Starting phenix.real_space_refine on Thu Mar 5 12:05:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wf4_32460/03_2026/7wf4_32460_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wf4_32460/03_2026/7wf4_32460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wf4_32460/03_2026/7wf4_32460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wf4_32460/03_2026/7wf4_32460.map" model { file = "/net/cci-nas-00/data/ceres_data/7wf4_32460/03_2026/7wf4_32460_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wf4_32460/03_2026/7wf4_32460_neut.cif" } resolution = 3.4 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= 0.015 sd= 1.348 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 K 3 8.98 5 P 12 5.49 5 S 120 5.16 5 C 14196 2.51 5 N 3736 2.21 5 O 4076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.02s 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: 22143 Number of models: 1 Model: "" Number of chains: 25 Chain: "D" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2017 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 242} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "O" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "o" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2017 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 242} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2017 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 242} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2017 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 242} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "I" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "M" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "o" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.37, per 1000 atoms: 0.24 Number of scatterers: 22143 At special positions: 0 Unit cell: (130.416, 131.274, 163.02, 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) K 3 19.00 S 120 16.00 P 12 15.00 O 4076 8.00 N 3736 7.00 C 14196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS J 101 " - pdb=" SG CYS J 123 " distance=2.03 Simple disulfide: pdb=" SG CYS N 101 " - pdb=" SG CYS N 123 " distance=2.03 Simple disulfide: pdb=" SG CYS O 101 " - pdb=" SG CYS O 123 " distance=2.04 Simple disulfide: pdb=" SG CYS P 101 " - pdb=" SG CYS P 123 " distance=2.03 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: 1.88 Conformation dependent library (CDL) restraints added in 1.2 seconds 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5104 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 12 sheets defined 60.9% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'D' and resid 216 through 226 Processing helix chain 'D' and resid 230 through 254 Processing helix chain 'D' and resid 293 through 316 removed outlier: 3.552A pdb=" N VAL D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL D 298 " --> pdb=" O PRO D 294 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 316 " --> pdb=" O VAL D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 326 removed outlier: 3.536A pdb=" N PHE D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 353 Proline residue: D 338 - end of helix removed outlier: 3.630A pdb=" N ALA D 348 " --> pdb=" O GLY D 344 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 370 removed outlier: 3.726A pdb=" N LEU D 368 " --> pdb=" O ARG D 364 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 369 " --> pdb=" O VAL D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 380 removed outlier: 3.544A pdb=" N ILE D 374 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 394 removed outlier: 3.873A pdb=" N GLN D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 419 Processing helix chain 'D' and resid 430 through 443 removed outlier: 3.714A pdb=" N PHE D 435 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TRP D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TRP D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR D 443 " --> pdb=" O VAL D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 473 removed outlier: 3.564A pdb=" N VAL D 460 " --> pdb=" O GLY D 456 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.655A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 78 Processing helix chain 'G' and resid 89 through 92 removed outlier: 3.761A pdb=" N ALA G 92 " --> pdb=" O VAL G 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 89 through 92' Processing helix chain 'G' and resid 93 through 107 removed outlier: 3.938A pdb=" N LYS G 105 " --> pdb=" O ASN G 101 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY G 107 " --> pdb=" O ILE G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.558A pdb=" N SER G 112 " --> pdb=" O ARG G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 129 removed outlier: 3.519A pdb=" N GLU G 128 " --> pdb=" O ALA G 125 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG G 129 " --> pdb=" O GLU G 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 125 through 129' Processing helix chain 'G' and resid 132 through 148 Processing helix chain 'G' and resid 165 through 179 removed outlier: 3.547A pdb=" N THR G 169 " --> pdb=" O PRO G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 205 Processing helix chain 'G' and resid 222 through 228 removed outlier: 3.570A pdb=" N GLU G 226 " --> pdb=" O ARG G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 236 removed outlier: 3.985A pdb=" N LEU G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 278 Processing helix chain 'G' and resid 280 through 300 removed outlier: 4.089A pdb=" N ARG G 284 " --> pdb=" O GLU G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 311 removed outlier: 3.868A pdb=" N CYS G 311 " --> pdb=" O ALA G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 335 removed outlier: 3.846A pdb=" N GLY G 335 " --> pdb=" O MET G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 356 Processing helix chain 'I' and resid 65 through 78 Processing helix chain 'I' and resid 89 through 92 removed outlier: 3.763A pdb=" N ALA I 92 " --> pdb=" O VAL I 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 89 through 92' Processing helix chain 'I' and resid 93 through 107 removed outlier: 3.937A pdb=" N LYS I 105 " --> pdb=" O ASN I 101 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY I 107 " --> pdb=" O ILE I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 113 removed outlier: 3.558A pdb=" N SER I 112 " --> pdb=" O ARG I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 129 removed outlier: 3.518A pdb=" N GLU I 128 " --> pdb=" O ALA I 125 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG I 129 " --> pdb=" O GLU I 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 125 through 129' Processing helix chain 'I' and resid 132 through 148 Processing helix chain 'I' and resid 165 through 179 removed outlier: 3.547A pdb=" N THR I 169 " --> pdb=" O PRO I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 205 Processing helix chain 'I' and resid 222 through 228 removed outlier: 3.570A pdb=" N GLU I 226 " --> pdb=" O ARG I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 236 removed outlier: 3.985A pdb=" N LEU I 232 " --> pdb=" O GLN I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 278 Processing helix chain 'I' and resid 280 through 300 removed outlier: 4.089A pdb=" N ARG I 284 " --> pdb=" O GLU I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 311 removed outlier: 3.867A pdb=" N CYS I 311 " --> pdb=" O ALA I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 335 removed outlier: 3.847A pdb=" N GLY I 335 " --> pdb=" O MET I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 344 through 356 Processing helix chain 'J' and resid 119 through 123 Processing helix chain 'J' and resid 136 through 138 No H-bonds generated for 'chain 'J' and resid 136 through 138' Processing helix chain 'J' and resid 155 through 166 removed outlier: 3.640A pdb=" N ILE J 159 " --> pdb=" O SER J 155 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR J 163 " --> pdb=" O ILE J 159 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY J 166 " --> pdb=" O TYR J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 188 Processing helix chain 'J' and resid 190 through 201 removed outlier: 3.502A pdb=" N MET J 194 " --> pdb=" O GLY J 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 78 Processing helix chain 'M' and resid 89 through 92 removed outlier: 3.761A pdb=" N ALA M 92 " --> pdb=" O VAL M 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 89 through 92' Processing helix chain 'M' and resid 93 through 107 removed outlier: 3.937A pdb=" N LYS M 105 " --> pdb=" O ASN M 101 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY M 107 " --> pdb=" O ILE M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 113 removed outlier: 3.557A pdb=" N SER M 112 " --> pdb=" O ARG M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 129 removed outlier: 3.518A pdb=" N GLU M 128 " --> pdb=" O ALA M 125 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG M 129 " --> pdb=" O GLU M 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 125 through 129' Processing helix chain 'M' and resid 132 through 148 Processing helix chain 'M' and resid 165 through 179 removed outlier: 3.548A pdb=" N THR M 169 " --> pdb=" O PRO M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 205 Processing helix chain 'M' and resid 222 through 228 removed outlier: 3.570A pdb=" N GLU M 226 " --> pdb=" O ARG M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 236 removed outlier: 3.986A pdb=" N LEU M 232 " --> pdb=" O GLN M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 278 Processing helix chain 'M' and resid 280 through 300 removed outlier: 4.089A pdb=" N ARG M 284 " --> pdb=" O GLU M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 311 removed outlier: 3.866A pdb=" N CYS M 311 " --> pdb=" O ALA M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 326 through 335 removed outlier: 3.847A pdb=" N GLY M 335 " --> pdb=" O MET M 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 344 through 356 Processing helix chain 'N' and