Starting phenix.real_space_refine on Thu Jun 19 07:02:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wf4_32460/06_2025/7wf4_32460_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wf4_32460/06_2025/7wf4_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_32460/06_2025/7wf4_32460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wf4_32460/06_2025/7wf4_32460.map" model { file = "/net/cci-nas-00/data/ceres_data/7wf4_32460/06_2025/7wf4_32460_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wf4_32460/06_2025/7wf4_32460_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'GLN:plan1': 2, 'ASN:plan1': 1} 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: {'GLN:plan1': 2, 'ARG:plan': 1} 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: {'GLN:plan1': 2, 'ARG:plan': 1} 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: {'GLN:plan1': 2, 'ARG:plan': 1} 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: {'GLN:plan1': 2, 'ARG:plan': 1} 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, 'GLN:plan1': 2, 'ASN:plan1': 1} 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, 'GLN:plan1': 2, 'ASN:plan1': 1} 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, 'GLN:plan1': 2, 'ASN:plan1': 1} 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: 14.10, per 1000 atoms: 0.64 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: 4.94 Conformation dependent library (CDL) restraints added in 2.8 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: 2.17 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: 6.61 Time building geometry restraints manager: 5.86 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: 5.620 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: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 47.810 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.110 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.590 ------------------------------------------------------------------------------- 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 : 6.38 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (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 TRP 0.014 0.002 TRP o 243 HIS 0.009 0.001 HIS I 135 PHE 0.020 0.002 PHE H 296 TYR 0.016 0.002 TYR H 487 ARG 0.004 0.001 ARG F 313 Details of bonding type rmsd hydrogen bonds : bond 0.19273 ( 1096) hydrogen bonds : angle 6.04255 ( 3204) SS BOND : bond 0.00380 ( 4) SS BOND : angle 1.28417 ( 8) covalent geometry : bond 0.00887 (22548) covalent geometry : angle 1.04742 (30552) *********************** 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 : 2.311 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: 0.7132 (m-10) REVERT: D 260 ARG cc_start: 0.5410 (OUTLIER) cc_final: 0.4494 (ttm170) REVERT: D 351 GLN cc_start: 0.4956 (OUTLIER) cc_final: 0.3568 (mp10) REVERT: D 386 ILE cc_start: 0.8061 (mt) cc_final: 0.7821 (mt) REVERT: D 463 LEU cc_start: 0.7066 (mt) cc_final: 0.6740 (mt) REVERT: G 73 MET cc_start: 0.7728 (mtp) cc_final: 0.7476 (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: 0.7250 (ttmp) REVERT: G 124 LYS cc_start: 0.7357 (mtmt) cc_final: 0.7112 (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: 0.7232 (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: 0.7326 (mtp) REVERT: I 94 LYS cc_start: 0.6998 (mtpt) cc_final: 0.6642 (mtmm) REVERT: I 106 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8141 (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: 0.7381 (mtpp) REVERT: I 129 ARG cc_start: 0.7148 (ptm160) cc_final: 0.6775 (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: 0.8020 (ttpt) REVERT: I 274 LYS cc_start: 0.7655 (tttt) cc_final: 0.7376 (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: 0.6390 (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: 0.7719 (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: 0.7461 (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: 0.6773 (ttmp) REVERT: M 124 LYS cc_start: 0.7642 (mtmt) cc_final: 0.7376 (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: 0.8034 (ttpt) REVERT: M 274 LYS cc_start: 0.7674 (tttt) cc_final: 0.7431 (ttpt) REVERT: M 276 LYS cc_start: 0.7503 (tttt) cc_final: 0.7007 (ttmt) REVERT: M 331 MET cc_start: 0.6531 (mmt) cc_final: 0.6183 (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: 0.7372 (mtt-85) REVERT: N 181 SER cc_start: 0.7686 (t) cc_final: 0.7474 (m) REVERT: O 144 ARG cc_start: 0.7840 (mtm180) cc_final: 0.7537 (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: 0.7617 (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: 0.8093 (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: 0.7486 (mtt-85) REVERT: o 73 MET cc_start: 0.7579 (mtp) cc_final: 0.7269 (mtp) REVERT: o 94 LYS cc_start: 0.6993 (mtpt) cc_final: 0.6717 (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: 0.7447 (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: 0.7472 (t) REVERT: o 268 LYS cc_start: 0.8240 (tttt) cc_final: 0.7970 (ttpt) REVERT: o 276 LYS cc_start: 0.7401 (tttt) cc_final: 0.6877 (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: 0.5943 (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: 0.7381 (mm) REVERT: F 259 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6166 (m-10) REVERT: F 463 LEU cc_start: 0.7147 (mt) cc_final: 0.6911 (mt) REVERT: H 244 ILE cc_start: 0.7513 (mt) cc_final: 0.7043 (mt) REVERT: H 301 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5821 (tt) REVERT: H 309 GLU cc_start: 0.3583 (tm-30) cc_final: 0.2885 (tm-30) REVERT: H 341 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9023 (mt) REVERT: H 351 GLN cc_start: 0.5344 (OUTLIER) cc_final: 0.3167 (mp10) REVERT: H 376 LYS cc_start: 0.6759 (mtpp) cc_final: 0.6537 (mtpp) outliers start: 140 outliers final: 43 residues processed: 652 average time/residue: 0.4179 time to fit residues: 396.3077 Evaluate side-chains 509 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 449 time to evaluate : 2.464 ------------------------------------------------------------------------------- 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 226 optimal weight: 2.9990 chunk 203 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 210 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 