Starting phenix.real_space_refine on Sat Mar 7 11:33:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vz8_21487/03_2026/6vz8_21487.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vz8_21487/03_2026/6vz8_21487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vz8_21487/03_2026/6vz8_21487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vz8_21487/03_2026/6vz8_21487.map" model { file = "/net/cci-nas-00/data/ceres_data/6vz8_21487/03_2026/6vz8_21487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vz8_21487/03_2026/6vz8_21487.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 8 5.21 5 S 200 5.16 5 C 26664 2.51 5 N 7372 2.21 5 O 7856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 275 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42132 Number of models: 1 Model: "" Number of chains: 32 Chain: "D" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 3910 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 495} Chain breaks: 6 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'HIS:plan': 4, 'GLU:plan': 6, 'TYR:plan': 2, 'ASP:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 105 Chain: "E" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 3953 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 505} Chain breaks: 4 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 6, 'ASP:plan': 8, 'TYR:plan': 2, 'HIS:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 121 Chain: "F" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1266 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 3, 'TRANS': 155} Chain: "G" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1228 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "H" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 3910 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 495} Chain breaks: 6 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'HIS:plan': 4, 'GLU:plan': 6, 'TYR:plan': 2, 'ASP:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 105 Chain: "I" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 3953 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 505} Chain breaks: 4 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 6, 'ASP:plan': 8, 'TYR:plan': 2, 'HIS:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 121 Chain: "J" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1266 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 3, 'TRANS': 155} Chain: "K" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1228 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "L" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 3910 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 495} Chain breaks: 6 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'HIS:plan': 4, 'GLU:plan': 6, 'TYR:plan': 2, 'ASP:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 105 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 3953 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 505} Chain breaks: 4 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 6, 'ASP:plan': 8, 'TYR:plan': 2, 'HIS:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 121 Chain: "N" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1266 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 3, 'TRANS': 155} Chain: "O" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1228 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "P" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 3910 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 495} Chain breaks: 6 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'HIS:plan': 4, 'GLU:plan': 6, 'TYR:plan': 2, 'ASP:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 105 Chain: "Q" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 3953 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 505} Chain breaks: 4 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 6, 'ASP:plan': 8, 'TYR:plan': 2, 'HIS:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 121 Chain: "R" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1266 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 3, 'TRANS': 155} Chain: "S" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1228 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "D" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "H" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "L" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "O" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "S" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 11.39, per 1000 atoms: 0.27 Number of scatterers: 42132 At special positions: 0 Unit cell: (228.78, 228.78, 96.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 200 16.00 P 32 15.00 Mg 8 11.99 O 7856 8.00 N 7372 7.00 C 26664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 2.0 seconds 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10232 Finding SS restraints... Secondary structure from input PDB file: 263 helices and 52 sheets defined 46.7% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'D' and resid 99 through 110 Processing helix chain 'D' and resid 123 through 133 Processing helix chain 'D' and resid 143 through 159 Processing helix chain 'D' and resid 169 through 186 removed outlier: 3.918A pdb=" N VAL D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER D 177 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 210 through 216 Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 256 through 261 Processing helix chain 'D' and resid 273 through 280 removed outlier: 3.514A pdb=" N SER D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 293 Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 316 through 323 Processing helix chain 'D' and resid 354 through 364 Processing helix chain 'D' and resid 375 through 380 Processing helix chain 'D' and resid 414 through 428 Processing helix chain 'D' and resid 429 through 434 Processing helix chain 'D' and resid 437 through 438 No H-bonds generated for 'chain 'D' and resid 437 through 438' Processing helix chain 'D' and resid 440 through 440 No H-bonds generated for 'chain 'D' and resid 440 through 440' Processing helix chain 'D' and resid 441 through 451 Processing helix chain 'D' and resid 463 through 474 Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.868A pdb=" N MET D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 527 Processing helix chain 'D' and resid 537 through 543 Processing helix chain 'D' and resid 544 through 546 No H-bonds generated for 'chain 'D' and resid 544 through 546' Processing helix chain 'D' and resid 547 through 555 removed outlier: 3.693A pdb=" N ILE D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 578 Processing helix chain 'D' and resid 600 through 608 removed outlier: 3.533A pdb=" N CYS D 608 " --> pdb=" O PHE D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 631 removed outlier: 4.328A pdb=" N ARG D 622 " --> pdb=" O LYS D 618 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU D 623 " --> pdb=" O ALA D 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 110 Processing helix chain 'E' and resid 123 through 133 Processing helix chain 'E' and resid 143 through 159 removed outlier: 3.557A pdb=" N PHE E 149 " --> pdb=" O GLN E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 186 removed outlier: 3.557A pdb=" N LEU E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER E 177 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLY E 178 " --> pdb=" O ASN E 174 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU E 184 " --> pdb=" O ALA E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 201 Processing helix chain 'E' and resid 210 through 216 Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'E' and resid 230 through 244 Processing helix chain 'E' and resid 256 through 261 Processing helix chain 'E' and resid 273 through 280 Processing helix chain 'E' and resid 285 through 296 Processing helix chain 'E' and resid 308 through 311 Processing helix chain 'E' and resid 313 through 323 Processing helix chain 'E' and resid 354 through 364 Processing helix chain 'E' and resid 375 through 380 Processing helix chain 'E' and resid 414 through 428 Processing helix chain 'E' and resid 429 through 434 Processing helix chain 'E' and resid 437 through 451 Processing helix chain 'E' and resid 463 through 474 Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.979A