi-restraints excluded: chain 4 residue 82 THR Chi-restraints excluded: chain 4 residue 130 THR Chi-restraints excluded: chain 4 residue 375 VAL Chi-restraints excluded: chain 4 residue 391 LEU Chi-restraints excluded: chain 4 residue 432 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 294 LEU Chi-restraints excluded: chain M residue 395 LYS Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 589 VAL Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 73 THR Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 432 TYR Chi-restraints excluded: chain b residue 133 GLN Chi-restraints excluded: chain b residue 323 MET Chi-restraints excluded: chain b residue 328 VAL Chi-restraints excluded: chain b residue 335 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 116 optimal weight: 0.8980 chunk 226 optimal weight: 0.6980 chunk 188 optimal weight: 0.0030 chunk 287 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.111573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.083609 restraints weight = 52632.197| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.90 r_work: 0.3163 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31300 Z= 0.113 Angle : 0.510 7.424 42503 Z= 0.252 Chirality : 0.043 0.207 4646 Planarity : 0.004 0.054 5517 Dihedral : 9.285 178.063 4694 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.56 % Allowed : 12.94 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.14), residues: 3805 helix: 1.14 (0.13), residues: 1667 sheet: 0.18 (0.20), residues: 620 loop : -0.54 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 264 TYR 0.030 0.001 TYR C 36 PHE 0.018 0.001 PHE M 236 TRP 0.021 0.001 TRP A 388 HIS 0.007 0.001 HIS M 360 Details of bonding type rmsd covalent geometry : bond 0.00258 (31300) covalent geometry : angle 0.50956 (42503) hydrogen bonds : bond 0.03597 ( 1384) hydrogen bonds : angle 4.22133 ( 4005) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7610 Ramachandran restraints generated. 3805 Oldfield, 0 Emsley, 3805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: 1 1 MET cc_start: 0.7165 (tpt) cc_final: 0.6946 (mmm) REVERT: 1 313 MET cc_start: 0.9014 (mtt) cc_final: 0.8795 (mtp) REVERT: 3 79 ARG cc_start: 0.8319 (ttp-170) cc_final: 0.8089 (ttp80) REVERT: 3 323 MET cc_start: 0.8746 (ptp) cc_final: 0.8171 (ptp) REVERT: 4 432 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.7755 (t80) REVERT: A 31 GLN cc_start: 0.8317 (mt0) cc_final: 0.7734 (mp10) REVERT: A 117 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8477 (tt) REVERT: A 255 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.6479 (p90) REVERT: A 313 MET cc_start: 0.9181 (mtm) cc_final: 0.8895 (mtp) REVERT: A 339 ARG cc_start: 0.8295 (mmp-170) cc_final: 0.8068 (mmm160) REVERT: B 75 MET cc_start: 0.8556 (mmm) cc_final: 0.8153 (mmm) REVERT: C 48 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7309 (ttm170) REVERT: C 149 MET cc_start: 0.8196 (ttt) cc_final: 0.7863 (ttt) REVERT: C 301 MET cc_start: 0.8730 (mmp) cc_final: 0.8521 (mmp) REVERT: a 26 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8739 (tp) REVERT: a 36 MET cc_start: 0.8448 (mtp) cc_final: 0.8051 (mtp) REVERT: a 117 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8449 (tt) REVERT: a 432 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.8007 (t80) REVERT: b 59 ASN cc_start: 0.8806 (t0) cc_final: 0.8331 (t0) outliers start: 51 outliers final: 40 residues processed: 233 average time/residue: 0.1826 time to fit residues: 70.5475 Evaluate side-chains 224 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 82 THR Chi-restraints excluded: chain 1 residue 375 VAL Chi-restraints excluded: chain 1 residue 379 SER Chi-restraints excluded: chain 1 residue 428 LEU Chi-restraints excluded: chain 3 residue 120 ASP Chi-restraints excluded: chain 3 residue 291 LEU Chi-restraints excluded: chain 4 residue 9 VAL Chi-restraints excluded: chain 4 residue 73 THR Chi-restraints excluded: chain 4 residue 82 THR Chi-restraints excluded: chain 4 residue 130 THR Chi-restraints excluded: chain 4 residue 391 LEU Chi-restraints excluded: chain 4 residue 432 TYR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 294 LEU Chi-restraints excluded: chain M residue 395 LYS Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 589 VAL Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 73 THR Chi-restraints excluded: chain a residue 94 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain a residue 391 LEU Chi-restraints excluded: chain a residue 432 TYR Chi-restraints excluded: chain b residue 133 GLN Chi-restraints excluded: chain b residue 300 ASN Chi-restraints excluded: chain b residue 323 MET Chi-restraints excluded: chain b residue 328 VAL Chi-restraints excluded: chain b residue 335 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 49 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 267 optimal weight: 0.0980 chunk 234 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 225 optimal weight: 0.8980 chunk 237 optimal weight: 0.7980 chunk 334 optimal weight: 4.9990 chunk 301 optimal weight: 0.8980 chunk 351 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.113097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.085409 restraints weight = 52563.420| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.91 r_work: 0.3194 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 31300 Z= 0.092 Angle : 0.500 7.547 42503 Z= 0.247 Chirality : 0.042 0.200 4646 Planarity : 0.004 0.055 5517 Dihedral : 9.125 179.306 4694 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.28 % Allowed : 13.15 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3805 helix: 1.25 (0.13), residues: 1667 sheet: 0.25 (0.20), residues: 639 loop : -0.47 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 1 123 TYR 0.030 0.001 TYR C 36 PHE 0.017 0.001 PHE M 236 TRP 0.019 0.001 TRP A 388 HIS 0.006 0.001 HIS M 360 Details of bonding type rmsd covalent geometry : bond 0.00195 (31300) covalent geometry : angle 0.50044 (42503) hydrogen bonds : bond 0.03235 ( 1384) hydrogen bonds : angle 4.11733 ( 4005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7148.56 seconds wall clock time: 123 minutes 11.98 seconds (7391.98 seconds total)