243 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 329 ASN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 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 = 0.3595 r_free = 0.3595 target = 0.152546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.130508 restraints weight = 26638.650| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.56 r_work: 0.3040 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22552 Z= 0.160 Angle : 0.636 7.722 30560 Z= 0.333 Chirality : 0.043 0.140 3392 Planarity : 0.005 0.047 3864 Dihedral : 11.025 62.767 3411 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.44 % Allowed : 2.86 % Favored : 96.70 % Rotamer: Outliers : 3.26 % Allowed : 10.95 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2728 helix: 1.18 (0.13), residues: 1552 sheet: 0.75 (0.35), residues: 216 loop : -2.08 (0.16), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 243 HIS 0.007 0.001 HIS G 135 PHE 0.025 0.001 PHE D 314 TYR 0.022 0.002 TYR D 339 ARG 0.006 0.001 ARG F 373 Details of bonding type rmsd hydrogen bonds : bond 0.06018 ( 1096) hydrogen bonds : angle 3.95327 ( 3204) SS BOND : bond 0.00118 ( 4) SS BOND : angle 0.46897 ( 8) covalent geometry : bond 0.00365 (22548) covalent geometry : angle 0.63585 (30552) *********************** 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 570 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 494 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 308 PHE cc_start: 0.8234 (t80) cc_final: 0.8024 (t80) REVERT: D 364 ARG cc_start: 0.8056 (tpp80) cc_final: 0.7533 (ttp-170) REVERT: G 94 LYS cc_start: 0.7912 (mtpt) cc_final: 0.7561 (mtmm) REVERT: G 129 ARG cc_start: 0.8270 (ptm160) cc_final: 0.7739 (ptt-90) REVERT: G 141 LYS cc_start: 0.8235 (mttt) cc_final: 0.7856 (mttm) REVERT: G 227 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7949 (t) REVERT: G 276 LYS cc_start: 0.8406 (tttt) cc_final: 0.7827 (ttmm) REVERT: G 331 MET cc_start: 0.7913 (mmt) cc_final: 0.7448 (mtm) REVERT: I 73 MET cc_start: 0.8366 (mtp) cc_final: 0.8158 (mtp) REVERT: I 129 ARG cc_start: 0.8221 (ptm160) cc_final: 0.7708 (ptt-90) REVERT: I 141 LYS cc_start: 0.8153 (mttt) cc_final: 0.7766 (mttm) REVERT: I 161 ASP cc_start: 0.8612 (t0) cc_final: 0.8404 (t0) REVERT: I 276 LYS cc_start: 0.8382 (tttt) cc_final: 0.7789 (ttmm) REVERT: I 331 MET cc_start: 0.7998 (mmt) cc_final: 0.7428 (mtm) REVERT: I 338 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7344 (mm-40) REVERT: J 144 ARG cc_start: 0.8300 (mtm180) cc_final: 0.8056 (mtt90) REVERT: J 170 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7735 (mtt-85) REVERT: M 67 GLU cc_start: 0.6989 (mp0) cc_final: 0.6759 (mp0) REVERT: M 73 MET cc_start: 0.8499 (mtp) cc_final: 0.8278 (mtp) REVERT: M 104 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7675 (tppt) REVERT: M 129 ARG cc_start: 0.8304 (ptm160) cc_final: 0.7756 (ptt-90) REVERT: M 141 LYS cc_start: 0.8225 (mttt) cc_final: 0.7872 (mttm) REVERT: M 276 LYS cc_start: 0.8395 (tttt) cc_final: 0.7838 (ttmt) REVERT: M 331 MET cc_start: 0.8011 (mmt) cc_final: 0.7511 (mtm) REVERT: N 144 ARG cc_start: 0.8299 (mtm180) cc_final: 0.8058 (mtt90) REVERT: N 170 ARG cc_start: 0.7968 (mtt180) cc_final: 0.7201 (mmt-90) REVERT: O 144 ARG cc_start: 0.8299 (mtm180) cc_final: 0.8051 (mtt90) REVERT: O 170 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7317 (mmt-90) REVERT: O 181 SER cc_start: 0.8254 (t) cc_final: 0.8008 (m) REVERT: O 195 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6875 (tm-30) REVERT: O 199 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6514 (mm-30) REVERT: P 127 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7806 (pm20) REVERT: P 144 ARG cc_start: 0.8322 (mtm180) cc_final: 0.8039 (mtt90) REVERT: P 170 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7929 (mtt-85) REVERT: o 73 MET cc_start: 0.8338 (mtp) cc_final: 0.8105 (mtp) REVERT: o 104 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7740 (tppt) REVERT: o 129 ARG cc_start: 0.8277 (ptm160) cc_final: 0.7730 (ptt-90) REVERT: o 141 LYS cc_start: 0.8223 (mttt) cc_final: 0.7859 (mttm) REVERT: o 161 ASP cc_start: 0.8616 (t0) cc_final: 0.8390 (t0) REVERT: o 276 LYS cc_start: 0.8248 (tttt) cc_final: 0.7664 (ttmt) REVERT: o 331 MET cc_start: 0.8021 (mmt) cc_final: 0.7494 (mtm) REVERT: o 338 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7340 (mm-40) REVERT: B 262 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5984 (mt-10) REVERT: B 489 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7681 (ttm170) REVERT: F 309 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8544 (tm-30) REVERT: F 325 ARG cc_start: 0.7847 (mmt180) cc_final: 0.7167 (tpt170) REVERT: F 433 ASP cc_start: 0.8360 (t0) cc_final: 0.8048 (t0) REVERT: H 301 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7798 (tt) outliers start: 76 outliers final: 45 residues processed: 541 average time/residue: 0.3998 time to fit residues: 313.1667 Evaluate side-chains 501 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 449 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 224 PHE 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 410 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 227 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 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 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 330 LEU 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 454 THR Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 336 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 407 ILE Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 472 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 161 optimal weight: 0.7980 chunk 206 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 267 optimal weight: 0.7980 chunk 237 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 124 GLN F 451 HIS F 484 ASN H 451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.145240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.115683 restraints weight = 27303.946| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.67 r_work: 0.2926 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22552 Z= 0.132 Angle : 