pdb=" N MET E 490 " --> pdb=" O GLY E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 527 Processing helix chain 'E' and resid 537 through 543 removed outlier: 4.063A pdb=" N MET E 543 " --> pdb=" O GLY E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 546 No H-bonds generated for 'chain 'E' and resid 544 through 546' Processing helix chain 'E' and resid 547 through 555 removed outlier: 3.736A pdb=" N ILE E 551 " --> pdb=" O GLU E 547 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 578 removed outlier: 3.539A pdb=" N TRP E 574 " --> pdb=" O MET E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 608 removed outlier: 3.501A pdb=" N PHE E 604 " --> pdb=" O ASN E 600 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS E 608 " --> pdb=" O PHE E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 631 removed outlier: 4.439A pdb=" N ARG E 622 " --> pdb=" O LYS E 618 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU E 623 " --> pdb=" O ALA E 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 111 removed outlier: 3.696A pdb=" N ARG F 102 " --> pdb=" O GLY F 98 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL F 106 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG F 110 " --> pdb=" O VAL F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 146 removed outlier: 3.678A pdb=" N GLN F 140 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 149 No H-bonds generated for 'chain 'F' and resid 147 through 149' Processing helix chain 'F' and resid 176 through 191 removed outlier: 3.544A pdb=" N TRP F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 221 Processing helix chain 'G' and resid 331 through 343 removed outlier: 4.123A pdb=" N ILE G 335 " --> pdb=" O GLY G 331 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE G 340 " --> pdb=" O VAL G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 382 removed outlier: 3.837A pdb=" N SER G 375 " --> pdb=" O ASP G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 426 removed outlier: 3.989A pdb=" N ARG G 416 " --> pdb=" O ALA G 412 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP G 417 " --> pdb=" O ALA G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 455 Processing helix chain 'H' and resid 99 through 110 Processing helix chain 'H' and resid 123 through 133 Processing helix chain 'H' and resid 143 through 159 Processing helix chain 'H' and resid 169 through 186 removed outlier: 3.917A pdb=" N VAL H 176 " --> pdb=" O ALA H 172 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER H 177 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLY H 178 " --> pdb=" O ASN H 174 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP H 181 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 201 Processing helix chain 'H' and resid 210 through 216 Processing helix chain 'H' and resid 227 through 229 No H-bonds generated for 'chain 'H' and resid 227 through 229' Processing helix chain 'H' and resid 230 through 244 Processing helix chain 'H' and resid 256 through 261 Processing helix chain 'H' and resid 273 through 280 removed outlier: 3.515A pdb=" N SER H 278 " --> pdb=" O PRO H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 293 Processing helix chain 'H' and resid 308 through 311 Processing helix chain 'H' and resid 316 through 323 Processing helix chain 'H' and resid 354 through 364 Processing helix chain 'H' and resid 375 through 380 Processing helix chain 'H' and resid 414 through 428 Processing helix chain 'H' and resid 429 through 434 Processing helix chain 'H' and resid 437 through 438 No H-bonds generated for 'chain 'H' and resid 437 through 438' Processing helix chain 'H' and resid 440 through 440 No H-bonds generated for 'chain 'H' and resid 440 through 440' Processing helix chain 'H' and resid 441 through 451 Processing helix chain 'H' and resid 463 through 474 Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.868A pdb=" N MET H 490 " --> pdb=" O GLY H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 527 Processing helix chain 'H' and resid 537 through 543 Processing helix chain 'H' and resid 544 through 546 No H-bonds generated for 'chain 'H' and resid 544 through 546' Processing helix chain 'H' and resid 547 through 555 removed outlier: 3.693A pdb=" N ILE H 551 " --> pdb=" O GLU H 547 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG H 552 " --> pdb=" O LEU H 548 " (cutoff:3.500A) Processing helix chain 'H' and resid 568 through 578 Processing helix chain 'H' and resid 600 through 608 removed outlier: 3.533A pdb=" N CYS H 608 " --> pdb=" O PHE H 604 " (cutoff:3.500A) Processing helix chain 'H' and resid 617 through 631 removed outlier: 4.328A pdb=" N ARG H 622 " --> pdb=" O LYS H 618 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU H 623 " --> pdb=" O ALA H 619 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 110 Processing helix chain 'I' and resid 123 through 133 Processing helix chain 'I' and resid 143 through 159 removed outlier: 3.557A pdb=" N PHE I 149 " --> pdb=" O GLN I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 186 removed outlier: 3.557A pdb=" N LEU I 175 " --> pdb=" O GLY I 171 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL I 176 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER I 177 " --> pdb=" O THR I 173 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLY I 178 " --> pdb=" O ASN I 174 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP I 181 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU I 184 " --> pdb=" O ALA I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 201 Processing helix chain 'I' and resid 210 through 216 Processing helix chain 'I' and resid 227 through 229 No H-bonds generated for 'chain 'I' and resid 227 through 229' Processing helix chain 'I' and resid 230 through 244 Processing helix chain 'I' and resid 256 through 261 Processing helix chain 'I' and resid 273 through 280 Processing helix chain 'I' and resid 285 through 296 Processing helix chain 'I' and resid 308 through 311 Processing helix chain 'I' and resid 313 through 323 Processing helix chain 'I' and resid 354 through 364 Processing helix chain 'I' and resid 375 through 380 Processing helix chain 'I' and resid 414 through 428 Processing helix chain 'I' and resid 429 through 434 Processing helix chain 'I' and resid 437 through 451 Processing helix chain 'I' and resid 463 through 474 Processing helix chain 'I' and resid 486 through 495 removed outlier: 3.979A pdb=" N MET I 490 " --> pdb=" O GLY I 486 " (cutoff:3.500A) Processing helix chain 'I' and resid 515 through 527 Processing helix chain 'I' and resid 537 through 543 removed outlier: 4.063A pdb=" N MET I 543 " --> pdb=" O GLY I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 544 through 546 No H-bonds generated for 'chain 'I' and resid 544 through 546' Processing helix chain 'I' and resid 547 through 555 removed outlier: 3.734A pdb=" N ILE I 551 " --> pdb=" O GLU I 547 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG I 552 " --> pdb=" O LEU I 548 " (cutoff:3.500A) Processing helix chain 'I' and resid 568 through 578 removed outlier: 3.539A pdb=" N TRP I 574 " --> pdb=" O MET I 570 " (cutoff:3.500A) Processing helix chain 'I' and resid 600 through 608 removed outlier: 3.621A pdb=" N CYS I 608 " --> pdb=" O PHE I 604 " (cutoff:3.500A) Processing helix chain 'I' and resid 617 through 631 removed outlier: 4.438A pdb=" N ARG I 622 " --> pdb=" O LYS I 618 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU I 623 " --> pdb=" O ALA I 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 111 removed outlier: 3.831A pdb=" N VAL J 106 " --> pdb=" O ARG J 102 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE J 107 " --> pdb=" O ILE J 103 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG J 110 " --> pdb=" O VAL J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 146 removed outlier: 3.615A pdb=" N GLN J 140 " --> pdb=" O GLU J 136 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN J 141 " --> pdb=" O ARG J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 149 No H-bonds generated for 'chain 'J' and resid 147 through 149' Processing helix chain 'J' and resid 176 through 191 removed outlier: 3.545A pdb=" N TRP J 185 " --> pdb=" O ALA J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 221 Processing helix chain 'K' and resid 331 through 344 removed