resid 119 through 123 Processing helix chain 'N' and resid 136 through 138 No H-bonds generated for 'chain 'N' and resid 136 through 138' Processing helix chain 'N' and resid 155 through 166 removed outlier: 3.640A pdb=" N ILE N 159 " --> pdb=" O SER N 155 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR N 163 " --> pdb=" O ILE N 159 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY N 166 " --> pdb=" O TYR N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 188 Processing helix chain 'N' and resid 190 through 201 removed outlier: 3.503A pdb=" N MET N 194 " --> pdb=" O GLY N 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 123 Processing helix chain 'O' and resid 136 through 138 No H-bonds generated for 'chain 'O' and resid 136 through 138' Processing helix chain 'O' and resid 155 through 166 removed outlier: 3.641A pdb=" N ILE O 159 " --> pdb=" O SER O 155 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR O 163 " --> pdb=" O ILE O 159 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY O 166 " --> pdb=" O TYR O 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 188 Processing helix chain 'O' and resid 190 through 201 removed outlier: 3.503A pdb=" N MET O 194 " --> pdb=" O GLY O 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 119 through 123 Processing helix chain 'P' and resid 136 through 138 No H-bonds generated for 'chain 'P' and resid 136 through 138' Processing helix chain 'P' and resid 155 through 166 removed outlier: 3.640A pdb=" N ILE P 159 " --> pdb=" O SER P 155 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR P 163 " --> pdb=" O ILE P 159 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY P 166 " --> pdb=" O TYR P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 188 Processing helix chain 'P' and resid 190 through 201 removed outlier: 3.504A pdb=" N MET P 194 " --> pdb=" O GLY P 190 " (cutoff:3.500A) Processing helix chain 'o' and resid 65 through 78 Processing helix chain 'o' and resid 89 through 92 removed outlier: 3.762A pdb=" N ALA o 92 " --> pdb=" O VAL o 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 89 through 92' Processing helix chain 'o' and resid 93 through 107 removed outlier: 3.938A pdb=" N LYS o 105 " --> pdb=" O ASN o 101 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY o 107 " --> pdb=" O ILE o 103 " (cutoff:3.500A) Processing helix chain 'o' and resid 109 through 113 removed outlier: 3.558A pdb=" N SER o 112 " --> pdb=" O ARG o 109 " (cutoff:3.500A) Processing helix chain 'o' and resid 125 through 129 removed outlier: 3.518A pdb=" N GLU o 128 " --> pdb=" O ALA o 125 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG o 129 " --> pdb=" O GLU o 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 125 through 129' Processing helix chain 'o' and resid 132 through 148 Processing helix chain 'o' and resid 165 through 179 removed outlier: 3.548A pdb=" N THR o 169 " --> pdb=" O PRO o 165 " (cutoff:3.500A) Processing helix chain 'o' and resid 191 through 205 Processing helix chain 'o' and resid 222 through 228 removed outlier: 3.570A pdb=" N GLU o 226 " --> pdb=" O ARG o 222 " (cutoff:3.500A) Processing helix chain 'o' and resid 228 through 236 removed outlier: 3.985A pdb=" N LEU o 232 " --> pdb=" O GLN o 228 " (cutoff:3.500A) Processing helix chain 'o' and resid 270 through 278 Processing helix chain 'o' and resid 280 through 300 removed outlier: 4.088A pdb=" N ARG o 284 " --> pdb=" O GLU o 280 " (cutoff:3.500A) Processing helix chain 'o' and resid 302 through 311 removed outlier: 3.867A pdb=" N CYS o 311 " --> pdb=" O ALA o 307 " (cutoff:3.500A) Processing helix chain 'o' and resid 326 through 335 removed outlier: 3.847A pdb=" N GLY o 335 " --> pdb=" O MET o 331 " (cutoff:3.500A) Processing helix chain 'o' and resid 344 through 356 Processing helix chain 'B' and resid 216 through 226 Processing helix chain 'B' and resid 230 through 254 Processing helix chain 'B' and resid 293 through 316 removed outlier: 3.553A pdb=" N VAL B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 316 " --> pdb=" O VAL B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 326 removed outlier: 3.537A pdb=" N PHE B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 353 Proline residue: B 338 - end of helix removed outlier: 3.630A pdb=" N ALA B 348 " --> pdb=" O GLY B 344 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 370 removed outlier: 3.727A pdb=" N LEU B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 380 removed outlier: 3.544A pdb=" N ILE B 374 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 394 removed outlier: 3.873A pdb=" N GLN B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 419 Processing helix chain 'B' and resid 430 through 443 removed outlier: 3.714A pdb=" N PHE B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TRP B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 473 removed outlier: 3.564A pdb=" N VAL B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.654A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 226 Processing helix chain 'F' and resid 230 through 254 Processing helix chain 'F' and resid 293 through 316 removed outlier: 3.552A pdb=" N VAL F 297 " --> pdb=" O ASP F 293 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL F 298 " --> pdb=" O PRO F 294 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU F 299 " --> pdb=" O PHE F 295 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR F 300 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA F 316 " --> pdb=" O VAL F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 326 removed outlier: 3.537A pdb=" N PHE F 323 " --> pdb=" O SER F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 353 Proline residue: F 338 - end of helix removed outlier: 3.630A pdb=" N ALA F 348 " --> pdb=" O GLY F 344 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN F 351 " --> pdb=" O LEU F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 370 removed outlier: 3.726A pdb=" N LEU F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 369 " --> pdb=" O VAL F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 380 removed outlier: 3.543A pdb=" N ILE F 374 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG F 379 " --> pdb=" O LYS F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 394 removed outlier: 3.873A pdb=" N GLN F 385 " --> pdb=" O SER F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 419 Processing helix chain 'F' and resid 430 through 443 removed outlier: 3.715A pdb=" N PHE F 435 " --> pdb=" O ILE F 431 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP F 436 " --> pdb=" O PRO F 432 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TRP F 437 " --> pdb=" O ASP F 433 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 443 " --> pdb=" O VAL F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 473 removed outlier: 3.564A pdb=" N VAL F 460 " --> pdb=" O GLY F 456 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL F 469 " --> pdb=" O ALA F 465 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU F 470 " --> pdb=" O ILE F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 3.656A pdb=" N ILE F 479 " --> pdb=" O PRO F 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 226 Processing helix chain 'H' and resid 230 through 254 Processing helix chain 'H' and resid 293 through 316 removed outlier: 3.552A pdb=" N VAL H 297 " --> pdb=" O ASP H 293 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL H 298 " --> pdb=" O PRO H 294 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU H 299 " --> pdb=" O PHE H 295 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR H 300 " --> pdb=" O PHE H 296 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA H 316 " --> pdb=" O VAL H 312 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 326 removed outlier: 3.536A pdb=" N PHE H 323 " --> pdb=" O SER H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 353 Proline residue: H 338 - end of helix removed outlier: 3.629A pdb=" N ALA H 348 " --> pdb=" O GLY H 344 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN H 351 " --> pdb=" O LEU H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 370 removed outlier: 3.725A pdb=" N LEU H 368 " --> pdb=" O ARG H 364 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 369 " --> pdb=" O VAL H 365 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 380 removed outlier: 3.543A pdb=" N ILE H 374 " --> pdb=" O VAL H 371 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG H 379 " --> pdb=" O LYS H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 394 removed outlier: 3.873A pdb=" N GLN H 385 " --> pdb=" O SER H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 419 Processing helix chain 'H' and resid 430 through 443 removed outlier: 3.714A pdb=" N PHE H 435 " --> pdb=" O ILE H 431 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP H 436 " --> pdb=" O PRO H 432 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TRP H 437 " --> pdb=" O ASP H 433 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR H 443 " --> pdb=" O VAL H 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 473 removed outlier: 3.565A pdb=" N VAL H 460 " --> pdb=" O GLY H 456 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU H 463 " --> pdb=" O ILE H 459 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL H 469 " --> pdb=" O ALA H 465 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU H 470 " --> pdb=" O ILE H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 489 removed outlier: 3.656A pdb=" N ILE H 479 " --> pdb=" O PRO H 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 55 removed outlier: 4.975A pdb=" N LEU G 83 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE G 115 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N PHE G 156 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR G 117 " --> pdb=" O PHE G 156 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP G 153 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLY G 186 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL G 155 " --> pdb=" O GLY G 186 