0.557 7.528 30560 Z= 0.293 Chirality : 0.041 0.138 3392 Planarity : 0.004 0.046 3864 Dihedral : 10.282 62.278 3330 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.90 % Favored : 96.81 % Rotamer: Outliers : 2.49 % Allowed : 11.60 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.16), residues: 2728 helix: 1.72 (0.14), residues: 1556 sheet: 1.00 (0.37), residues: 196 loop : -1.94 (0.16), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 305 HIS 0.007 0.001 HIS G 135 PHE 0.018 0.001 PHE F 406 TYR 0.019 0.001 TYR D 339 ARG 0.005 0.000 ARG M 40 Details of bonding type rmsd hydrogen bonds : bond 0.05359 ( 1096) hydrogen bonds : angle 3.72477 ( 3204) SS BOND : bond 0.00215 ( 4) SS BOND : angle 0.57073 ( 8) covalent geometry : bond 0.00297 (22548) covalent geometry : angle 0.55724 (30552) *********************** 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 518 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 460 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 328 MET cc_start: 0.7480 (mmm) cc_final: 0.7203 (mpp) REVERT: D 364 ARG cc_start: 0.7937 (tpp80) cc_final: 0.7294 (ttt-90) REVERT: D 488 HIS cc_start: 0.7464 (m170) cc_final: 0.7248 (m170) REVERT: G 94 LYS cc_start: 0.7594 (mtpt) cc_final: 0.7210 (mtmm) REVERT: G 129 ARG cc_start: 0.8057 (ptm160) cc_final: 0.7431 (ptt-90) REVERT: G 141 LYS cc_start: 0.7962 (mttt) cc_final: 0.7584 (mttm) REVERT: G 227 VAL cc_start: 0.7859 (OUTLIER) cc_final: 0.7648 (t) REVERT: G 331 MET cc_start: 0.7566 (mmt) cc_final: 0.7051 (mtm) REVERT: I 73 MET cc_start: 0.8080 (mtp) cc_final: 0.7859 (mtp) REVERT: I 94 LYS cc_start: 0.7485 (mtpt) cc_final: 0.7131 (mtmm) REVERT: I 129 ARG cc_start: 0.8017 (ptm160) cc_final: 0.7409 (ptt-90) REVERT: I 141 LYS cc_start: 0.7839 (mttt) cc_final: 0.7448 (mttm) REVERT: I 161 ASP cc_start: 0.8464 (t0) cc_final: 0.8212 (t0) REVERT: I 331 MET cc_start: 0.7613 (mmt) cc_final: 0.7060 (mtm) REVERT: J 144 ARG cc_start: 0.8169 (mtm180) cc_final: 0.7940 (mtt90) REVERT: J 170 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7723 (mtt-85) REVERT: M 73 MET cc_start: 0.8176 (mtp) cc_final: 0.7953 (mtp) REVERT: M 129 ARG cc_start: 0.8128 (ptm160) cc_final: 0.7483 (ptt-90) REVERT: M 141 LYS cc_start: 0.7932 (mttt) cc_final: 0.7547 (mttm) REVERT: M 331 MET cc_start: 0.7653 (mmt) cc_final: 0.7134 (mtm) REVERT: N 144 ARG cc_start: 0.8160 (mtm180) cc_final: 0.7929 (mtt90) REVERT: N 170 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7727 (mtt-85) REVERT: O 144 ARG cc_start: 0.8136 (mtm180) cc_final: 0.7904 (mtt90) REVERT: O 170 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7239 (mmt-90) REVERT: O 181 SER cc_start: 0.7932 (t) cc_final: 0.7648 (m) REVERT: O 195 GLU cc_start: 0.6787 (mm-30) cc_final: 0.5922 (mt-10) REVERT: O 199 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6353 (mm-30) REVERT: P 127 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7699 (pm20) REVERT: P 144 ARG cc_start: 0.8163 (mtm180) cc_final: 0.7921 (mtt90) REVERT: P 170 ARG cc_start: 0.8028 (mtt180) cc_final: 0.7815 (mtt-85) REVERT: o 73 MET cc_start: 0.8064 (mtp) cc_final: 0.7836 (mtp) REVERT: o 129 ARG cc_start: 0.8040 (ptm160) cc_final: 0.7405 (ptt-90) REVERT: o 141 LYS cc_start: 0.7872 (mttt) cc_final: 0.7517 (mttm) REVERT: o 161 ASP cc_start: 0.8492 (t0) cc_final: 0.8248 (t0) REVERT: o 331 MET cc_start: 0.7630 (mmt) cc_final: 0.7105 (mtm) REVERT: B 364 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7381 (ttp-170) REVERT: B 489 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7664 (ttm170) REVERT: F 433 ASP cc_start: 0.8468 (t0) cc_final: 0.8228 (t0) REVERT: H 362 ILE cc_start: 0.7809 (mt) cc_final: 0.7587 (mt) outliers start: 58 outliers final: 38 residues processed: 496 average time/residue: 0.3905 time to fit residues: 280.9413 Evaluate side-chains 481 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 440 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 307 SER 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 410 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 154 VAL Chi-restraints excluded: chain G residue 227 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 N residue 157 ASP Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 196 LYS Chi-restraints excluded: chain O residue 199 GLU Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain o residue 154 VAL 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 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 358 MET 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 H residue 216 PHE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 472 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 191 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.145031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.113731 restraints weight = 27321.569| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.65 r_work: 0.2806 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22552 Z= 0.128 Angle : 0.544 7.061 30560 Z= 0.285 Chirality : 0.041 0.136 3392 Planarity : 0.004 0.045 3864 Dihedral : 9.858 60.432 3300 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.01 % Favored : 96.70 % Rotamer: Outliers : 2.23 % Allowed : 12.76 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.16), residues: 2728 helix: 1.94 (0.14), residues: 1556 sheet: 0.71 (0.35), residues: 216 loop : -1.83 (0.17), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 243 HIS 0.006 0.001 HIS I 135 PHE 0.022 0.001 PHE H 315 TYR 0.015 0.001 TYR D 339 ARG 0.009 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.05110 ( 1096) hydrogen bonds : angle 3.63227 ( 3204) SS BOND : bond 0.00165 ( 4) SS BOND : angle 0.58855 ( 8) covalent geometry : bond 0.00293 (22548) covalent geometry : angle 0.54394 (30552) *********************** 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 524 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 472 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 364 ARG cc_start: 0.7899 (tpp80) cc_final: 0.7237 (ttt-90) REVERT: D 433 ASP cc_start: 0.8635 (t0) cc_final: 0.8403 (t0) REVERT: G 129 ARG cc_start: 0.8068 (ptm160) cc_final: 0.7408 (ptt-90) REVERT: G 141 LYS cc_start: 0.7998 (mttt) cc_final: 0.7629 (mttm) REVERT: G 331 MET cc_start: 0.7568 (mmt) cc_final: 0.7066 (mtm) REVERT: I 73 MET cc_start: 0.8114 (mtp) cc_final: 0.7908 (mtp) REVERT: I 129 ARG cc_start: 0.8017 (ptm160) cc_final: 0.7400 (ptt-90) REVERT: I 141 LYS cc_start: 0.7929 (mttt) cc_final: 0.7545 (mttm) REVERT: I 161 ASP cc_start: 0.8428 (t0) cc_final: 0.8165 (t0) REVERT: I 331 MET cc_start: 0.7549 (mmt) cc_final: 0.7035 (mtm) REVERT: J 144 ARG cc_start: 0.8160 (mtm180) cc_final: 0.7944 (mtt90) REVERT: J 170 ARG cc_start: 0.8004 (mtt180) cc_final: 0.7783 (mtt-85) REVERT: M 73 MET cc_start: 0.8182 (mtp) cc_final: 0.7975 (mtp) REVERT: M 129 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7443 (ptt-90) REVERT: M 141 LYS cc_start: 0.7962 (mttt) cc_final: 0.7603 (mttm) REVERT: M 276 LYS cc_start: 0.8093 (tttm) cc_final: 0.7611 (ttmt) REVERT: M 331 MET cc_start: 0.7574 (mmt) cc_final: 0.7044 (mtm) REVERT: N 144 ARG cc_start: 0.8154 (mtm180) cc_final: 0.7925 (mtt90) REVERT: N 170 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7770 (mtt-85) REVERT: N 194 MET cc_start: 0.7454 (tpt) cc_final: 0.7229 (tpt) REVERT: O 144 ARG cc_start: 0.8103 (mtm180) cc_final: 0.7876 (mtt90) REVERT: O 170 ARG cc_start: 0.8031 (mtt180) cc_final: 0.7829 (mtt-85) REVERT: O 181 SER cc_start: 0.7876 (t) cc_final: 0.7624 (m) REVERT: O 195 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6050 (mt-10) REVERT: O 199 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6279 (mm-30) REVERT: P 127 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7766 (pm20) REVERT: P 144 ARG cc_start: 0.8131 (mtm180) cc_final: 0.7905 (mtt90) REVERT: P 170 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7851 (mtt-85) REVERT: o 73 MET cc_start: 0.8137 (mtp) cc_final: 0.7935 (mtp) REVERT: o 129 ARG cc_start: 0.8034 (ptm160) cc_final: 0.7397 (ptt-90) REVERT: o 141 LYS cc_start: 0.7971 (mttt) cc_final: 0.7634 (mttm) REVERT: o 161 ASP cc_start: 0.8465 (t0) cc_final: 0.8207 (t0) REVERT: o 331 MET cc_start: 0.7576 (mmt) cc_final: 0.7067 (mtm) REVERT: B 364 ARG cc_start: 0.7963 (ttm-80) cc_final: 0.7289 (ttp-170) REVERT: F 433 ASP cc_start: 0.8577 (t0) cc_final: 0.8324 (t0) REVERT: H 226 TYR cc_start: 0.8625 (m-80) cc_final: 0.8409 (m-80) outliers start: 52 outliers final: 43 residues processed: 500 average time/residue: 0.4018 time to fit residues: 292.0281 Evaluate side-chains 489 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 445 time to evaluate : 2.285 ------------------------------------------------------------------------------- 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 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 410 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 I residue 346 SER Chi-restraints excluded: chain J residue 157 ASP 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 O residue 196 LYS Chi-restraints excluded: chain O residue 199 GLU Chi-restraints excluded: chain P residue 157 ASP 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 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 F residue 330 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 358 MET 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 H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 374 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 472 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 58 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.148677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.120884 restraints weight = 26671.635| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.15 r_work: 0.2852 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22552 Z= 0.200 Angle : 0.620 8.021 30560 Z= 0.327 Chirality : 0.044 0.144 3392 Planarity : 0.005 0.047 3864 Dihedral : 10.499 68.481 3299 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.59 % Favored : 95.82 % Rotamer: Outliers : 3.14 % Allowed : 12.54 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2728 helix: 1.66 (0.14), residues: 1584 sheet: 0.78 (0.36), residues: 192 loop : -1.80 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 243 HIS 0.007 0.001 HIS o 135 PHE 0.018 0.002 PHE H 315 TYR 0.014 0.002 TYR D 339 ARG 0.006 0.000 ARG F 218 Details of bonding type rmsd hydrogen bonds : bond 0.06654 ( 1096) hydrogen bonds : angle 3.89029 ( 3204) SS BOND : bond 0.00062 ( 4) SS BOND : angle 0.76320 ( 8) covalent geometry : bond 0.00481 (22548) covalent geometry : angle 0.61987 (30552) *********************** 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 522 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 449 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 364 ARG cc_start: 0.8118 (tpp80) cc_final: 0.7424 (ttt180) REVERT: D 433 ASP cc_start: 0.8725 (t0) cc_final: 0.8415 (t0) REVERT: G 94 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7386 (mttt) REVERT: G 129 ARG cc_start: 0.8166 (ptm160) cc_final: 0.7541 (ptt-90) REVERT: G 141 LYS cc_start: 0.8113 (mttt) cc_final: 0.7753 (mttm) REVERT: G 331 MET cc_start: 0.7858 (mmt) cc_final: 0.7259 (mtm) REVERT: I 73 MET cc_start: 0.8314 (mtp) cc_final: 0.8083 (mtp) REVERT: I 94 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7362 (mttt) REVERT: I 129 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7533 (ptt-90) REVERT: I 141 LYS cc_start: 0.8041 (mttt) cc_final: 0.7652 (mttm) REVERT: I 276 LYS cc_start: 0.8243 (tttm) cc_final: 0.7749 (ttmt) REVERT: I 331 MET cc_start: 0.7866 (mmt) cc_final: 0.7258 (mtm) REVERT: J 144 ARG cc_start: 0.8336 (mtm180) cc_final: 0.8131 (mtt90) REVERT: J 170 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7812 (mtt-85) REVERT: M 73 MET cc_start: 0.8349 (mtp) cc_final: 0.8123 (mtp) REVERT: M 94 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7353 (mttp) REVERT: M 129 ARG cc_start: 0.8234 (ptm160) cc_final: 0.7572 (ptt-90) REVERT: M 276 LYS cc_start: 0.8210 (tttm) cc_final: 0.7715 (ttmt) REVERT: M 331 MET cc_start: 0.7888 (mmt) cc_final: 0.7286 (mtm) REVERT: N 144 ARG cc_start: 0.8281 (mtm180) cc_final: 0.8053 (mtt90) REVERT: N 170 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7751 (mtt-85) REVERT: N 191 GLU cc_start: 0.7400 (tp30) cc_final: 0.7084 (tp30) REVERT: N 199 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6466 (mm-30) REVERT: O 124 GLN cc_start: 0.8651 (mt0) cc_final: 0.8448 (mt0) REVERT: O 144 ARG cc_start: 0.8257 (mtm180) cc_final: 0.8031 (mtt90) REVERT: O 170 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7810 (mtt-85) REVERT: O 181 SER cc_start: 0.7974 (t) cc_final: 0.7748 (m) REVERT: P 127 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7840 (pm20) REVERT: P 144 ARG cc_start: 0.8294 (mtm180) cc_final: 0.8083 (mtt90) REVERT: P 170 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7769 (mtt-85) REVERT: o 73 MET cc_start: 0.8322 (mtp) cc_final: 0.8093 (mtp) REVERT: o 94 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7336 (mttt) REVERT: o 129 ARG cc_start: 0.8134 (ptm160) cc_final: 0.7505 (ptt-90) REVERT: o 276 LYS cc_start: 0.8094 (tttm) cc_final: 0.7575 (ttmt) REVERT: o 331 MET cc_start: 0.7882 (mmt) cc_final: 0.7276 (mtm) REVERT: B 364 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7486 (tmt170) REVERT: H 323 PHE cc_start: 0.8177 (t80) cc_final: 0.7915 (t80) outliers start: 73 outliers final: 53 residues processed: 496 average time/residue: 0.4117 time to fit residues: 295.4533 Evaluate side-chains 477 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 424 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 307 SER 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 154 VAL Chi-restraints excluded: chain G residue 289 LEU 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 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 O residue 196 LYS Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain o residue 154 VAL 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 454 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 304 ILE 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 454 THR Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 347 LEU 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 472 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 228 optimal weight: 1.9990 chunk 258 optimal weight: 0.5980 chunk 265 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 196 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 204 optimal weight: 5.9990 chunk 200 optimal weight: 0.5980 chunk 150 optimal weight: 0.9990 chunk 216 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.144877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.113844 restraints weight = 27140.197| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.62 r_work: 0.2901 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22552 Z= 0.112 Angle : 0.533 8.974 30560 Z= 0.275 Chirality : 0.040 0.129 3392 Planarity : 0.004 0.045 3864 Dihedral : 9.462 59.361 3292 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.75 % Favored : 96.99 % Rotamer: Outliers : 2.32 % Allowed : 13.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.16), residues: 2728 helix: 1.83 (0.14), residues: 1608 sheet: 0.17 (0.39), residues: 152 loop : -1.57 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 305 HIS 0.006 0.001 HIS G 135 PHE 0.022 0.001 PHE H 315 TYR 0.014 0.001 TYR D 339 ARG 0.004 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 1096) hydrogen bonds : angle 3.56097 ( 3204) SS BOND : bond 0.00222 ( 4) SS BOND : angle 0.55351 ( 8) covalent geometry : bond 0.00247 (22548) covalent geometry : angle 0.53261 (30552) *********************** 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 508 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 454 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 364 ARG cc_start: 0.7923 (tpp80) cc_final: 0.7272 (ttt180) REVERT: D 433 ASP cc_start: 0.8510 (t0) cc_final: 0.8227 (t0) REVERT: G 129 ARG cc_start: 0.8048 (ptm160) cc_final: 0.7396 (ptt-90) REVERT: G 141 LYS cc_start: 0.8010 (mttt) cc_final: 0.7612 (mttm) REVERT: G 331 MET cc_start: 0.7579 (mmt) cc_final: 0.7037 (mtm) REVERT: I 73 MET cc_start: 0.8111 (mtp) cc_final: 0.7884 (mtp) REVERT: I 129 ARG cc_start: 0.7964 (ptm160) cc_final: 0.7375 (ptt-90) REVERT: I 141 LYS cc_start: 0.7957 (mttt) cc_final: 0.7559 (mttm) REVERT: I 161 ASP cc_start: 0.8453 (t0) cc_final: 0.8207 (t0) REVERT: I 331 MET cc_start: 0.7590 (mmt) cc_final: 0.7069 (mtm) REVERT: J 144 ARG cc_start: 0.8162 (mtm180) cc_final: 0.7960 (mtt90) REVERT: J 170 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7750 (mtt-85) REVERT: M 73 MET cc_start: 0.8138 (mtp) cc_final: 0.7925 (mtp) REVERT: M 129 ARG cc_start: 0.8083 (ptm160) cc_final: 0.7430 (ptt-90) REVERT: M 141 LYS cc_start: 0.7993 (mttt) cc_final: 0.7642 (mttm) REVERT: M 331 MET cc_start: 0.7593 (mmt) cc_final: 0.7049 (mtm) REVERT: N 144 ARG cc_start: 0.8146 (mtm180) cc_final: 0.7933 (mtt90) REVERT: O 124 GLN cc_start: 0.8468 (mt0) cc_final: 0.8267 (mt0) REVERT: O 170 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7744 (mtt-85) REVERT: P 127 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7804 (pm20) REVERT: o 73 MET cc_start: 0.8118 (mtp) cc_final: 0.7892 (mtp) REVERT: o 129 ARG cc_start: 0.7983 (ptm160) cc_final: 0.7378 (ptt-90) REVERT: o 141 LYS cc_start: 0.7999 (mttt) cc_final: 0.7654 (mttm) REVERT: o 161 ASP cc_start: 0.8484 (t0) cc_final: 0.8247 (t0) REVERT: o 331 MET cc_start: 0.7612 (mmt) cc_final: 0.7091 (mtm) REVERT: B 364 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7208 (tmt170) REVERT: F 218 ARG cc_start: 0.7558 (tpp-160) cc_final: 0.7123 (ttp-170) REVERT: F 330 LEU cc_start: 0.8163 (mm) cc_final: 0.7934 (tp) REVERT: F 358 MET cc_start: 0.6472 (tpp) cc_final: 0.6060 (tpt) REVERT: H 218 ARG cc_start: 0.8206 (ttt180) cc_final: 0.7991 (tpt-90) outliers start: 54 outliers final: 43 residues processed: 482 average time/residue: 0.4125 time to fit residues: 290.7861 Evaluate side-chains 480 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 437 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU 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 410 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 466 ILE 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 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 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 293 ASP Chi-restraints excluded: chain B residue 307 SER 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 374 