outlier: 4.242A pdb=" N ILE K 335 " --> pdb=" O GLY K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 382 removed outlier: 3.838A pdb=" N SER K 375 " --> pdb=" O ASP K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 411 through 426 removed outlier: 4.150A pdb=" N ARG K 416 " --> pdb=" O ALA K 412 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP K 417 " --> pdb=" O ALA K 413 " (cutoff:3.500A) Processing helix chain 'K' and resid 444 through 455 Processing helix chain 'L' and resid 99 through 110 Processing helix chain 'L' and resid 123 through 133 Processing helix chain 'L' and resid 143 through 159 Processing helix chain 'L' and resid 169 through 186 removed outlier: 3.918A pdb=" N VAL L 176 " --> pdb=" O ALA L 172 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER L 177 " --> pdb=" O THR L 173 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLY L 178 " --> pdb=" O ASN L 174 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP L 181 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU L 184 " --> pdb=" O ALA L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 201 Processing helix chain 'L' and resid 210 through 216 Processing helix chain 'L' and resid 217 through 219 No H-bonds generated for 'chain 'L' and resid 217 through 219' Processing helix chain 'L' and resid 227 through 229 No H-bonds generated for 'chain 'L' and resid 227 through 229' Processing helix chain 'L' and resid 230 through 244 Processing helix chain 'L' and resid 256 through 261 Processing helix chain 'L' and resid 273 through 280 removed outlier: 3.516A pdb=" N SER L 278 " --> pdb=" O PRO L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 293 Processing helix chain 'L' and resid 308 through 311 Processing helix chain 'L' and resid 316 through 323 Processing helix chain 'L' and resid 354 through 364 Processing helix chain 'L' and resid 375 through 380 Processing helix chain 'L' and resid 414 through 428 Processing helix chain 'L' and resid 429 through 434 Processing helix chain 'L' and resid 437 through 438 No H-bonds generated for 'chain 'L' and resid 437 through 438' Processing helix chain 'L' and resid 440 through 440 No H-bonds generated for 'chain 'L' and resid 440 through 440' Processing helix chain 'L' and resid 441 through 451 Processing helix chain 'L' and resid 463 through 474 Processing helix chain 'L' and resid 486 through 495 removed outlier: 3.869A pdb=" N MET L 490 " --> pdb=" O GLY L 486 " (cutoff:3.500A) Processing helix chain 'L' and resid 515 through 527 Processing helix chain 'L' and resid 537 through 543 Processing helix chain 'L' and resid 544 through 546 No H-bonds generated for 'chain 'L' and resid 544 through 546' Processing helix chain 'L' and resid 547 through 555 removed outlier: 3.693A pdb=" N ILE L 551 " --> pdb=" O GLU L 547 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG L 552 " --> pdb=" O LEU L 548 " (cutoff:3.500A) Processing helix chain 'L' and resid 568 through 578 Processing helix chain 'L' and resid 600 through 608 removed outlier: 3.532A pdb=" N CYS L 608 " --> pdb=" O PHE L 604 " (cutoff:3.500A) Processing helix chain 'L' and resid 617 through 631 removed outlier: 4.328A pdb=" N ARG L 622 " --> pdb=" O LYS L 618 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU L 623 " --> pdb=" O ALA L 619 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 110 Processing helix chain 'M' and resid 123 through 133 Processing helix chain 'M' and resid 143 through 159 removed outlier: 3.558A pdb=" N PHE M 149 " --> pdb=" O GLN M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 186 removed outlier: 3.556A pdb=" N LEU M 175 " --> pdb=" O GLY M 171 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL M 176 " --> pdb=" O ALA M 172 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER M 177 " --> pdb=" O THR M 173 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLY M 178 " --> pdb=" O ASN M 174 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP M 181 " --> pdb=" O SER M 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU M 184 " --> pdb=" O ALA M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 201 Processing helix chain 'M' and resid 210 through 216 Processing helix chain 'M' and resid 227 through 229 No H-bonds generated for 'chain 'M' and resid 227 through 229' Processing helix chain 'M' and resid 230 through 244 Processing helix chain 'M' and resid 256 through 261 Processing helix chain 'M' and resid 273 through 280 Processing helix chain 'M' and resid 285 through 296 Processing helix chain 'M' and resid 308 through 311 Processing helix chain 'M' and resid 313 through 323 Processing helix chain 'M' and resid 354 through 364 Processing helix chain 'M' and resid 375 through 380 Processing helix chain 'M' and resid 414 through 428 Processing helix chain 'M' and resid 429 through 434 Processing helix chain 'M' and resid 437 through 451 Processing helix chain 'M' and resid 463 through 474 Processing helix chain 'M' and resid 486 through 495 removed outlier: 3.979A pdb=" N MET M 490 " --> pdb=" O GLY M 486 " (cutoff:3.500A) Processing helix chain 'M' and resid 515 through 527 Processing helix chain 'M' and resid 537 through 543 removed outlier: 4.063A pdb=" N MET M 543 " --> pdb=" O GLY M 539 " (cutoff:3.500A) Processing helix chain 'M' and resid 544 through 546 No H-bonds generated for 'chain 'M' and resid 544 through 546' Processing helix chain 'M' and resid 547 through 555 removed outlier: 3.734A pdb=" N ILE M 551 " --> pdb=" O GLU M 547 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG M 552 " --> pdb=" O LEU M 548 " (cutoff:3.500A) Processing helix chain 'M' and resid 568 through 578 removed outlier: 3.539A pdb=" N TRP M 574 " --> pdb=" O MET M 570 " (cutoff:3.500A) Processing helix chain 'M' and resid 600 through 608 removed outlier: 3.501A pdb=" N PHE M 604 " --> pdb=" O ASN M 600 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS M 608 " --> pdb=" O PHE M 604 " (cutoff:3.500A) Processing helix chain 'M' and resid 617 through 631 removed outlier: 4.439A pdb=" N ARG M 622 " --> pdb=" O LYS M 618 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU M 623 " --> pdb=" O ALA M 619 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 111 removed outlier: 3.574A pdb=" N ARG N 102 " --> pdb=" O GLY N 98 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE N 107 " --> pdb=" O ILE N 103 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG N 110 " --> pdb=" O VAL N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 146 removed outlier: 3.650A pdb=" N GLN N 140 " --> pdb=" O GLU N 136 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN N 141 " --> pdb=" O ARG N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 149 No H-bonds generated for 'chain 'N' and resid 147 through 149' Processing helix chain 'N' and resid 176 through 191 removed outlier: 3.544A pdb=" N TRP N 185 " --> pdb=" O ALA N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 209 through 221 Processing helix chain 'O' and resid 331 through 344 removed outlier: 4.235A pdb=" N ILE O 335 " --> pdb=" O GLY O 331 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE O 340 " --> pdb=" O VAL O 336 " (cutoff:3.500A) Processing helix chain 'O' and resid 370 through 382 removed outlier: 3.837A pdb=" N SER O 375 " --> pdb=" O ASP O 371 " (cutoff:3.500A) Processing helix chain 'O' and resid 411 through 426 removed outlier: 3.991A pdb=" N ARG O 416 " --> pdb=" O ALA O 412 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP O 417 " --> pdb=" O ALA O 413 " (cutoff:3.500A) Processing helix chain 'O' and resid 444 through 455 Processing helix chain 'P' and resid 99 through 110 Processing helix chain 'P' and resid 123 through 133 Processing helix chain 'P' and resid 143 through 159 Processing helix chain 'P' and resid 169 through 186 removed outlier: 3.918A pdb=" N VAL P 176 " --> pdb=" O ALA P 172 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER P 177 " --> pdb=" O THR P 173 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY P 178 " --> pdb=" O ASN P 174 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP P 181 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU P 184 " --> pdb=" O ALA P 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 201 Processing helix chain 'P' and resid 210 through 216 Processing helix chain 'P' and resid 217 through 219 No