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N SER G 188 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA G 157 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS G 212 " --> pdb=" O TRP G 185 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU G 213 " --> pdb=" O MET G 241 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N TRP G 243 " --> pdb=" O GLU G 213 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA G 215 " --> pdb=" O TRP G 243 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA G 240 " --> pdb=" O SER G 318 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL G 320 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR G 242 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU G 322 " --> pdb=" O THR G 242 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY G 53 " --> pdb=" O LEU G 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'I' and resid 52 through 55 removed outlier: 4.974A pdb=" N LEU I 83 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE I 115 " --> pdb=" O VAL I 154 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N PHE I 156 " --> pdb=" O ILE I 115 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR I 117 " --> pdb=" O PHE I 156 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP I 153 " --> pdb=" O TYR I 184 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLY I 186 " --> pdb=" O ASP I 153 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL I 155 " --> pdb=" O GLY I 186 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER I 188 " --> pdb=" O VAL I 155 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA I 157 " --> pdb=" O SER I 188 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS I 212 " --> pdb=" O TRP I 185 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU I 213 " --> pdb=" O MET I 241 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N TRP I 243 " --> pdb=" O GLU I 213 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA I 215 " --> pdb=" O TRP I 243 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA I 240 " --> pdb=" O SER I 318 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL I 320 " --> pdb=" O ALA I 240 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR I 242 " --> pdb=" O VAL I 320 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU I 322 " --> pdb=" O THR I 242 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY I 53 " --> pdb=" O LEU I 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 113 through 118 removed outlier: 3.576A pdb=" N GLU J 146 " --> pdb=" O ASP J 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 39 through 41 Processing sheet with id=AA7, first strand: chain 'M' and resid 52 through 55 removed outlier: 4.976A pdb=" N LEU M 83 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE M 115 " --> pdb=" O VAL M 154 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N PHE M 156 " --> pdb=" O ILE M 115 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR M 117 " --> pdb=" O PHE M 156 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP M 153 " --> pdb=" O TYR M 184 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLY M 186 " --> pdb=" O ASP M 153 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL M 155 " --> pdb=" O GLY M 186 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER M 188 " --> pdb=" O VAL M 155 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA M 157 " --> pdb=" O SER M 188 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS M 212 " --> pdb=" O TRP M 185 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU M 213 " --> pdb=" O MET M 241 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N TRP M 243 " --> pdb=" O GLU M 213 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA M 215 " --> pdb=" O TRP M 243 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA M 240 " --> pdb=" O SER M 318 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL M 320 " --> pdb=" O ALA M 240 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR M 242 " --> pdb=" O VAL M 320 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU M 322 " --> pdb=" O THR M 242 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY M 53 " --> pdb=" O LEU M 322 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 113 through 118 removed outlier: 3.576A pdb=" N GLU N 146 " --> pdb=" O ASP N 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 113 through 118 removed outlier: 3.576A pdb=" N GLU O 146 " --> pdb=" O ASP O 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 113 through 118 removed outlier: 3.576A pdb=" N GLU P 146 " --> pdb=" O ASP P 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'o' and resid 39 through 41 Processing sheet with id=AB3, first strand: chain 'o' and resid 52 through 55 removed outlier: 4.975A pdb=" N LEU o 83 " --> pdb=" O LEU o 52 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE o 115 " --> pdb=" O VAL o 154 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N PHE o 156 " --> pdb=" O ILE o 115 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR o 117 " --> pdb=" O PHE o 156 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP o 153 " --> pdb=" O TYR o 184 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLY o 186 " --> pdb=" O ASP o 153 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL o 155 " --> pdb=" O GLY o 186 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N SER o 188 " --> pdb=" O VAL o 155 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA o 157 " --> pdb=" O SER o 188 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N CYS o 212 " --> pdb=" O TRP o 185 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU o 213 " --> pdb=" O MET o 241 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N TRP o 243 " --> pdb=" O GLU o 213 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA o 215 " --> pdb=" O TRP o 243 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA o 240 " --> pdb=" O SER o 318 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL o 320 " --> pdb=" O ALA o 240 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR o 242 " --> pdb=" O VAL o 320 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU o 322 " --> pdb=" O THR o 242 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLY o 53 " --> pdb=" O LEU o 322 " (cutoff:3.500A) 1096 hydrogen bonds defined for protein. 3204 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: 3.78 Time building geometry restraints manager: 2.45 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: 3536 1.31 - 1.44: 6180 1.44 - 1.57: 12620 1.57 - 1.70: 20 1.70 - 1.83: 192 Bond restraints: 22548 Sorted by residual: bond pdb=" C1B NAP I 401 " pdb=" C2B NAP I 401 " ideal model delta sigma weight residual 1.528 1.309 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C1B NAP G 401 " pdb=" C2B NAP G 401 " ideal model delta sigma weight residual 1.528 1.309 0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C1B NAP o 401 " pdb=" C2B NAP o 401 " ideal model delta sigma weight residual 1.528 1.310 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C1B NAP M 401 " pdb=" C2B NAP M 401 " ideal model delta sigma weight residual 1.528 1.311 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C4D NAP I 401 " pdb=" O4D NAP I 401 " ideal model delta sigma weight residual 1.447 1.304 0.143 2.00e-02 2.50e+03 5.08e+01 ... (remaining 22543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 29817 2.81 - 5.62: 558 5.62 - 8.43: 114 8.43 - 11.24: 35 11.24 - 14.05: 28 Bond angle restraints: 30552 Sorted by residual: angle pdb=" N GLU B 349 " pdb=" CA GLU B 349 " pdb=" C GLU B 349 " ideal model delta sigma weight residual 111.14 119.64 -8.50 1.08e+00 8.57e-01 6.19e+01 angle pdb=" N GLU F 349 " pdb=" CA GLU F 349 " pdb=" C GLU F 349 " ideal model delta sigma weight residual 111.14 119.59 -8.45 1.08e+00 8.57e-01 6.13e+01 angle pdb=" N GLU D 349 " pdb=" CA GLU D 349 " pdb=" C GLU D 349 " ideal model delta sigma weight residual 111.14 119.59 -8.45 1.08e+00 8.57e-01 6.12e+01 angle pdb=" N GLU H 349 " pdb=" CA GLU H 349 " pdb=" C GLU H 349 " ideal model delta sigma weight residual 111.14 119.56 -8.42 1.08e+00 8.57e-01 6.08e+01 angle pdb=" N MET D 358 " pdb=" CA MET D 358 " pdb=" C MET D 358 " ideal model delta sigma weight residual 110.80 96.75 14.05 2.13e+00 2.20e-01 4.35e+01 ... (remaining 30547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 12187 17.03 - 34.06: 1047 34.06 - 51.09: 260 51.09 - 68.12: 78 68.12 - 85.15: 24 Dihedral angle restraints: 13596 sinusoidal: 5656 harmonic: 7940 Sorted by residual: dihedral pdb=" CA TRP G 57 " pdb=" C TRP G 57 " pdb=" N VAL G 58 " pdb=" CA VAL G 58 " ideal model delta harmonic sigma weight residual -180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA TRP I 57 " pdb=" C TRP I 57 " pdb=" N VAL I 58 " pdb=" CA VAL I 58 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA TRP o 57 " pdb=" C TRP o 57 " pdb=" N VAL o 58 " pdb=" CA VAL o 58 " ideal model delta harmonic sigma weight residual -180.00 -151.11 -28.89 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 13593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3120 0.101 - 0.202: 220 0.202 - 0.303: 24 0.303 - 0.404: 12 0.404 - 0.505: 16 Chirality restraints: 3392 Sorted by residual: chirality pdb=" CA GLU B 349 " pdb=" N GLU B 349 " pdb=" C GLU B 349 " pdb=" CB GLU B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" CA GLU D 349 " pdb=" N GLU D 349 " pdb=" C GLU D 349 " pdb=" CB GLU D 349 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" CA GLU H 349 " pdb=" N GLU H 349 " pdb=" C GLU H 349 " pdb=" CB GLU H 349 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.31e+00 ... (remaining 3389 not shown) Planarity restraints: 3864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY G 100 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C GLY G 100 " 0.048 2.00e-02 2.50e+03 pdb=" O GLY G 100 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN G 101 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 100 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C GLY M 100 