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain F residue 222 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 472 ILE Chi-restraints excluded: chain H residue 243 VAL 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 454 THR Chi-restraints excluded: chain H residue 472 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 72 optimal weight: 0.6980 chunk 266 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 267 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 265 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 124 GLN N 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 = 0.3497 r_free = 0.3497 target = 0.144408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.113248 restraints weight = 27174.626| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.63 r_work: 0.2911 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22552 Z= 0.118 Angle : 0.536 9.392 30560 Z= 0.277 Chirality : 0.040 0.133 3392 Planarity : 0.004 0.045 3864 Dihedral : 9.360 59.991 3290 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.78 % Favored : 95.97 % Rotamer: Outliers : 2.32 % Allowed : 14.09 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.16), residues: 2728 helix: 1.92 (0.14), residues: 1608 sheet: 0.72 (0.36), residues: 192 loop : -1.66 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 185 HIS 0.006 0.001 HIS o 135 PHE 0.034 0.001 PHE H 323 TYR 0.012 0.001 TYR D 339 ARG 0.007 0.000 ARG P 170 Details of bonding type rmsd hydrogen bonds : bond 0.04821 ( 1096) hydrogen bonds : angle 3.54020 ( 3204) SS BOND : bond 0.00200 ( 4) SS BOND : angle 0.56312 ( 8) covalent geometry : bond 0.00267 (22548) covalent geometry : angle 0.53641 (30552) *********************** 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 499 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 445 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 364 ARG cc_start: 0.7887 (tpp80) cc_final: 0.7275 (ttt180) REVERT: D 422 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7010 (p0) REVERT: D 433 ASP cc_start: 0.8494 (t0) cc_final: 0.8206 (t0) REVERT: G 129 ARG cc_start: 0.8112 (ptm160) cc_final: 0.7434 (ptt-90) REVERT: G 141 LYS cc_start: 0.8006 (mttt) cc_final: 0.7626 (mttm) REVERT: G 331 MET cc_start: 0.7560 (mmt) cc_final: 0.6998 (mtm) REVERT: I 73 MET cc_start: 0.8108 (mtp) cc_final: 0.7891 (mtp) REVERT: I 129 ARG cc_start: 0.7959 (ptm160) cc_final: 0.7368 (ptt-90) REVERT: I 141 LYS cc_start: 0.7920 (mttt) cc_final: 0.7536 (mttm) REVERT: I 161 ASP cc_start: 0.8442 (t0) cc_final: 0.8184 (t0) REVERT: I 331 MET cc_start: 0.7531 (mmt) cc_final: 0.6987 (mtm) REVERT: J 170 ARG cc_start: 0.7963 (mtt180) cc_final: 0.7745 (mtt-85) REVERT: M 73 MET cc_start: 0.8118 (mtp) cc_final: 0.7899 (mtp) REVERT: M 129 ARG cc_start: 0.8131 (ptm160) cc_final: 0.7453 (ptt-90) REVERT: M 141 LYS cc_start: 0.7952 (mttt) cc_final: 0.7598 (mttm) REVERT: M 331 MET cc_start: 0.7582 (mmt) cc_final: 0.7004 (mtm) REVERT: N 124 GLN cc_start: 0.8364 (mt0) cc_final: 0.8119 (mt0) REVERT: N 144 ARG cc_start: 0.8155 (mtm180) cc_final: 0.7949 (mtt90) REVERT: N 199 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6547 (mm-30) REVERT: O 170 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7741 (mtt-85) REVERT: P 127 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7803 (pm20) REVERT: o 73 MET cc_start: 0.8100 (mtp) cc_final: 0.7874 (mtp) REVERT: o 129 ARG cc_start: 0.7999 (ptm160) cc_final: 0.7379 (ptt-90) REVERT: o 141 LYS cc_start: 0.7972 (mttt) cc_final: 0.7615 (mttm) REVERT: o 161 ASP cc_start: 0.8477 (t0) cc_final: 0.8227 (t0) REVERT: o 331 MET cc_start: 0.7545 (mmt) cc_final: 0.7001 (mtm) REVERT: B 364 ARG cc_start: 0.7806 (ttm-80) cc_final: 0.7144 (tmt170) REVERT: F 358 MET cc_start: 0.6601 (tpp) cc_final: 0.6245 (tpt) REVERT: H 218 ARG cc_start: 0.8306 (ttt180) cc_final: 0.7915 (tpt-90) outliers start: 54 outliers final: 49 residues processed: 476 average time/residue: 0.3915 time to fit residues: 273.1258 Evaluate side-chains 488 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 438 time to evaluate : 2.522 ------------------------------------------------------------------------------- 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 243 VAL Chi-restraints excluded: chain D residue 307 SER 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 410 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 466 ILE 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 G residue 346 SER Chi-restraints excluded: chain J residue 157 ASP 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 O residue 196 LYS Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain B residue 307 SER 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 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 B residue 472 ILE Chi-restraints excluded: chain F residue 222 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 472 ILE Chi-restraints excluded: chain F residue 488 HIS Chi-restraints excluded: chain H residue 243 VAL 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 472 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 194 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 238 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 202 optimal weight: 0.0770 chunk 112 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 chunk 213 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.145575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.116943 restraints weight = 27268.274| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.67 r_work: 0.2938 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 22552 Z= 0.106 Angle : 0.525 9.641 30560 Z= 0.270 Chirality : 0.040 0.131 3392 Planarity : 0.004 0.045 3864 Dihedral : 9.073 59.302 3290 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.90 % Favored : 96.85 % Rotamer: Outliers : 2.32 % Allowed : 14.39 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.16), residues: 2728 helix: 2.01 (0.14), residues: 1608 sheet: 0.16 (0.39), residues: 152 loop : -1.47 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 185 HIS 0.005 0.001 HIS G 135 PHE 0.025 0.001 PHE H 323 TYR 0.012 0.001 TYR D 339 ARG 0.006 0.000 ARG P 170 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 1096) hydrogen bonds : angle 3.46486 ( 3204) SS BOND : bond 0.00250 ( 4) SS BOND : angle 0.48793 ( 8) covalent geometry : bond 0.00234 (22548) covalent geometry : angle 0.52526 (30552) *********************** 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 504 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 450 time to evaluate : 4.