H-bonds generated for 'chain 'P' and resid 217 through 219' Processing helix chain 'P' and resid 227 through 229 No H-bonds generated for 'chain 'P' and resid 227 through 229' Processing helix chain 'P' and resid 230 through 244 Processing helix chain 'P' and resid 256 through 261 Processing helix chain 'P' and resid 273 through 280 removed outlier: 3.515A pdb=" N SER P 278 " --> pdb=" O PRO P 274 " (cutoff:3.500A) Processing helix chain 'P' and resid 285 through 293 Processing helix chain 'P' and resid 308 through 311 Processing helix chain 'P' and resid 316 through 323 Processing helix chain 'P' and resid 354 through 364 Processing helix chain 'P' and resid 375 through 380 Processing helix chain 'P' and resid 414 through 428 Processing helix chain 'P' and resid 429 through 434 Processing helix chain 'P' and resid 437 through 438 No H-bonds generated for 'chain 'P' and resid 437 through 438' Processing helix chain 'P' and resid 440 through 440 No H-bonds generated for 'chain 'P' and resid 440 through 440' Processing helix chain 'P' and resid 441 through 451 Processing helix chain 'P' and resid 463 through 474 Processing helix chain 'P' and resid 486 through 495 removed outlier: 3.867A pdb=" N MET P 490 " --> pdb=" O GLY P 486 " (cutoff:3.500A) Processing helix chain 'P' and resid 515 through 527 Processing helix chain 'P' and resid 537 through 543 Processing helix chain 'P' and resid 544 through 546 No H-bonds generated for 'chain 'P' and resid 544 through 546' Processing helix chain 'P' and resid 547 through 555 removed outlier: 3.693A pdb=" N ILE P 551 " --> pdb=" O GLU P 547 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG P 552 " --> pdb=" O LEU P 548 " (cutoff:3.500A) Processing helix chain 'P' and resid 568 through 578 Processing helix chain 'P' and resid 600 through 608 removed outlier: 3.532A pdb=" N CYS P 608 " --> pdb=" O PHE P 604 " (cutoff:3.500A) Processing helix chain 'P' and resid 617 through 631 removed outlier: 4.328A pdb=" N ARG P 622 " --> pdb=" O LYS P 618 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU P 623 " --> pdb=" O ALA P 619 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 110 Processing helix chain 'Q' and resid 123 through 133 Processing helix chain 'Q' and resid 143 through 159 removed outlier: 3.558A pdb=" N PHE Q 149 " --> pdb=" O GLN Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 186 removed outlier: 3.557A pdb=" N LEU Q 175 " --> pdb=" O GLY Q 171 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL Q 176 " --> pdb=" O ALA Q 172 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SER Q 177 " --> pdb=" O THR Q 173 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLY Q 178 " --> pdb=" O ASN Q 174 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP Q 181 " --> pdb=" O SER Q 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU Q 184 " --> pdb=" O ALA Q 180 " (cutoff:3.500A) Processing helix chain 'Q' and resid 197 through 201 Processing helix chain 'Q' and resid 210 through 216 Processing helix chain 'Q' and resid 227 through 229 No H-bonds generated for 'chain 'Q' and resid 227 through 229' Processing helix chain 'Q' and resid 230 through 244 Processing helix chain 'Q' and resid 256 through 261 Processing helix chain 'Q' and resid 273 through 280 Processing helix chain 'Q' and resid 285 through 296 Processing helix chain 'Q' and resid 308 through 311 Processing helix chain 'Q' and resid 313 through 323 Processing helix chain 'Q' and resid 354 through 364 Processing helix chain 'Q' and resid 375 through 380 Processing helix chain 'Q' and resid 414 through 428 Processing helix chain 'Q' and resid 429 through 434 Processing helix chain 'Q' and resid 437 through 451 Processing helix chain 'Q' and resid 463 through 474 Processing helix chain 'Q' and resid 486 through 495 removed outlier: 3.978A pdb=" N MET Q 490 " --> pdb=" O GLY Q 486 " (cutoff:3.500A) Processing helix chain 'Q' and resid 515 through 527 Processing helix chain 'Q' and resid 537 through 543 removed outlier: 4.063A pdb=" N MET Q 543 " --> pdb=" O GLY Q 539 " (cutoff:3.500A) Processing helix chain 'Q' and resid 544 through 546 No H-bonds generated for 'chain 'Q' and resid 544 through 546' Processing helix chain 'Q' and resid 547 through 555 removed outlier: 3.735A pdb=" N ILE Q 551 " --> pdb=" O GLU Q 547 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG Q 552 " --> pdb=" O LEU Q 548 " (cutoff:3.500A) Processing helix chain 'Q' and resid 568 through 578 removed outlier: 3.540A pdb=" N TRP Q 574 " --> pdb=" O MET Q 570 " (cutoff:3.500A) Processing helix chain 'Q' and resid 600 through 608 removed outlier: 3.501A pdb=" N PHE Q 604 " --> pdb=" O ASN Q 600 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS Q 608 " --> pdb=" O PHE Q 604 " (cutoff:3.500A) Processing helix chain 'Q' and resid 617 through 631 removed outlier: 4.439A pdb=" N ARG Q 622 " --> pdb=" O LYS Q 618 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU Q 623 " --> pdb=" O ALA Q 619 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 111 removed outlier: 3.624A pdb=" N VAL R 106 " --> pdb=" O ARG R 102 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE R 107 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG R 110 " --> pdb=" O VAL R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 146 removed outlier: 3.651A pdb=" N GLN R 140 " --> pdb=" O GLU R 136 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN R 141 " --> pdb=" O ARG R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 149 No H-bonds generated for 'chain 'R' and resid 147 through 149' Processing helix chain 'R' and resid 176 through 191 removed outlier: 3.545A pdb=" N TRP R 185 " --> pdb=" O ALA R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 221 Processing helix chain 'S' and resid 331 through 344 removed outlier: 3.824A pdb=" N ILE S 335 " --> pdb=" O GLY S 331 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL S 339 " --> pdb=" O ILE S 335 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE S 340 " --> pdb=" O VAL S 336 " (cutoff:3.500A) Processing helix chain 'S' and resid 370 through 382 removed outlier: 3.839A pdb=" N SER S 375 " --> pdb=" O ASP S 371 " (cutoff:3.500A) Processing helix chain 'S' and resid 411 through 426 removed outlier: 3.991A pdb=" N ARG S 416 " --> pdb=" O ALA S 412 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP S 417 " --> pdb=" O ALA S 413 " (cutoff:3.500A) Processing helix chain 'S' and resid 444 through 455 Processing sheet with id=AA1, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AA2, first strand: chain 'D' and resid 137 through 139 removed outlier: 7.545A pdb=" N THR D 114 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N ILE D 165 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE D 116 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY D 162 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE D 192 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N CYS D 164 " --> pdb=" O ILE D 192 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLY D 194 " --> pdb=" O CYS D 164 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ALA D 166 " --> pdb=" O GLY D 194 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU D 189 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL D 252 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA D 191 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL D 254 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR D 193 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS D 221 " --> pdb=" O PRO D 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 345 through 348 removed outlier: 7.980A pdb=" N VAL D 328 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET D 348 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER D 330 " --> pdb=" O MET D 348 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ALA D 329 " --> pdb=" O PRO D 302 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU D 304 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU D 367 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE D 394 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA D 369 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS D 393 " --> pdb=" O VAL D 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 504 through 505 removed outlier: 6.628A pdb=" N ILE D 481 " --> pdb=" O LEU D 505 