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY M 100 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN M 101 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY o 100 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" C GLY o 100 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY o 100 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN o 101 " 0.016 2.00e-02 2.50e+03 ... (remaining 3861 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.70: 659 2.70 - 3.31: 23508 3.31 - 3.92: 41039 3.92 - 4.53: 55941 4.53 - 5.14: 86630 Nonbonded interactions: 207777 Sorted by model distance: nonbonded pdb=" OH TYR F 447 " pdb=" OG1 THR H 441 " model vdw 2.085 3.040 nonbonded pdb=" N ASP B 293 " pdb=" OD1 ASP B 293 " model vdw 2.108 3.120 nonbonded pdb=" N ASP D 293 " pdb=" OD1 ASP D 293 " model vdw 2.109 3.120 nonbonded pdb=" N ASP F 293 " pdb=" OD1 ASP F 293 " model vdw 2.109 3.120 nonbonded pdb=" N ASP H 293 " pdb=" OD1 ASP H 293 " model vdw 2.109 3.120 ... (remaining 207772 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 'B' and resid 208 through 490) selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'M' selection = chain 'o' } ncs_group { reference = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 7.100 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: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 21.050 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 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 : 0.009 0.219 22552 Z= 0.466 Angle : 1.047 14.051 30560 Z= 0.583 Chirality : 0.067 0.505 3392 Planarity : 0.006 0.064 3864 Dihedral : 14.446 85.149 8480 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.44 % Allowed : 3.85 % Favored : 95.71 % Rotamer: Outliers : 6.01 % Allowed : 7.90 % Favored : 86.08 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % 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: -1.41 (0.14), residues: 2728 helix: -0.29 (0.12), residues: 1516 sheet: 0.99 (0.38), residues: 196 loop : -2.29 (0.15), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 313 TYR 0.016 0.002 TYR H 487 PHE 0.020 0.002 PHE H 296 TRP 0.014 0.002 TRP o 243 HIS 0.009 0.001 HIS I 135 Details of bonding type rmsd covalent geometry : bond 0.00887 (22548) covalent geometry : angle 1.04742 (30552) SS BOND : bond 0.00380 ( 4) SS BOND : angle 1.28417 ( 8) hydrogen bonds : bond 0.19273 ( 1096) hydrogen bonds : angle 6.04255 ( 3204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 549 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 259 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7134 (m-10) REVERT: D 260 ARG cc_start: 0.5410 (OUTLIER) cc_final: 0.4519 (ttm170) REVERT: D 351 GLN cc_start: 0.4956 (OUTLIER) cc_final: 0.3569 (mp10) REVERT: D 386 ILE cc_start: 0.8061 (mt) cc_final: 0.7818 (mt) REVERT: D 463 LEU cc_start: 0.7066 (mt) cc_final: 0.6739 (mt) REVERT: G 73 MET cc_start: 0.7728 (mtp) cc_final: 0.7478 (mtp) REVERT: G 94 LYS cc_start: 0.6982 (mtpt) cc_final: 0.6654 (mtmm) REVERT: G 104 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7248 (ttmp) REVERT: G 124 LYS cc_start: 0.7357 (mtmt) cc_final: 0.7113 (mtpp) REVERT: G 129 ARG cc_start: 0.7148 (ptm160) cc_final: 0.6797 (ptt-90) REVERT: G 276 LYS cc_start: 0.7739 (tttt) cc_final: 0.7230 (ttmm) REVERT: G 331 MET cc_start: 0.6438 (mmt) cc_final: 0.6200 (mtm) REVERT: I 73 MET cc_start: 0.7570 (mtp) cc_final: 0.7327 (mtp) REVERT: I 94 LYS cc_start: 0.6998 (mtpt) cc_final: 0.6641 (mtmm) REVERT: I 106 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8143 (mtpt) REVERT: I 119 ILE cc_start: 0.8184 (mt) cc_final: 0.7809 (mm) REVERT: I 124 LYS cc_start: 0.7604 (mtmt) cc_final: 0.7380 (mtpp) REVERT: I 129 ARG cc_start: 0.7148 (ptm160) cc_final: 0.6774 (ptt-90) REVERT: I 141 LYS cc_start: 0.7719 (mttt) cc_final: 0.7369 (mttm) REVERT: I 227 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7585 (t) REVERT: I 268 LYS cc_start: 0.8279 (tttt) cc_final: 0.8021 (ttpt) REVERT: I 274 LYS cc_start: 0.7655 (tttt) cc_final: 0.7377 (ttpt) REVERT: I 276 LYS cc_start: 0.7571 (tttt) cc_final: 0.7055 (ttmt) REVERT: I 290 LYS cc_start: 0.6638 (mtmt) cc_final: 0.6389 (mmtp) REVERT: I 331 MET cc_start: 0.6666 (mmt) cc_final: 0.6171 (mtm) REVERT: J 138 ARG cc_start: 0.8203 (ptm160) cc_final: 0.7718 (ptm160) REVERT: J 144 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7572 (mtt90) REVERT: J 170 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7394 (mtt-85) REVERT: J 181 SER cc_start: 0.7683 (t) cc_final: 0.7442 (m) REVERT: M 73 MET cc_start: 0.7747 (mtp) cc_final: 0.7460 (mtp) REVERT: M 94 LYS cc_start: 0.6987 (mtpt) cc_final: 0.6669 (mtmm) REVERT: M 104 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.6771 (ttmp) REVERT: M 124 LYS cc_start: 0.7642 (mtmt) cc_final: 0.7375 (mtpp) REVERT: M 129 ARG cc_start: 0.7301 (ptm160) cc_final: 0.6886 (ptt-90) REVERT: M 141 LYS cc_start: 0.7571 (mttt) cc_final: 0.7170 (mttm) REVERT: M 227 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7731 (t) REVERT: M 268 LYS cc_start: 0.8263 (tttt) cc_final: 0.8035 (ttpt) REVERT: M 274 LYS cc_start: 0.7674 (tttt) cc_final: 0.7432 (ttpt) REVERT: M 276 LYS cc_start: 0.7503 (tttt) cc_final: 0.7010 (ttmt) REVERT: M 331 MET cc_start: 0.6531 (mmt) cc_final: 0.6184 (mtm) REVERT: N 144 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7555 (mtt90) REVERT: N 170 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7373 (mtt-85) REVERT: N 181 SER cc_start: 0.7686 (t) cc_final: 0.7476 (m) REVERT: O 144 ARG cc_start: 0.7840 (mtm180) cc_final: 0.7536 (mtt90) REVERT: O 168 ARG cc_start: 0.8130 (mtm180) cc_final: 0.7827 (mtm-85) REVERT: O 170 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7078 (mmt-90) REVERT: O 181 SER cc_start: 0.7961 (t) cc_final: 0.7618 (m) REVERT: O 199 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6415 (mm-30) REVERT: P 124 GLN cc_start: 0.8299 (mt0) cc_final: 0.8092 (mt0) REVERT: P 144 ARG cc_start: 0.7815 (mtm180) cc_final: 0.7489 (mtt90) REVERT: P 161 TYR cc_start: 0.6559 (t80) cc_final: 0.6161 (t80) REVERT: P 168 ARG cc_start: 0.8022 (mtm180) cc_final: 0.7641 (mtm-85) REVERT: P 170 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7489 (mtt-85) REVERT: o 73 MET cc_start: 0.7579 (mtp) cc_final: 0.7271 (mtp) REVERT: o 94 LYS cc_start: 0.6993 (mtpt) cc_final: 0.6716 (mtmm) REVERT: o 104 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7329 (tppt) REVERT: o 119 ILE cc_start: 0.8203 (mt) cc_final: 0.7856 (mm) REVERT: o 124 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7448 (mtpp) REVERT: o 129 ARG cc_start: 0.7302 (ptm160) cc_final: 0.6838 (ptt-90) REVERT: o 227 VAL cc_start: 0.7794 (OUTLIER) cc_final: 0.7473 (t) REVERT: o 268 LYS cc_start: 0.8240 (tttt) cc_final: 0.7969 (ttpt) REVERT: o 276 LYS cc_start: 0.7401 (tttt) cc_final: 0.6878 (ttmt) REVERT: o 331 MET cc_start: 0.6613 (mmt) cc_final: 0.6227 (mtm) REVERT: B 260 ARG cc_start: 0.5318 (OUTLIER) cc_final: 0.4748 (ttm170) REVERT: B 337 ILE cc_start: 0.6270 (mt) cc_final: 0.5944 (mt) REVERT: B 350 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.6351 (mmt180) REVERT: B 407 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7383 (mm) REVERT: F 259 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6167 (m-10) REVERT: F 463 LEU cc_start: 0.7147 (mt) cc_final: 0.6913 (mt) REVERT: H 244 ILE cc_start: 0.7513 (mt) cc_final: 0.7039 (mt) REVERT: H 301 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5805 (tt) REVERT: H 309 GLU cc_start: 0.3583 (tm-30) cc_final: 0.2819 (tm-30) REVERT: H 337 ILE cc_start: 0.5876 (mt) cc_final: 0.5675 (mt) REVERT: H 341 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9024 (mt) REVERT: H 351 GLN cc_start: 0.5344 (OUTLIER) cc_final: 0.3165 (mp10) REVERT: H 376 LYS cc_start: 0.6759 (mtpp) cc_final: 0.6505 (mtpp) outliers start: 140 outliers final: 43 residues processed: 652 average time/residue: 0.1816 time to fit residues: 171.9030 Evaluate side-chains 510 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 450 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 LYS Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 LYS Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain O residue 199 GLU Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain o residue 104 LYS Chi-restraints excluded: chain o residue 227 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain F residue 259 PHE Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 358 MET Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain H residue 358 MET Chi-restraints excluded: chain H residue 359 SER Chi-restraints excluded: chain H residue 407 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.0570 chunk 111 optimal weight: 0.7980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 HIS F 451 HIS H 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.150273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.120979 restraints weight = 27538.528| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.73 r_work: 0.2903 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22552 Z= 0.128 Angle : 0.596 7.500 30560 Z= 0.310 Chirality : 0.041 0.131 3392 Planarity : 0.005 0.047 3864 Dihedral : 11.206 60.709 3411 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.46 % Favored : 97.25 % Rotamer: Outliers : 2.96 % Allowed : 11.04 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.16), residues: 2728 helix: 1.14 (0.13), residues: 1560 sheet: 0.68 (0.36), residues: 216 loop : -2.00 (0.16), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 313 TYR 0.019 0.001 TYR D 339 PHE 0.024 0.001 PHE D 314 TRP 0.012 0.001 TRP H 305 HIS 0.004 0.001 HIS o 135 Details of bonding type rmsd covalent geometry : bond 0.00269 (22548) covalent geometry : angle 0.59604 (30552) SS BOND : bond 0.00323 ( 4) SS BOND : angle 0.49128 ( 8) hydrogen bonds : bond 0.05541 ( 1096) hydrogen bonds : angle 3.93039 ( 3204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 488 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 217 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.7031 (pm20) REVERT: D 308 PHE cc_start: 0.8231 (t80) cc_final: 0.8011 (t80) REVERT: D 364 ARG cc_start: 0.8034 (tpp80) cc_final: 0.7365 (ttp-170) REVERT: G 94 LYS cc_start: 0.7618 (mtpt) cc_final: 0.7254 (mtmm) REVERT: G 129 ARG cc_start: 0.7985 (ptm160) cc_final: 0.7398 (ptt-90) REVERT: G 141 LYS cc_start: 0.7913 (mttt) cc_final: 0.7593 (mttm) REVERT: G 276 LYS cc_start: 0.8045 (tttt) cc_final: 0.7433 (ttmm) REVERT: G 331 MET cc_start: 0.7353 (mmt) cc_final: 0.6956 (mtm) REVERT: I 129 ARG cc_start: 0.7930 (ptm160) cc_final: 0.7343 (ptt-90) REVERT: I 141 LYS cc_start: 0.7836 (mttt) cc_final: 0.7502 (mttm) REVERT: I 161 ASP cc_start: 0.8464 (t0) cc_final: 0.8223 (t0) REVERT: I 268 LYS cc_start: 0.8354 (tttt) cc_final: 0.8152 (ttpt) REVERT: I 276 LYS cc_start: 0.8033 (tttt) cc_final: 0.7420 (ttmm) REVERT: I 331 MET cc_start: 0.7585 (mmt) cc_final: 0.6994 (mtm) REVERT: I 338 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7058 (mm-40) REVERT: J 144 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7732 (mtt90) REVERT: J 170 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7706 (mtt-85) REVERT: M 67 GLU cc_start: 0.6791 (mp0) cc_final: 0.6541 (mp0) REVERT: M 73 MET cc_start: 0.8278 (mtp) cc_final: 0.8077 (mtp) REVERT: M 129 ARG cc_start: 0.8074 (ptm160) cc_final: 0.7462 (ptt-90) REVERT: M 141 LYS cc_start: 0.7974 (mttt) cc_final: 0.7614 (mttm) REVERT: M 276 LYS cc_start: 0.8039 (tttt) cc_final: 0.7460 (ttmt) REVERT: M 331 MET cc_start: 0.7620 (mmt) cc_final: 0.7136 (mtm) REVERT: N 144 ARG cc_start: 0.8007 (mtm180) cc_final: 0.7769 (mtt90) REVERT: N 170 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7673 (mtt-85) REVERT: O 144 ARG cc_start: 0.7937 (mtm180) cc_final: 0.7668 (mtt90) REVERT: O 170 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7252 (mmt-90) REVERT: O 181 SER cc_start: 0.7880 (t) cc_final: 0.7558 (m) REVERT: O 195 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6455 (tm-30) REVERT: O 199 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6567 (mm-30) REVERT: P 144 ARG cc_start: 0.8017 (mtm180) cc_final: 0.7704 (mtt90) REVERT: P 168 ARG cc_start: 0.8419 (mtm180) cc_final: 0.8189 (mtm180) REVERT: P 170 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7893 (mtt-85) REVERT: o 73 MET cc_start: 0.8075 (mtp) cc_final: 0.7859 (mtp) REVERT: o 104 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7461 (tppt) REVERT: o 129 ARG cc_start: 0.7997 (ptm160) cc_final: 0.7382 (ptt-90) REVERT: o 141 LYS cc_start: 0.7969 (mttt) cc_final: 0.7639 (mttm) REVERT: o 161 ASP cc_start: 0.8487 (t0) cc_final: 0.8247 (t0) REVERT: o 268 LYS cc_start: 0.8342 (tttt) cc_final: 0.8122 (ttpt) REVERT: o 276 LYS cc_start: 0.7877 (tttt) cc_final: 0.7295 (ttmt) REVERT: o 331 MET cc_start: 0.7606 (mmt) cc_final: 0.7101 (mtm) REVERT: B 262 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.6264 (mt-10) REVERT: B 362 ILE cc_start: 0.7872 (mt) cc_final: 0.7659 (mt) REVERT: B 489 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7680 (ttm170) REVERT: F 313 ARG cc_start: 0.7831 (ttt180) cc_final: 0.7501 (ttm-80) REVERT: F 325 ARG cc_start: 0.7921 (mmt180) cc_final: 0.7023 (tpt170) REVERT: F 433 ASP cc_start: 0.8310 (t0) cc_final: 0.8010 (t0) outliers start: 69 outliers final: 36 residues processed: 535 average time/residue: 0.1747 time to fit residues: 136.5039 Evaluate side-chains 497 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 456 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 GLN Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain O residue 199 GLU Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain o residue 104 LYS Chi-restraints excluded: chain o residue 346 SER Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 ARG Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 358 MET Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 358 MET Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 440 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 56 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 48 optimal weight: 0.0770 chunk 240 optimal weight: 0.7980 chunk 188 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 264 optimal weight: 0.2980 chunk 21 optimal weight: 0.1980 chunk 128 optimal weight: 6.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 329 ASN D 451 HIS D 484 ASN J 124 GLN P 124 GLN H 451 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.149421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.119336 restraints weight = 27378.993| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.67 r_work: 0.2889 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22552 Z= 0.104 Angle : 0.524 7.264 30560 Z= 0.271 Chirality : 0.039 0.130 3392 Planarity : 0.004 0.045 3864 Dihedral : 9.342 56.045 3321 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.49 % Favored : 97.21 % Rotamer: Outliers : 1.93 % Allowed : 12.76 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.16), residues: 2728 helix: 1.68 (0.14), residues: 1580 sheet: 0.65 (0.37), residues: 192 loop : -1.70 (0.17), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 364 TYR 0.013 0.001 TYR F 485 PHE 0.032 0.001 PHE F 296 TRP 0.012 0.001 TRP H 305 HIS 0.005 0.001 HIS G 135 Details of bonding type rmsd covalent geometry : bond 0.00222 (22548) covalent geometry : angle 0.52394 (30552) SS BOND : bond 0.00254 ( 4) SS BOND : angle 0.47642 ( 8) hydrogen bonds : bond 0.04423 ( 1096) hydrogen bonds : angle 3.57979 ( 3204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 489 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 217 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: D 328 MET cc_start: 0.7564 (mmm) cc_final: 0.7245 (mmm) REVERT: D 364 ARG cc_start: 0.7799 (tpp80) cc_final: 0.7154 (ttt-90) REVERT: G 94 LYS cc_start: 0.7464 (mtpt) cc_final: 0.7054 (mtmm) REVERT: G 129 ARG cc_start: 0.7967 (ptm160) cc_final: 0.7345 (ptt-90) REVERT: G 141 LYS cc_start: 0.7939 (mttt) cc_final: 0.7615 (mttm) REVERT: G 331 MET cc_start: 0.7237 (mmt) cc_final: 0.6860 (mtm) REVERT: I 129 ARG cc_start: 0.7937 (ptm160) cc_final: 0.7334 (ptt-90) REVERT: I 141 LYS cc_start: 0.7827 (mttt) cc_final: 0.7481 (mttm) REVERT: I 161 ASP cc_start: 0.8465 (t0) cc_final: 0.8242 (t0) REVERT: I 268 LYS cc_start: 0.8356 (tttt) cc_final: 0.8129 (ttpt) REVERT: I 331 MET cc_start: 0.7523 (mmt) cc_final: 0.7004 (mtm) REVERT: J 144 ARG cc_start: 0.7993 (mtm180) cc_final: 0.7728 (mtt90) REVERT: J 170 ARG cc_start: 0.7907 (mtt180) cc_final: 0.7705 (mtt-85) REVERT: M 129 ARG cc_start: 0.8111 (ptm160) cc_final: 0.7456 (ptt-90) REVERT: M 141 LYS cc_start: 0.7960 (mttt) cc_final: 0.7606 (mttm) REVERT: M 331 MET cc_start: 0.7444 (mmt) cc_final: 0.6992 (mtm) REVERT: N 144 ARG cc_start: 0.7993 (mtm180) cc_final: 0.7757 (mtt90) REVERT: N 170 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7727 (mtt-85) REVERT: O 127 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7507 (pm20) REVERT: O 144 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7689 (mtt90) REVERT: O 170 ARG cc_start: 0.8037 (mtt180) cc_final: 0.7273 (mmt-90) REVERT: O 181 SER cc_start: 0.7844 (t) cc_final: 0.7598 (m) REVERT: O 195 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6493 (tm-30) REVERT: O 199 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6274 (mm-30) REVERT: P 144 ARG cc_start: 0.7977 (mtm180) cc_final: 0.7723 (mtt90) REVERT: o 129 ARG cc_start: 0.7990 (ptm160) cc_final: 0.7370 (ptt-90) REVERT: o 141 LYS cc_start: 0.7899 (mttt) cc_final: 0.7562 (mttm) REVERT: o 161 ASP cc_start: 0.8460 (t0) cc_final: 0.8250 (t0) REVERT: o 268 LYS cc_start: 0.8384 (tttt) cc_final: 0.8159 (ttpt) REVERT: o 276 LYS cc_start: 0.7859 (tttt) cc_final: 0.7637 (tttm) REVERT: o 331 MET cc_start: 0.7447 (mmt) cc_final: 0.6984 (mtm) REVERT: o 338 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7240 (mm-40) REVERT: B 364 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7261 (ttp-170) REVERT: B 470 LEU cc_start: 0.8211 (tp) cc_final: 0.7665 (mp) REVERT: F 313 ARG cc_start: 0.7913 (ttt180) cc_final: 0.7544 (ttm-80) REVERT: F 325 ARG cc_start: 0.8027 (mmt180) cc_final: 0.7175 (tpt170) REVERT: F 433 ASP cc_start: 0.8386 (t0) cc_final: 0.8138 (t0) REVERT: H 209 ARG cc_start: 0.7452 (mtm180) cc_final: 0.7191 (mpp80) REVERT: H 362 ILE cc_start: 0.7768 (mt) cc_final: 0.7546 (mt) outliers start: 45 outliers final: 28 residues processed: 519 average time/residue: 0.1832 time to fit residues: 138.6145 Evaluate side-chains 477 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 447 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 217 GLN Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 295 ILE Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 199 GLU Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 440 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 3 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 124 GLN P 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.140059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.108620 restraints weight = 27344.366| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.64 r_work: 0.2735 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 22552 Z= 0.255 Angle : 0.684 8.367 30560 Z= 0.363 Chirality : 0.046 0.251 3392 Planarity : 0.005 0.052 3864 Dihedral : 10.976 70.811 3300 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.63 % Favored : 95.78 % Rotamer: Outliers : 3.14 % Allowed : 12.33 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.16), residues: 2728 helix: 1.45 (0.13), residues: 1584 sheet: 0.30 (0.40), residues: 152 loop : -1.73 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 214 TYR 0.020 0.002 TYR D 339 PHE 0.021 0.002 PHE H 315 TRP 0.022 0.003 TRP M 57 HIS 0.008 0.001 HIS o 135 Details of bonding type rmsd covalent geometry : bond 0.00619 (22548) covalent geometry : angle 0.68433 (30552) SS BOND : bond 0.00054 ( 4) SS BOND : angle 0.83482 ( 8) hydrogen bonds : bond 0.07361 ( 1096) hydrogen bonds : angle 4.02703 ( 3204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 452 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 328 MET cc_start: 0.7736 (mmm) cc_final: 0.7484 (mmm) REVERT: D 364 ARG cc_start: 0.8050 (tpp80) cc_final: 0.7363 (ttt180) REVERT: G 94 LYS cc_start: 0.7767 (mtpt) cc_final: 0.7359 (mtmm) REVERT: G 129 ARG cc_start: 0.8069 (ptm160) cc_final: 0.7446 (ptt-90) REVERT: G 141 LYS cc_start: 0.8022 (mttt) cc_final: 0.7640 (mttm) REVERT: G 331 MET cc_start: 0.7663 (mmt) cc_final: 0.7135 (mtm) REVERT: I 94 LYS cc_start: 0.7698 (mtpt) cc_final: 0.7322 (mtmm) REVERT: I 129 ARG cc_start: 0.8007 (ptm160) cc_final: 0.7366 (ptt-90) REVERT: I 141 LYS cc_start: 0.7932 (mttt) cc_final: 0.7547 (mttm) REVERT: I 268 LYS cc_start: 0.8338 (tttt) cc_final: 0.8096 (ttpt) REVERT: I 276 LYS cc_start: 0.8123 (tttm) cc_final: 0.7619 (ttmt) REVERT: I 297 GLU cc_start: 0.7538 (tt0) cc_final: 0.7329 (mt-10) REVERT: I 331 MET cc_start: 0.7691 (mmt) cc_final: 0.7153 (mtm) REVERT: I 338 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7583 (mm-40) REVERT: J 144 ARG cc_start: 0.8191 (mtm180) cc_final: 0.7941 (mtt90) REVERT: J 170 ARG cc_start: 0.8008 (mtt180) cc_final: 0.7805 (mtt-85) REVERT: M 94 LYS cc_start: 0.7736 (mtpt) cc_final: 0.7342 (mtmm) REVERT: M 129 ARG cc_start: 0.8138 (ptm160) cc_final: 0.7457 (ptt-90) REVERT: M 276 LYS cc_start: 0.8147 (tttm) cc_final: 0.7649 (ttmt) REVERT: M 331 MET cc_start: 0.7726 (mmt) cc_final: 0.7178 (mtm) REVERT: N 144 ARG cc_start: 0.8178 (mtm180) cc_final: 0.7913 (mtt90) REVERT: N 170 ARG cc_start: 0.8017 (mtt180) cc_final: 0.7747 (mtt-85) REVERT: N 191 GLU cc_start: 0.7369 (tp30) cc_final: 0.6776 (tp30) REVERT: O 144 ARG cc_start: 0.8141 (mtm180) cc_final: 0.7883 (mtt90) REVERT: O 170 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7764 (mtt-85) REVERT: O 181 SER cc_start: 0.7926 (t) cc_final: 0.7663 (m) REVERT: O 191 GLU cc_start: 0.7200 (tp30) cc_final: 0.6889 (tp30) REVERT: O 195 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6459 (mt-10) REVERT: P 127 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7708 (pm20) REVERT: P 144 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7937 (mtt90) REVERT: o 94 LYS cc_start: 0.7722 (mtpt) cc_final: 0.7316 (mtmm) REVERT: o 129 ARG cc_start: 0.8026 (ptm160) cc_final: 0.7365 (ptt-90) REVERT: o 141 LYS cc_start: 0.7961 (mttt) cc_final: 0.7591 (mttm) REVERT: o 276 LYS cc_start: 0.7946 (tttt) cc_final: 0.7352 (ttmt) REVERT: o 297 GLU cc_start: 0.7558 (tt0) cc_final: 0.7346 (mt-10) REVERT: o 331 MET cc_start: 0.7679 (mmt) cc_final: 0.7141 (mtm) REVERT: B 364 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7533 (ttp-170) REVERT: F 313 ARG cc_start: 0.8060 (ttt180) cc_final: 0.7806 (ttm-80) REVERT: F 332 ASP cc_start: 0.8627 (m-30) cc_final: 0.8423 (m-30) REVERT: F 376 LYS cc_start: 0.9325 (mtmt) cc_final: 0.9071 (mtpp) REVERT: H 209 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7311 (mpp80) REVERT: H 218 ARG cc_start: 0.8254 (ttt90) cc_final: 0.7988 (tpt-90) outliers start: 73 outliers final: 49 residues processed: 507 average time/residue: 0.1810 time to fit residues: 134.1197 Evaluate side-chains 476 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 427 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 313 ARG Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 489 ARG Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 196 LYS Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain o residue 279 SER Chi-restraints excluded: chain o residue 346 SER Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 407 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 471 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 48 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 chunk 258 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 169 optimal weight: 0.4980 chunk 235 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 488 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.144402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.113056 restraints weight = 27287.320| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.66 r_work: 0.2805 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22552 Z= 0.123 Angle : 0.544 6.120 30560 Z= 0.287 Chirality : 0.041 0.139 3392 Planarity : 0.004 0.045 3864 Dihedral : 9.706 60.568 3291 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.90 % Favored : 96.85 % Rotamer: Outliers : 2.15 % Allowed : 13.79 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.84 (0.16), residues: 2728 helix: 1.81 (0.14), residues: 1580 sheet: 0.21 (0.39), residues: 152 loop : -1.52 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.020 0.001 TYR H 485 PHE 0.021 0.001 PHE H 315 TRP 0.010 0.001 TRP I 185 HIS 0.006 0.001 HIS o 135 Details of bonding type rmsd covalent geometry : bond 0.00274 (22548) covalent geometry : angle 0.54422 (30552) SS BOND : bond 0.00232 ( 4) SS BOND : angle 0.58786 ( 8) hydrogen bonds : bond 0.04955 ( 1096) hydrogen bonds : angle 3.61632 ( 3204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 453 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 328 MET cc_start: 0.7389 (mmm) cc_final: 0.7121 (mmm) REVERT: D 364 ARG cc_start: 0.7900 (tpp80) cc_final: 0.7261 (ttt180) REVERT: D 433 ASP cc_start: 0.8570 (t0) cc_final: 0.8366 (t0) REVERT: G 129 ARG cc_start: 0.8082 (ptm160) cc_final: 0.7433 (ptt-90) REVERT: G 141 LYS cc_start: 0.8034 (mttt) cc_final: 0.7656 (mttm) REVERT: G 331 MET cc_start: 0.7641 (mmt) cc_final: 0.7127 (mtm) REVERT: I 129 ARG cc_start: 0.7998 (ptm160) cc_final: 0.7384 (ptt-90) REVERT: I 141 LYS cc_start: 0.7949 (mttt) cc_final: 0.7565 (mttm) REVERT: I 161 ASP cc_start: 0.8428 (t0) cc_final: 0.8163 (t0) REVERT: I 268 LYS cc_start: 0.8366 (tttt) cc_final: 0.8148 (ttpt) REVERT: I 331 MET cc_start: 0.7604 (mmt) cc_final: 0.7053 (mtm) REVERT: J 144 ARG cc_start: 0.8141 (mtm180) cc_final: 0.7914 (mtt90) REVERT: J 170 ARG cc_start: 0.7957 (mtt180) cc_final: 0.7723 (mtt-85) REVERT: M 129 ARG cc_start: 0.8111 (ptm160) cc_final: 0.7438 (ptt-90) REVERT: M 141 LYS cc_start: 0.7982 (mttt) cc_final: 0.7620 (mttm) REVERT: M 331 MET cc_start: 0.7634 (mmt) cc_final: 0.7100 (mtm) REVERT: N 144 ARG cc_start: 0.8134 (mtm180) cc_final: 0.7890 (mtt90) REVERT: N 170 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7724 (mtt-85) REVERT: O 124 GLN cc_start: 0.8406 (mt0) cc_final: 0.8202 (mt0) REVERT: O 127 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7476 (pm20) REVERT: O 144 ARG cc_start: 0.8120 (mtm180) cc_final: 0.7872 (mtt90) REVERT: O 170 ARG cc_start: 0.8007 (mtt180) cc_final: 0.7780 (mtt-85) REVERT: O 181 SER cc_start: 0.7860 (t) cc_final: 0.7618 (m) REVERT: O 195 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6346 (mt-10) REVERT: P 127 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7780 (pm20) REVERT: P 144 ARG cc_start: 0.8162 (mtm180) cc_final: 0.7935 (mtt90) REVERT: P 161 TYR cc_start: 0.7460 (t80) cc_final: 0.7077 (t80) REVERT: o 129 ARG cc_start: 0.7996 (ptm160) cc_final: 0.7379 (ptt-90) REVERT: o 141 LYS cc_start: 0.7984 (mttt) cc_final: 0.7632 (mttm) REVERT: o 161 ASP cc_start: 0.8462 (t0) cc_final: 0.8210 (t0) REVERT: o 331 MET cc_start: 0.7580 (mmt) cc_final: 0.7047 (mtm) REVERT: B 364 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7251 (ttp-170) REVERT: F 313 ARG cc_start: 0.8068 (ttt180) cc_final: 0.7860 (ttm-80) REVERT: F 332 ASP cc_start: 0.8609 (m-30) cc_final: 0.8400 (m-30) REVERT: F 376 LYS cc_start: 0.9252 (mtmt) cc_final: 0.8983 (mtpp) outliers start: 50 outliers final: 41 residues processed: 482 average time/residue: 0.1865 time to fit residues: 131.0403 Evaluate side-chains 471 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 430 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 488 HIS Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 295 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain o residue 295 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 454 THR Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 488 HIS Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 416 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 129 optimal weight: 0.6980 chunk 99 optimal weight: 0.0980 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 231 optimal weight: 0.0770 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.146003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.116271 restraints weight = 27221.951| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.66 r_work: 0.2957 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22552 Z= 0.106 Angle : 0.526 9.045 30560 Z= 0.272 Chirality : 0.040 0.181 3392 Planarity : 0.004 0.045 3864 Dihedral : 9.264 58.853 3291 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.01 % Favored : 96.74 % Rotamer: Outliers : 1.76 % Allowed : 14.26 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.99 (0.16), residues: 2728 helix: 1.93 (0.14), residues: 1604 sheet: 0.26 (0.39), residues: 152 loop : -1.53 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 218 TYR 0.021 0.001 TYR H 485 PHE 0.034 0.001 PHE H 323 TRP 0.009 0.001 TRP M 185 HIS 0.017 0.001 HIS D 488 Details of bonding type rmsd covalent geometry : bond 0.00227 (22548) covalent geometry : angle 0.52567 (30552) SS BOND : bond 0.00248 ( 4) SS BOND : angle 0.54698 ( 8) hydrogen bonds : bond 0.04379 ( 1096) hydrogen bonds : angle 3.48204 ( 3204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 454 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 328 MET cc_start: 0.7189 (mmm) cc_final: 0.6953 (mmm) REVERT: D 364 ARG cc_start: 0.7751 (tpp80) cc_final: 0.7186 (ttt-90) REVERT: G 129 ARG cc_start: 0.8042 (ptm160) cc_final: 0.7395 (ptt-90) REVERT: G 141 LYS cc_start: 0.7965 (mttt) cc_final: 0.7581 (mttm) REVERT: G 331 MET cc_start: 0.7521 (mmt) cc_final: 0.7000 (mtm) REVERT: I 129 ARG cc_start: 0.7955 (ptm160) cc_final: 0.7343 (ptt-90) REVERT: I 141 LYS cc_start: 0.7884 (mttt) cc_final: 0.7487 (mttm) REVERT: I 161 ASP cc_start: 0.8433 (t0) cc_final: 0.8192 (t0) REVERT: I 268 LYS cc_start: 0.8354 (tttt) cc_final: 0.8151 (ttpt) REVERT: I 331 MET cc_start: 0.7454 (mmt) cc_final: 0.6905 (mtm) REVERT: J 144 ARG cc_start: 0.8042 (mtm180) cc_final: 0.7825 (mtt90) REVERT: J 170 