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 364 ARG cc_start: 0.7898 (tpp80) cc_final: 0.7254 (ttt180) REVERT: G 129 ARG cc_start: 0.8090 (ptm160) cc_final: 0.7415 (ptt-90) REVERT: G 141 LYS cc_start: 0.8014 (mttt) cc_final: 0.7629 (mttm) REVERT: G 331 MET cc_start: 0.7588 (mmt) cc_final: 0.7035 (mtm) REVERT: I 129 ARG cc_start: 0.7970 (ptm160) cc_final: 0.7357 (ptt-90) REVERT: I 141 LYS cc_start: 0.7941 (mttt) cc_final: 0.7548 (mttm) REVERT: I 331 MET cc_start: 0.7541 (mmt) cc_final: 0.6985 (mtm) REVERT: M 129 ARG cc_start: 0.8102 (ptm160) cc_final: 0.7426 (ptt-90) REVERT: M 141 LYS cc_start: 0.7963 (mttt) cc_final: 0.7598 (mttm) REVERT: M 331 MET cc_start: 0.7625 (mmt) cc_final: 0.7060 (mtm) REVERT: N 124 GLN cc_start: 0.8359 (mt0) cc_final: 0.8148 (mt0) REVERT: N 144 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7909 (mtt90) REVERT: O 170 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7748 (mtt-85) REVERT: P 127 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7837 (pm20) REVERT: o 129 ARG cc_start: 0.8035 (ptm160) cc_final: 0.7389 (ptt-90) REVERT: o 141 LYS cc_start: 0.7984 (mttt) cc_final: 0.7613 (mttm) REVERT: o 331 MET cc_start: 0.7545 (mmt) cc_final: 0.6986 (mtm) REVERT: B 364 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7084 (tmt170) REVERT: F 218 ARG cc_start: 0.7576 (tpp-160) cc_final: 0.7118 (ttp-170) REVERT: F 330 LEU cc_start: 0.8144 (mm) cc_final: 0.7934 (tp) REVERT: F 358 MET cc_start: 0.6574 (tpp) cc_final: 0.6304 (tpt) REVERT: F 364 ARG cc_start: 0.6889 (tmt170) cc_final: 0.6459 (ttp-170) REVERT: H 374 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8909 (pt) outliers start: 54 outliers final: 44 residues processed: 480 average time/residue: 0.4969 time to fit residues: 356.6472 Evaluate side-chains 486 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 441 time to evaluate : 7.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 307 SER 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 374 ILE Chi-restraints excluded: chain D residue 410 ILE 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 295 ILE 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 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 243 VAL Chi-restraints excluded: chain B residue 293 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 369 VAL 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 B residue 472 ILE 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 416 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 243 VAL 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 416 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 131 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 198 optimal weight: 0.3980 chunk 155 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.144345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.113137 restraints weight = 27156.681| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.66 r_work: 0.2888 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3444 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= 0.122 Angle : 0.539 8.699 30560 Z= 0.279 Chirality : 0.041 0.140 3392 Planarity : 0.004 0.045 3864 Dihedral : 9.219 59.793 3289 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.70 % Favored : 96.04 % Rotamer: Outliers : 2.36 % Allowed : 14.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.16), residues: 2728 helix: 2.01 (0.14), residues: 1608 sheet: 0.17 (0.39), residues: 152 loop : -1.46 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 243 HIS 0.006 0.001 HIS G 135 PHE 0.025 0.001 PHE H 323 TYR 0.011 0.001 TYR G 270 ARG 0.008 0.000 ARG J 170 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 1096) hydrogen bonds : angle 3.51710 ( 3204) SS BOND : bond 0.00191 ( 4) SS BOND : angle 0.54822 ( 8) covalent geometry : bond 0.00279 (22548) covalent geometry : angle 0.53919 (30552) *********************** 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 506 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 451 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 364 ARG cc_start: 0.7869 (tpp80) cc_final: 0.7226 (ttt180) REVERT: D 422 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7057 (p0) REVERT: G 129 ARG cc_start: 0.8127 (ptm160) cc_final: 0.7431 (ptt-90) REVERT: G 141 LYS cc_start: 0.8006 (mttt) cc_final: 0.7610 (mttm) REVERT: G 331 MET cc_start: 0.7528 (mmt) cc_final: 0.6961 (mtm) REVERT: I 129 ARG cc_start: 0.8018 (ptm160) cc_final: 0.7387 (ptt-90) REVERT: I 141 LYS cc_start: 0.7927 (mttt) cc_final: 0.7526 (mttm) REVERT: I 331 MET cc_start: 0.7480 (mmt) cc_final: 0.6927 (mtm) REVERT: M 129 ARG cc_start: 0.8133 (ptm160) cc_final: 0.7447 (ptt-90) REVERT: M 141 LYS cc_start: 0.7956 (mttt) cc_final: 0.7580 (mttm) REVERT: M 276 LYS cc_start: 0.7997 (tttm) cc_final: 0.7506 (ttmt) REVERT: M 331 MET cc_start: 0.7534 (mmt) cc_final: 0.6958 (mtm) REVERT: O 170 ARG cc_start: 0.7942 (mtt180) cc_final: 0.7732 (mtt-85) REVERT: P 127 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7826 (pm20) REVERT: o 129 ARG cc_start: 0.8050 (ptm160) cc_final: 0.7395 (ptt-90) REVERT: o 141 LYS cc_start: 0.7959 (mttt) cc_final: 0.7587 (mttm) REVERT: o 331 MET cc_start: 0.7499 (mmt) cc_final: 0.6933 (mtm) REVERT: B 364 ARG cc_start: 0.7757 (ttm-80) cc_final: 0.7054 (tmt170) REVERT: F 330 LEU cc_start: 0.8201 (mm) cc_final: 0.7961 (tp) REVERT: F 358 MET cc_start: 0.6757 (tpp) cc_final: 0.6489 (tpt) REVERT: F 364 ARG cc_start: 0.6941 (tmt170) cc_final: 0.6225 (ttp-170) outliers start: 55 outliers final: 47 residues processed: 481 average time/residue: 0.3934 time to fit residues: 274.9296 Evaluate side-chains 487 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 439 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 307 SER 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 374 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 