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE D 480 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE D 535 " --> pdb=" O ILE D 480 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SER D 482 " --> pdb=" O ILE D 535 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL D 532 " --> pdb=" O LYS D 559 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU D 561 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP D 534 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL D 560 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL D 639 " --> pdb=" O VAL D 560 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU D 562 " --> pdb=" O VAL D 639 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA D 613 " --> pdb=" O ASP D 638 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'E' and resid 137 through 139 removed outlier: 7.544A pdb=" N THR E 114 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ILE E 165 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE E 116 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLY E 162 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE E 192 " --> pdb=" O GLY E 162 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N CYS E 164 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLY E 194 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA E 166 " --> pdb=" O GLY E 194 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU E 189 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL E 252 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA E 191 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL E 254 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR E 193 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N HIS E 221 " --> pdb=" O PRO E 249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 345 through 348 removed outlier: 7.979A pdb=" N VAL E 328 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N MET E 348 " --> pdb=" O VAL E 328 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER E 330 " --> pdb=" O MET E 348 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ALA E 329 " --> pdb=" O PRO E 302 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU E 304 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU E 367 " --> pdb=" O VAL E 392 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE E 394 " --> pdb=" O LEU E 367 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA E 369 " --> pdb=" O ILE E 394 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS E 393 " --> pdb=" O VAL E 411 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 504 through 506 removed outlier: 6.421A pdb=" N ILE E 481 " --> pdb=" O LEU E 505 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE E 480 " --> pdb=" O VAL E 533 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE E 535 " --> pdb=" O ILE E 480 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SER E 482 " --> pdb=" O ILE E 535 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL E 532 " --> pdb=" O LYS E 559 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU E 561 " --> pdb=" O VAL E 532 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP E 534 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU E 563 " --> pdb=" O ASP E 534 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP E 536 " --> pdb=" O LEU E 563 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL E 560 " --> pdb=" O LEU E 637 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL E 639 " --> pdb=" O VAL E 560 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU E 562 " --> pdb=" O VAL E 639 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA E 613 " --> pdb=" O ASP E 638 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE E 640 " --> pdb=" O ALA E 613 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL E 615 " --> pdb=" O ILE E 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 152 through 157 removed outlier: 6.129A pdb=" N VAL F 152 " --> pdb=" O GLY F 94 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY F 94 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU F 127 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL F 119 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR F 129 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU F 117 " --> pdb=" O THR F 129 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL F 131 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 11.086A pdb=" N GLU F 115 " --> pdb=" O HIS G 354 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N HIS G 354 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER G 349 " --> pdb=" O VAL G 366 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR G 321 " --> pdb=" O ASP G 392 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP G 392 " --> pdb=" O THR G 321 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER G 323 " --> pdb=" O VAL G 390 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL G 390 " --> pdb=" O SER G 323 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU G 325 " --> pdb=" O HIS G 388 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 193 through 197 removed outlier: 6.750A pdb=" N THR F 203 " --> pdb=" O VAL F 195 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE F 197 " --> pdb=" O ALA F 201 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA F 201 " --> pdb=" O ILE F 197 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASN F 174 " --> pdb=" O ILE F 225 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE F 225 " --> pdb=" O ASN F 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 193 through 197 removed outlier: 6.750A pdb=" N THR F 203 " --> pdb=" O VAL F 195 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE F 197 " --> pdb=" O ALA F 201 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA F 201 " --> pdb=" O ILE F 197 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 428 through 432 removed outlier: 6.495A pdb=" N THR G 438 " --> pdb=" O VAL G 430 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL G 432 " --> pdb=" O THR G 436 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR G 436 " --> pdb=" O VAL G 432 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU G 405 " --> pdb=" O VAL G 463 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL G 463 " --> pdb=" O LEU G 405 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS G 407 " --> pdb=" O CYS G 461 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY G 459 " --> pdb=" O ALA G 409 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 428 through 432 removed outlier: 6.495A pdb=" N THR G 438 " --> pdb=" O VAL G 430 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL G 432 " --> pdb=" O THR G 436 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR G 436 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 97 through 98 Processing sheet with id=AB6, first strand: chain 'H' and resid 137 through 139 removed outlier: 7.544A pdb=" N THR H 114 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ILE H 165 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE H 116 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY H 162 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE H 192 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N CYS H 164 " --> pdb=" O ILE H 192 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLY H 194 " --> pdb=" O CYS H 164 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA H 166 " --> pdb=" O GLY H 194 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU H 189 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL H 252 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA H 191 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL H 254 " --> pdb=" O ALA H 191 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR H 193 " --> pdb=" O VAL H 254 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS H 221 " --> pdb=" O PRO H 249 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 345 through 348 removed outlier: 7.980A pdb=" N VAL H 328 " --> pdb=" O LEU H 346 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N MET H 348 " --> pdb=" O VAL H 328 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER H 330 " --> pdb=" O MET H 348 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ALA H 329 " --> pdb=" O PRO H 302 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU H 304 " --> pdb=" O ALA H 329 