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7683 (mtt-85) REVERT: J 191 GLU cc_start: 0.7189 (tp30) cc_final: 0.6827 (tp30) REVERT: M 129 ARG cc_start: 0.8068 (ptm160) cc_final: 0.7395 (ptt-90) REVERT: M 141 LYS cc_start: 0.7908 (mttt) cc_final: 0.7528 (mttm) REVERT: M 331 MET cc_start: 0.7537 (mmt) cc_final: 0.7019 (mtm) REVERT: N 144 ARG cc_start: 0.8032 (mtm180) cc_final: 0.7803 (mtt90) REVERT: N 170 ARG cc_start: 0.7899 (mtt180) cc_final: 0.7696 (mtt-85) REVERT: O 127 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7470 (pm20) REVERT: O 144 ARG cc_start: 0.8013 (mtm180) cc_final: 0.7793 (mtt90) REVERT: O 170 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7733 (mtt-85) REVERT: O 181 SER cc_start: 0.7807 (t) cc_final: 0.7602 (m) REVERT: O 182 GLU cc_start: 0.6868 (tp30) cc_final: 0.6628 (mt-10) REVERT: O 195 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6344 (mt-10) REVERT: P 127 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7759 (pm20) REVERT: P 144 ARG cc_start: 0.8049 (mtm180) cc_final: 0.7800 (mtt90) REVERT: P 161 TYR cc_start: 0.7466 (t80) cc_final: 0.6988 (t80) REVERT: o 129 ARG cc_start: 0.7980 (ptm160) cc_final: 0.7355 (ptt-90) REVERT: o 141 LYS cc_start: 0.7906 (mttt) cc_final: 0.7530 (mttm) REVERT: o 331 MET cc_start: 0.7461 (mmt) cc_final: 0.6914 (mtm) REVERT: B 364 ARG cc_start: 0.7792 (ttm-80) cc_final: 0.7156 (tmt170) REVERT: B 470 LEU cc_start: 0.8208 (tp) cc_final: 0.7735 (mp) REVERT: F 330 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7827 (tp) REVERT: F 332 ASP cc_start: 0.8550 (m-30) cc_final: 0.8350 (m-30) REVERT: F 376 LYS cc_start: 0.9249 (mtmt) cc_final: 0.8989 (mtpp) REVERT: H 218 ARG cc_start: 0.7936 (tpt-90) cc_final: 0.7412 (mmm160) outliers start: 41 outliers final: 35 residues processed: 476 average time/residue: 0.1858 time to fit residues: 129.1277 Evaluate side-chains 478 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 442 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 295 ILE Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 295 ILE Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain o residue 295 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 488 HIS Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 440 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 139 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 223 optimal weight: 0.0170 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 174 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 124 GLN O 124 GLN P 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.142925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.114136 restraints weight = 27179.079| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.49 r_work: 0.2768 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22552 Z= 0.150 Angle : 0.571 7.887 30560 Z= 0.297 Chirality : 0.042 0.139 3392 Planarity : 0.004 0.045 3864 Dihedral : 9.750 61.779 3291 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.70 % Favored : 96.08 % Rotamer: Outliers : 2.02 % Allowed : 14.30 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.01 (0.16), residues: 2728 helix: 1.93 (0.14), residues: 1584 sheet: 0.36 (0.37), residues: 176 loop : -1.49 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 170 TYR 0.021 0.002 TYR H 485 PHE 0.025 0.001 PHE H 323 TRP 0.012 0.002 TRP o 243 HIS 0.007 0.001 HIS o 135 Details of bonding type rmsd covalent geometry : bond 0.00352 (22548) covalent geometry : angle 0.57114 (30552) SS BOND : bond 0.00160 ( 4) SS BOND : angle 0.63657 ( 8) hydrogen bonds : bond 0.05484 ( 1096) hydrogen bonds : angle 3.62441 ( 3204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 451 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 364 ARG cc_start: 0.7940 (tpp80) cc_final: 0.7217 (ttt180) REVERT: G 94 LYS cc_start: 0.7636 (mtpt) cc_final: 0.7175 (mttt) REVERT: G 129 ARG cc_start: 0.8104 (ptm160) cc_final: 0.7420 (ptt-90) REVERT: G 141 LYS cc_start: 0.8023 (mttt) cc_final: 0.7646 (mttm) REVERT: G 331 MET cc_start: 0.7616 (mmt) cc_final: 0.7056 (mtm) REVERT: I 94 LYS cc_start: 0.7579 (mtpt) cc_final: 0.7118 (mttt) REVERT: I 129 ARG cc_start: 0.8014 (ptm160) cc_final: 0.7373 (ptt-90) REVERT: I 141 LYS cc_start: 0.7927 (mttt) cc_final: 0.7539 (mttm) REVERT: I 268 LYS cc_start: 0.8318 (tttt) cc_final: 0.8097 (ttpt) REVERT: I 331 MET cc_start: 0.7576 (mmt) cc_final: 0.7022 (mtm) REVERT: J 127 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7414 (pm20) REVERT: J 144 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7921 (mtt90) REVERT: J 170 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7761 (mtt-85) REVERT: M 104 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7295 (tppt) REVERT: M 129 ARG cc_start: 0.8130 (ptm160) cc_final: 0.7431 (ptt-90) REVERT: M 141 LYS cc_start: 0.7950 (mttt) cc_final: 0.7590 (mttm) REVERT: M 276 LYS cc_start: 0.7913 (tttm) cc_final: 0.7426 (ttmt) REVERT: M 331 MET cc_start: 0.7625 (mmt) cc_final: 0.7059 (mtm) REVERT: N 144 ARG cc_start: 0.8139 (mtm180) cc_final: 0.7906 (mtt90) REVERT: N 170 ARG cc_start: 0.8018 (mtt180) cc_final: 0.7799 (mtt-85) REVERT: O 124 GLN cc_start: 0.8415 (mt0) cc_final: 0.8210 (mt0) REVERT: O 127 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7415 (pm20) REVERT: O 144 ARG cc_start: 0.8107 (mtm180) cc_final: 0.7893 (mtt90) REVERT: O 170 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7808 (mtt-85) REVERT: O 182 GLU cc_start: 0.6918 (tp30) cc_final: 0.6580 (mt-10) REVERT: O 195 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6325 (mt-10) REVERT: P 127 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7750 (pm20) REVERT: P 144 ARG cc_start: 0.8147 (mtm180) cc_final: 0.7937 (mtt90) REVERT: P 161 TYR cc_start: 0.7443 (t80) cc_final: 0.6970 (t80) REVERT: o 94 LYS cc_start: 0.7596 (mtpt) cc_final: 0.7131 (mttt) REVERT: o 129 ARG cc_start: 0.8042 (ptm160) cc_final: 0.7385 (ptt-90) REVERT: o 141 LYS cc_start: 0.7943 (mttt) cc_final: 0.7590 (mttm) REVERT: o 331 MET cc_start: 0.7595 (mmt) cc_final: 0.7032 (mtm) REVERT: B 364 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7147 (tmt170) REVERT: F 332 ASP cc_start: 0.8678 (m-30) cc_final: 0.8476 (m-30) REVERT: F 376 LYS cc_start: 0.9307 (mtmt) cc_final: 0.9051 (mtpp) REVERT: H 218 ARG cc_start: 0.8097 (tpt-90) cc_final: 0.7599 (mmm160) outliers start: 47 outliers final: 39 residues processed: 483 average time/residue: 0.1887 time to fit residues: 132.4327 Evaluate side-chains 476 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 436 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 488 HIS Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 407 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 471 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 169 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 265 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 226 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.144316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.115575 restraints weight = 27032.578| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.61 r_work: 0.2868 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22552 Z= 0.120 Angle : 0.540 8.683 30560 Z= 0.278 Chirality : 0.041 0.134 3392 Planarity : 0.004 0.045 3864 Dihedral : 9.493 59.371 3291 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.08 % Favored : 96.70 % Rotamer: Outliers : 2.02 % Allowed : 14.60 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.05 (0.16), residues: 2728 helix: 1.95 (0.14), residues: 1608 sheet: 0.31 (0.39), residues: 152 loop : -1.47 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 170 TYR 0.023 0.001 TYR H 485 PHE 0.023 0.001 PHE H 323 TRP 0.010 0.001 TRP I 185 HIS 0.006 0.001 HIS o 135 Details of bonding type rmsd covalent geometry : bond 0.00273 (22548) covalent geometry : angle 0.54026 (30552) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.56637 ( 8) hydrogen bonds : bond 0.04833 ( 1096) hydrogen bonds : angle 3.52776 ( 3204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 439 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 364 ARG cc_start: 0.7919 (tpp80) cc_final: 0.7236 (ttt180) REVERT: G 129 ARG cc_start: 0.8131 (ptm160) cc_final: 0.7442 (ptt-90) REVERT: G 141 LYS cc_start: 0.7975 (mttt) cc_final: 0.7608 (mttm) REVERT: G 331 MET cc_start: 0.7619 (mmt) cc_final: 0.7039 (mtm) REVERT: I 129 ARG cc_start: 0.8009 (ptm160) cc_final: 0.7374 (ptt-90) REVERT: I 141 LYS cc_start: 0.7873 (mttt) cc_final: 0.7473 (mttm) REVERT: I 268 LYS cc_start: 0.8375 (tttt) cc_final: 0.8169 (ttpt) REVERT: I 331 MET cc_start: 0.7509 (mmt) cc_final: 0.6943 (mtm) REVERT: J 127 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7385 (pm20) REVERT: J 144 ARG cc_start: 0.8133 (mtm180) cc_final: 0.7933 (mtt90) REVERT: J 170 ARG cc_start: 0.7927 (mtt180) cc_final: 0.7715 (mtt-85) REVERT: M 104 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7373 (tppt) REVERT: M 129 ARG cc_start: 0.8121 (ptm160) cc_final: 0.7425 (ptt-90) REVERT: M 141 LYS cc_start: 0.7899 (mttt) cc_final: 0.7523 (mttm) REVERT: M 331 MET cc_start: 0.7559 (mmt) cc_final: 0.6972 (mtm) REVERT: N 144 ARG cc_start: 0.8130 (mtm180) cc_final: 0.7915 (mtt90) REVERT: N 170 ARG cc_start: 0.7956 (mtt180) cc_final: 0.7746 (mtt-85) REVERT: O 127 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7468 (pm20) REVERT: O 144 ARG cc_start: 0.8093 (mtm180) cc_final: 0.7884 (mtt90) REVERT: O 182 GLU cc_start: 0.6890 (tp30) cc_final: 0.6168 (tt0) REVERT: O 195 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6332 (mt-10) REVERT: P 127 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7768 (pm20) REVERT: P 161 TYR cc_start: 0.7460 (t80) cc_final: 0.7141 (t80) REVERT: o 129 ARG cc_start: 0.8026 (ptm160) cc_final: 0.7379 (ptt-90) REVERT: o 141 LYS cc_start: 0.7905 (mttt) cc_final: 0.7553 (mttm) REVERT: o 331 MET cc_start: 0.7540 (mmt) cc_final: 0.6954 (mtm) REVERT: B 364 ARG cc_start: 0.7839 (ttm-80) cc_final: 0.7112 (tmt170) REVERT: F 330 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7940 (tp) REVERT: F 376 LYS cc_start: 0.9277 (mtmt) cc_final: 