422 ASP 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 295 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain I residue 154 VAL 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 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 243 VAL Chi-restraints excluded: chain B residue 293 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 369 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain F residue 307 SER 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 416 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 243 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 173 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 226 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 145 optimal weight: 0.0770 chunk 165 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.145079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.113861 restraints weight = 27278.643| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.69 r_work: 0.2878 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22552 Z= 0.112 Angle : 0.531 9.599 30560 Z= 0.274 Chirality : 0.040 0.152 3392 Planarity : 0.004 0.045 3864 Dihedral : 9.090 59.952 3289 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.04 % Favored : 96.74 % Rotamer: Outliers : 2.23 % Allowed : 14.56 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.16), residues: 2728 helix: 2.05 (0.14), residues: 1608 sheet: 0.17 (0.38), residues: 152 loop : -1.44 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 185 HIS 0.005 0.001 HIS I 135 PHE 0.024 0.001 PHE H 323 TYR 0.011 0.001 TYR D 339 ARG 0.008 0.000 ARG D 209 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 1096) hydrogen bonds : angle 3.48463 ( 3204) SS BOND : bond 0.00223 ( 4) SS BOND : angle 0.48971 ( 8) covalent geometry : bond 0.00252 (22548) covalent geometry : angle 0.53113 (30552) ********************** 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 495 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 443 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 364 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7239 (ttt180) REVERT: D 422 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7025 (p0) REVERT: G 129 ARG cc_start: 0.8115 (ptm160) cc_final: 0.7408 (ptt-90) REVERT: G 141 LYS cc_start: 0.8018 (mttt) cc_final: 0.7632 (mttm) REVERT: G 331 MET cc_start: 0.7560 (mmt) cc_final: 0.7014 (mtm) REVERT: I 129 ARG cc_start: 0.8044 (ptm160) cc_final: 0.7397 (ptt-90) REVERT: I 141 LYS cc_start: 0.7940 (mttt) cc_final: 0.7551 (mttm) REVERT: I 331 MET cc_start: 0.7506 (mmt) cc_final: 0.6962 (mtm) REVERT: M 129 ARG cc_start: 0.8109 (ptm160) cc_final: 0.7423 (ptt-90) REVERT: M 141 LYS cc_start: 0.7971 (mttt) cc_final: 0.7601 (mttm) REVERT: M 276 LYS cc_start: 0.8007 (tttm) cc_final: 0.7521 (ttmt) REVERT: M 331 MET cc_start: 0.7544 (mmt) cc_final: 0.6979 (mtm) REVERT: P 127 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7834 (pm20) REVERT: o 129 ARG cc_start: 0.8042 (ptm160) cc_final: 0.7385 (ptt-90) REVERT: o 141 LYS cc_start: 0.7978 (mttt) cc_final: 0.7611 (mttm) REVERT: o 331 MET cc_start: 0.7516 (mmt) cc_final: 0.6964 (mtm) REVERT: B 358 MET cc_start: 0.6829 (tpp) cc_final: 0.6616 (tpp) REVERT: B 364 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7064 (tmt170) REVERT: F 218 ARG cc_start: 0.7618 (tpp-160) cc_final: 0.7119 (ttp-170) REVERT: F 330 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7931 (tp) REVERT: F 358 MET cc_start: 0.6769 (tpp) cc_final: 0.6528 (tpt) REVERT: F 364 ARG cc_start: 0.6986 (tmt170) cc_final: 0.6212 (ttp-170) REVERT: H 374 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8918 (pt) outliers start: 52 outliers final: 48 residues processed: 470 average time/residue: 0.4053 time to fit residues: 277.2922 Evaluate side-chains 488 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 437 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 307 SER 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 362 ILE Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 422 ASP 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 295 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain I residue 154 VAL 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 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 243 VAL Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 307 SER 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 410 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 472 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 416 VAL Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 489 ARG Chi-restraints excluded: chain H residue 243 VAL 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 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 190 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 chunk 224 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 133 optimal weight: 0.0470 chunk 192 optimal weight: 0.6980 overall best weight: 0.5880 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.145650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.114444 restraints weight = 27267.068| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.69 r_work: 0.2946 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 22552 Z= 0.109 Angle : 0.523 9.449 30560 Z= 0.270 Chirality : 0.040 0.148 3392 Planarity : 0.004 0.045 3864 Dihedral : 8.903 59.508 3289 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.59 % Favored : 96.19 % Rotamer: Outliers : 2.36 % Allowed : 14.52 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.16), residues: 2728 helix: 2.09 (0.14), residues: 1608 sheet: 0.17 (0.38), residues: 152 loop : -1.43 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 221 HIS 0.005 0.001 HIS I 135 PHE 0.023 0.001 PHE H 323 TYR 0.011 0.001 TYR D 339 ARG 0.010 0.000 ARG O 170 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 1096) hydrogen bonds : angle 3.44791 ( 3204) SS BOND : bond 0.00233 ( 4) SS BOND : angle 0.46595 ( 8) covalent geometry : bond 0.00241 (22548) covalent geometry : angle 0.52324 (30552) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12177.28 seconds wall clock time: 214 minutes 53.74 seconds (12893.74 seconds total)