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU H 367 " --> pdb=" O VAL H 392 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE H 394 " --> pdb=" O LEU H 367 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA H 369 " --> pdb=" O ILE H 394 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS H 393 " --> pdb=" O VAL H 411 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 504 through 505 removed outlier: 6.630A pdb=" N ILE H 481 " --> pdb=" O LEU H 505 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE H 480 " --> pdb=" O VAL H 533 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE H 535 " --> pdb=" O ILE H 480 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SER H 482 " --> pdb=" O ILE H 535 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL H 532 " --> pdb=" O LYS H 559 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU H 561 " --> pdb=" O VAL H 532 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP H 534 " --> pdb=" O LEU H 561 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL H 560 " --> pdb=" O LEU H 637 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL H 639 " --> pdb=" O VAL H 560 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU H 562 " --> pdb=" O VAL H 639 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA H 613 " --> pdb=" O ASP H 638 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 97 through 98 Processing sheet with id=AC1, first strand: chain 'I' and resid 137 through 139 removed outlier: 7.544A pdb=" N THR I 114 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N ILE I 165 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE I 116 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY I 162 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE I 192 " --> pdb=" O GLY I 162 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N CYS I 164 " --> pdb=" O ILE I 192 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLY I 194 " --> pdb=" O CYS I 164 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ALA I 166 " --> pdb=" O GLY I 194 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU I 189 " --> pdb=" O VAL I 250 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL I 252 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA I 191 " --> pdb=" O VAL I 252 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL I 254 " --> pdb=" O ALA I 191 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR I 193 " --> pdb=" O VAL I 254 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS I 221 " --> pdb=" O PRO I 249 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 345 through 348 removed outlier: 7.979A pdb=" N VAL I 328 " --> pdb=" O LEU I 346 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N MET I 348 " --> pdb=" O VAL I 328 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N SER I 330 " --> pdb=" O MET I 348 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ALA I 329 " --> pdb=" O PRO I 302 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU I 304 " --> pdb=" O ALA I 329 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU I 367 " --> pdb=" O VAL I 392 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE I 394 " --> pdb=" O LEU I 367 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA I 369 " --> pdb=" O ILE I 394 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS I 393 " --> pdb=" O VAL I 411 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 504 through 506 removed outlier: 6.421A pdb=" N ILE I 481 " --> pdb=" O LEU I 505 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE I 480 " --> pdb=" O VAL I 533 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE I 535 " --> pdb=" O ILE I 480 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SER I 482 " --> pdb=" O ILE I 535 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL I 532 " --> pdb=" O LYS I 559 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LEU I 561 " --> pdb=" O VAL I 532 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP I 534 " --> pdb=" O LEU I 561 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU I 563 " --> pdb=" O ASP I 534 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASP I 536 " --> pdb=" O LEU I 563 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL I 560 " --> pdb=" O LEU I 637 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL I 639 " --> pdb=" O VAL I 560 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU I 562 " --> pdb=" O VAL I 639 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA I 613 " --> pdb=" O ASP I 638 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE I 640 " --> pdb=" O ALA I 613 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL I 615 " --> pdb=" O ILE I 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'J' and resid 152 through 157 removed outlier: 6.267A pdb=" N VAL J 152 " --> pdb=" O GLY J 94 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY J 94 " --> pdb=" O VAL J 152 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU J 127 " --> pdb=" O VAL J 119 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL J 119 " --> pdb=" O LEU J 127 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR J 129 " --> pdb=" O LEU J 117 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU J 117 " --> pdb=" O THR J 129 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL J 131 " --> pdb=" O GLU J 115 " (cutoff:3.500A) removed outlier: 11.141A pdb=" N GLU J 115 " --> pdb=" O HIS K 354 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N HIS K 354 " --> pdb=" O GLU J 115 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER K 349 " --> pdb=" O VAL K 366 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N THR K 321 " --> pdb=" O ASP K 392 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP K 392 " --> pdb=" O THR K 321 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER K 323 " --> pdb=" O VAL K 390 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL K 390 " --> pdb=" O SER K 323 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU K 325 " --> pdb=" O HIS K 388 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 193 through 197 removed outlier: 6.750A pdb=" N THR J 203 " --> pdb=" O VAL J 195 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ILE J 197 " --> pdb=" O ALA J 201 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA J 201 " --> pdb=" O ILE J 197 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN J 174 " --> pdb=" O ILE J 225 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE J 225 " --> pdb=" O ASN J 174 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 193 through 197 removed outlier: 6.750A pdb=" N THR J 203 " --> pdb=" O VAL J 195 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ILE J 197 " --> pdb=" O ALA J 201 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA J 201 " --> pdb=" O ILE J 197 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 428 through 432 removed outlier: 6.432A pdb=" N THR K 438 " --> pdb=" O VAL K 430 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL K 432 " --> pdb=" O THR K 436 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR K 436 " --> pdb=" O VAL K 432 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU K 405 " --> pdb=" O VAL K 463 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL K 463 " --> pdb=" O LEU K 405 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS K 407 " --> pdb=" O CYS K 461 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY K 459 " --> pdb=" O ALA K 409 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 428 through 432 removed outlier: 6.432A pdb=" N THR K 438 " --> pdb=" O VAL K 430 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL K 432 " --> pdb=" O THR K 436 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR K 436 " --> pdb=" O VAL K 432 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 97 through 98 Processing sheet with id=AD1, first strand: chain 'L' and resid 137 through 139 removed outlier: 7.544A pdb=" N THR L 114 " --> pdb=" O ILE L 163 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ILE L 165 " --> pdb=" O THR L 114 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE L 116 " --> pdb=" O ILE L 165 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY L 162 " --> pdb=" O VAL L 190 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE L 192 " --> pdb=" O GLY L 162 