0.9026 (mtpp) REVERT: H 218 ARG cc_start: 0.8061 (tpt-90) cc_final: 0.7588 (mmm160) outliers start: 47 outliers final: 44 residues processed: 469 average time/residue: 0.1880 time to fit residues: 127.7047 Evaluate side-chains 484 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 438 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain M residue 295 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 488 HIS Chi-restraints excluded: chain F residue 489 ARG Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 407 ILE Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 454 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 229 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 212 optimal weight: 0.0070 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.0170 chunk 19 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.144164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.115458 restraints weight = 27175.280| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.53 r_work: 0.2917 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22552 Z= 0.124 Angle : 0.548 9.860 30560 Z= 0.282 Chirality : 0.041 0.134 3392 Planarity : 0.004 0.045 3864 Dihedral : 9.466 59.258 3291 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.41 % Favored : 96.41 % Rotamer: Outliers : 2.28 % Allowed : 14.56 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.09 (0.16), residues: 2728 helix: 1.99 (0.14), residues: 1608 sheet: 0.29 (0.39), residues: 152 loop : -1.47 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 170 TYR 0.024 0.001 TYR H 485 PHE 0.022 0.001 PHE H 323 TRP 0.010 0.001 TRP o 243 HIS 0.006 0.001 HIS o 135 Details of bonding type rmsd covalent geometry : bond 0.00283 (22548) covalent geometry : angle 0.54814 (30552) SS BOND : bond 0.00190 ( 4) SS BOND : angle 0.56173 ( 8) hydrogen bonds : bond 0.04901 ( 1096) hydrogen bonds : angle 3.53211 ( 3204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 442 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 364 ARG cc_start: 0.7930 (tpp80) cc_final: 0.7269 (ttt180) REVERT: G 129 ARG cc_start: 0.8118 (ptm160) cc_final: 0.7429 (ptt-90) REVERT: G 141 LYS cc_start: 0.7992 (mttt) cc_final: 0.7618 (mttm) REVERT: G 331 MET cc_start: 0.7600 (mmt) cc_final: 0.7009 (mtm) REVERT: I 129 ARG cc_start: 0.7980 (ptm160) cc_final: 0.7362 (ptt-90) REVERT: I 141 LYS cc_start: 0.7917 (mttt) cc_final: 0.7524 (mttm) REVERT: I 268 LYS cc_start: 0.8329 (tttt) cc_final: 0.8120 (ttpt) REVERT: I 331 MET cc_start: 0.7524 (mmt) cc_final: 0.6949 (mtm) REVERT: J 127 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7397 (pm20) REVERT: J 170 ARG cc_start: 0.7902 (mtt180) cc_final: 0.7693 (mtt-85) REVERT: M 104 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7381 (tppt) REVERT: M 129 ARG cc_start: 0.8111 (ptm160) cc_final: 0.7425 (ptt-90) REVERT: M 141 LYS cc_start: 0.7934 (mttt) cc_final: 0.7574 (mttm) REVERT: M 331 MET cc_start: 0.7579 (mmt) cc_final: 0.6994 (mtm) REVERT: N 144 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7914 (mtt90) REVERT: N 170 ARG cc_start: 0.7944 (mtt180) cc_final: 0.7731 (mtt-85) REVERT: O 127 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7474 (pm20) REVERT: O 182 GLU cc_start: 0.6872 (tp30) cc_final: 0.6664 (mt-10) REVERT: O 195 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6361 (mt-10) REVERT: P 127 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7759 (pm20) REVERT: P 161 TYR cc_start: 0.7458 (t80) cc_final: 0.7156 (t80) REVERT: o 129 ARG cc_start: 0.8024 (ptm160) cc_final: 0.7385 (ptt-90) REVERT: o 141 LYS cc_start: 0.7945 (mttt) cc_final: 0.7585 (mttm) REVERT: o 331 MET cc_start: 0.7536 (mmt) cc_final: 0.6958 (mtm) REVERT: B 364 ARG cc_start: 0.7837 (ttm-80) cc_final: 0.7143 (tmt170) REVERT: F 364 ARG cc_start: 0.6924 (tmt170) cc_final: 0.6347 (ttp-170) outliers start: 53 outliers final: 51 residues processed: 476 average time/residue: 0.1820 time to fit residues: 126.1379 Evaluate side-chains 484 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 432 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 295 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 199 GLU Chi-restraints excluded: chain o residue 346 SER Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 488 HIS Chi-restraints excluded: chain H residue 216 PHE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 407 ILE Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 454 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 106 optimal weight: 0.4980 chunk 234 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 216 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.142605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.113962 restraints weight = 27228.990| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.53 r_work: 0.2896 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22552 Z= 0.155 Angle : 0.587 10.102 30560 Z= 0.304 Chirality : 0.042 0.138 3392 Planarity : 0.004 0.045 3864 Dihedral : 9.820 62.157 3291 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.74 % Favored : 96.11 % Rotamer: Outliers : 2.41 % Allowed : 14.52 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.01 (0.16), residues: 2728 helix: 1.95 (0.14), residues: 1584 sheet: 0.15 (0.39), residues: 148 loop : -1.43 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 170 TYR 0.025 0.002 TYR H 485 PHE 0.022 0.001 PHE H 323 TRP 0.012 0.002 TRP M 243 HIS 0.007 0.001 HIS o 135 Details of bonding type rmsd covalent geometry : bond 0.00367 (22548) covalent geometry : angle 0.58732 (30552) SS BOND : bond 0.00139 ( 4) SS BOND : angle 0.64527 ( 8) hydrogen bonds : bond 0.05565 ( 1096) hydrogen bonds : angle 3.65103 ( 3204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 444 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 364 ARG cc_start: 0.7945 (tpp80) cc_final: 0.7279 (ttt180) REVERT: G 94 LYS cc_start: 0.7693 (mtpt) cc_final: 0.7221 (mttp) REVERT: G 129 ARG cc_start: 0.8139 (ptm160) cc_final: 0.7467 (ptt-90) REVERT: G 141 LYS cc_start: 0.8026 (mttt) cc_final: 0.7640 (mttm) REVERT: G 331 MET cc_start: 0.7726 (mmt) cc_final: 0.7147 (mtm) REVERT: I 94 LYS cc_start: 0.7664 (mtpt) cc_final: 0.7208 (mttp) REVERT: I 129 ARG cc_start: 0.8026 (ptm160) cc_final: 0.7417 (ptt-90) REVERT: I 141 LYS cc_start: 0.7939 (mttt) cc_final: 0.7540 (mttm) REVERT: I 268 LYS cc_start: 0.8341 (tttt) cc_final: 0.8139 (ttpt) REVERT: I 331 MET cc_start: 0.7657 (mmt) cc_final: 0.7099 (mtm) REVERT: J 170 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7713 (mtt-85) REVERT: M 104 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7410 (tppt) REVERT: M 129 ARG cc_start: 0.8133 (ptm160) cc_final: 0.7465 (ptt-90) REVERT: M 141 LYS cc_start: 0.7964 (mttt) cc_final: 0.7590 (mttm) REVERT: M 276 LYS cc_start: 0.8096 (tttm) cc_final: 0.7615 (ttmt) REVERT: M 331 MET cc_start: 0.7710 (mmt) cc_final: 0.7124 (mtm) REVERT: N 144 ARG cc_start: 0.8178 (mtm180) cc_final: 0.7969 (mtt90) REVERT: N 170 ARG cc_start: 0.7980 (mtt180) cc_final: 0.7751 (mtt-85) REVERT: O 127 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7498 (pm20) REVERT: O 182 GLU cc_start: 0.6957 (tp30) cc_final: 0.6283 (tt0) REVERT: O 195 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6418 (mt-10) REVERT: P 127 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7769 (pm20) REVERT: P 161 TYR cc_start: 0.7475 (t80) cc_final: 0.7186 (t80) REVERT: o 94 LYS cc_start: 0.7664 (mtpt) cc_final: 0.7182 (mttp) REVERT: o 129 ARG cc_start: 0.8045 (ptm160) cc_final: 0.7416 (ptt-90) REVERT: o 141 LYS cc_start: 0.7987 (mttt) cc_final: 0.7621 (mttm) REVERT: o 276 LYS cc_start: 0.8070 (tttm) cc_final: 0.7582 (ttmt) REVERT: o 331 MET cc_start: 0.7676 (mmt) cc_final: 0.7106 (mtm) REVERT: B 364 ARG cc_start: 0.7914 (ttm-80) cc_final: 0.7191 (ttt180) REVERT: F 364 ARG cc_start: 0.6996 (tmt170) cc_final: 0.6369 (ttp-170) REVERT: H 218 ARG cc_start: 0.8065 (tpt-90) cc_final: 0.7672 (mmm160) REVERT: H 358 MET cc_start: 0.6851 (tpp) cc_final: 0.6585 (tpp) outliers start: 56 outliers final: 54 residues processed: 483 average time/residue: 0.1872 time to fit residues: 132.0421 Evaluate side-chains 491 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 436 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain M residue 104 LYS Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 199 GLU Chi-restraints excluded: chain o residue 154 VAL Chi-restraints excluded: chain o residue 346 SER Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 489 ARG Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 407 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain H residue 471 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 203 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 250 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 89 optimal weight: 0.0770 chunk 265 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.145373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.116764 restraints weight = 27160.135| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.57 r_work: 0.2891 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22552 Z= 0.111 Angle : 0.537 9.835 30560 Z= 0.275 Chirality : 0.040 0.133 3392 Planarity : 0.004 0.044 3864 Dihedral : 9.280 59.901 3291 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.12 % Favored : 96.74 % Rotamer: Outliers : 2.23 % Allowed : 14.78 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.16), residues: 2728 helix: 2.05 (0.14), residues: 1608 sheet: 0.27 (0.39), residues: 152 loop : -1.47 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 170 TYR 0.025 0.001 TYR H 485 PHE 0.022 0.001 PHE H 323 TRP 0.009 0.001 TRP o 185 HIS 0.005 0.001 HIS M 135 Details of bonding type rmsd covalent geometry : bond 0.00246 (22548) covalent geometry : angle 0.53677 (30552) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.48129 ( 8) hydrogen bonds : bond 0.04452 ( 1096) hydrogen bonds : angle 3.47607 ( 3204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5066.00 seconds wall clock time: 87 minutes 13.21 seconds (5233.21 seconds total)