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS L 164 " --> pdb=" O ILE L 192 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLY L 194 " --> pdb=" O CYS L 164 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ALA L 166 " --> pdb=" O GLY L 194 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU L 189 " --> pdb=" O VAL L 250 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL L 252 " --> pdb=" O LEU L 189 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA L 191 " --> pdb=" O VAL L 252 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL L 254 " --> pdb=" O ALA L 191 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR L 193 " --> pdb=" O VAL L 254 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS L 221 " --> pdb=" O PRO L 249 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 345 through 348 removed outlier: 7.979A pdb=" N VAL L 328 " --> pdb=" O LEU L 346 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N MET L 348 " --> pdb=" O VAL L 328 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER L 330 " --> pdb=" O MET L 348 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ALA L 329 " --> pdb=" O PRO L 302 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU L 304 " --> pdb=" O ALA L 329 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU L 367 " --> pdb=" O VAL L 392 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE L 394 " --> pdb=" O LEU L 367 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA L 369 " --> pdb=" O ILE L 394 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N HIS L 393 " --> pdb=" O VAL L 411 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 504 through 505 removed outlier: 6.629A pdb=" N ILE L 481 " --> pdb=" O LEU L 505 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE L 480 " --> pdb=" O VAL L 533 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE L 535 " --> pdb=" O ILE L 480 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER L 482 " --> pdb=" O ILE L 535 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL L 532 " --> pdb=" O LYS L 559 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU L 561 " --> pdb=" O VAL L 532 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP L 534 " --> pdb=" O LEU L 561 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL L 560 " --> pdb=" O LEU L 637 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL L 639 " --> pdb=" O VAL L 560 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU L 562 " --> pdb=" O VAL L 639 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA L 613 " --> pdb=" O ASP L 638 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'M' and resid 97 through 98 Processing sheet with id=AD5, first strand: chain 'M' and resid 137 through 139 removed outlier: 7.545A pdb=" N THR M 114 " --> pdb=" O ILE M 163 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N ILE M 165 " --> pdb=" O THR M 114 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE M 116 " --> pdb=" O ILE M 165 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLY M 162 " --> pdb=" O VAL M 190 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE M 192 " --> pdb=" O GLY M 162 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N CYS M 164 " --> pdb=" O ILE M 192 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLY M 194 " --> pdb=" O CYS M 164 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ALA M 166 " --> pdb=" O GLY M 194 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU M 189 " --> pdb=" O VAL M 250 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL M 252 " --> pdb=" O LEU M 189 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA M 191 " --> pdb=" O VAL M 252 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL M 254 " --> pdb=" O ALA M 191 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR M 193 " --> pdb=" O VAL M 254 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N HIS M 221 " --> pdb=" O PRO M 249 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 345 through 348 removed outlier: 7.979A pdb=" N VAL M 328 " --> pdb=" O LEU M 346 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N MET M 348 " --> pdb=" O VAL M 328 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N SER M 330 " --> pdb=" O MET M 348 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ALA M 329 " --> pdb=" O PRO M 302 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU M 304 " --> pdb=" O ALA M 329 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU M 367 " --> pdb=" O VAL M 392 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE M 394 " --> pdb=" O LEU M 367 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA M 369 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N HIS M 393 " --> pdb=" O VAL M 411 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 504 through 506 removed outlier: 6.421A pdb=" N ILE M 481 " --> pdb=" O LEU M 505 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE M 480 " --> pdb=" O VAL M 533 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE M 535 " --> pdb=" O ILE M 480 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N SER M 482 " --> pdb=" O ILE M 535 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL M 532 " --> pdb=" O LYS M 559 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU M 561 " --> pdb=" O VAL M 532 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP M 534 " --> pdb=" O LEU M 561 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU M 563 " --> pdb=" O ASP M 534 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP M 536 " --> pdb=" O LEU M 563 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL M 560 " --> pdb=" O LEU M 637 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL M 639 " --> pdb=" O VAL M 560 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU M 562 " --> pdb=" O VAL M 639 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA M 613 " --> pdb=" O ASP M 638 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE M 640 " --> pdb=" O ALA M 613 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL M 615 " --> pdb=" O ILE M 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'N' and resid 152 through 157 removed outlier: 6.023A pdb=" N VAL N 152 " --> pdb=" O GLY N 94 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY N 94 " --> pdb=" O VAL N 152 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU N 127 " --> pdb=" O VAL N 119 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL N 119 " --> pdb=" O LEU N 127 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR N 129 " --> pdb=" O LEU N 117 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU N 117 " --> pdb=" O THR N 129 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL N 131 " --> pdb=" O GLU N 115 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N GLU N 115 " --> pdb=" O HIS O 354 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N HIS O 354 " --> pdb=" O GLU N 115 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER O 349 " --> pdb=" O VAL O 366 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N THR O 321 " --> pdb=" O ASP O 392 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP O 392 " --> pdb=" O THR O 321 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER O 323 " --> pdb=" O VAL O 390 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL O 390 " --> pdb=" O SER O 323 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU O 325 " --> pdb=" O HIS O 388 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 193 through 197 removed outlier: 6.751A pdb=" N THR N 203 " --> pdb=" O VAL N 195 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE N 197 " --> pdb=" O ALA N 201 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA N 201 " --> pdb=" O ILE N 197 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN N 174 " --> pdb=" O ILE N 225 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE N 225 " --> pdb=" O ASN N 174 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 193 through 197 removed outlier: 6.751A pdb=" N THR N 203 " --> pdb=" O VAL N 195 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE N 197 " --> pdb=" O ALA N 201 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA N 201 " --> pdb=" O ILE N 197 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 428 through 432 removed outlier: 6.486A pdb=" N THR O 438 " --> pdb=" O VAL O 430 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL O 432 " --> pdb=" O THR O 436 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR O 436 " --> pdb=" O VAL O 432 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU O 405 " --> pdb=" O VAL O 463 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL O 463 " --> pdb=" O LEU O 405 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS O 407 " --> pdb=" O CYS O 461 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY O 459 " --> pdb=" O ALA O 409 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 428 through 432 removed outlier: 6.486A pdb=" N THR O 438 " --> pdb=" O VAL O 430 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL O 432 " --> pdb=" O THR O 436 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR O 436 " --> pdb=" O VAL O 432 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 97 through 98 Processing sheet with id=AE5, first strand: chain 'P' and resid 137 through 139 removed outlier: 7.544A pdb=" N THR P 114 " --> pdb=" O ILE P 163 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N ILE P 165 " --> pdb=" O THR P 114 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE P 116 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY P 162 " --> pdb=" O VAL P 190 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE P 192 " --> pdb=" O GLY P 162 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS P 164 " --> pdb=" O ILE P 192 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLY P 194 " --> pdb=" O CYS P 164 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA P 166 " --> pdb=" O GLY P 194 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU P 189 " --> pdb=" O VAL P 250 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL P 252 " --> pdb=" O LEU P 189 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA P 191 " --> pdb=" O VAL P 252 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL P 254 " --> pdb=" O ALA P 191 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR P 193 " --> pdb=" O VAL P 254 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS P 221 " --> pdb=" O PRO P 249 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 345 through 348 removed outlier: 7.979A pdb=" N VAL P 328 " --> pdb=" O LEU P 346 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET P 348 " --> pdb=" O VAL P 328 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N SER P 330 " --> pdb=" O MET P 348 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ALA P 329 " --> pdb=" O PRO P 302 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU P 304 " --> pdb=" O ALA P 329 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU P 367 " --> pdb=" O VAL P 392 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE P 394 " --> pdb=" O LEU P 367 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA P 369 " --> pdb=" O ILE P 394 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N HIS P 393 " --> pdb=" O VAL P 411 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 504 through 505 removed outlier: 6.629A pdb=" N ILE P 481 " --> pdb=" O LEU P 505 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE P 480 " --> pdb=" O VAL P 533 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE P 535 " --> pdb=" O ILE P 480 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER P 482 " --> pdb=" O ILE P 535 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL P 532 " --> pdb=" O LYS P 559 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU P 561 " --> pdb=" O VAL P 532 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP P 534 " --> pdb=" O LEU P 561 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL P 560 " --> pdb=" O LEU P 637 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL P 639 " --> pdb=" O VAL P 560 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU P 562 " --> pdb=" O VAL P 639 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA P 613 " --> pdb=" O ASP P 638 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'Q' and resid 97 through 98 Processing sheet with id=AE9, first strand: chain 'Q' and resid 137 through 139 removed outlier: 7.545A pdb=" N THR Q 114 " --> pdb=" O ILE Q 163 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N ILE Q 165 " --> pdb=" O THR Q 114 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE Q 116 " --> pdb=" O ILE Q 165 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY Q 162 " --> pdb=" O VAL Q 190 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE Q 192 " --> pdb=" O GLY Q 162 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N CYS Q 164 " --> pdb=" O ILE Q 192 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLY Q 194 " --> pdb=" O CYS Q 164 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA Q 166 " --> pdb=" O GLY Q 194 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU Q 189 " --> pdb=" O VAL Q 250 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL Q 252 " --> pdb=" O LEU Q 189 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA Q 191 " --> pdb=" O VAL Q 252 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL Q 254 " --> pdb=" O ALA Q 191 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR Q 193 " --> pdb=" O VAL Q 254 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS Q 221 " --> pdb=" O PRO Q 249 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 345 through 348 removed outlier: 7.979A pdb=" N VAL Q 328 " --> pdb=" O LEU Q 346 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N MET Q 348 " --> pdb=" O VAL Q 328 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER Q 330 " --> pdb=" O MET Q 348 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ALA Q 329 " --> pdb=" O PRO Q 302 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU Q 304 " --> pdb=" O ALA Q 329 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU Q 367 " --> pdb=" O VAL Q 392 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE Q 394 " --> pdb=" O LEU Q 367 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA Q 369 " --> pdb=" O ILE Q 394 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N HIS Q 393 " --> pdb=" O VAL Q 411 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 504 through 506 removed outlier: 6.420A pdb=" N ILE Q 481 " --> pdb=" O LEU Q 505 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE Q 480 " --> pdb=" O VAL Q 533 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE Q 535 " --> pdb=" O ILE Q 480 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SER Q 482 " --> pdb=" O ILE Q 535 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL Q 532 " --> pdb=" O LYS Q 559 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU Q 561 " --> pdb=" O VAL Q 532 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP Q 534 " --> pdb=" O LEU Q 561 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU Q 563 " --> pdb=" O ASP Q 534 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP Q 536 " --> pdb=" O LEU Q 563 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL Q 560 " --> pdb=" O LEU Q 637 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL Q 639 " --> pdb=" O VAL Q 560 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU Q 562 " --> pdb=" O VAL Q 639 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA Q 613 " --> pdb=" O ASP Q 638 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE Q 640 " --> pdb=" O ALA Q 613 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL Q 615 " --> pdb=" O ILE Q 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'R' and resid 152 through 157 removed outlier: 6.061A pdb=" N VAL R 152 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLY R 94 " --> pdb=" O VAL R 152 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU R 127 " --> pdb=" O VAL R 119 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL R 119 " --> pdb=" O LEU R 127 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR R 129 " --> pdb=" O LEU R 117 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU R 117 " --> pdb=" O THR R 129 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL R 131 " --> pdb=" O GLU R 115 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N GLU R 115 " --> pdb=" O HIS S 354 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N HIS S 354 " --> pdb=" O GLU R 115 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER S 349 " --> pdb=" O VAL S 366 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR S 321 " --> pdb=" O ASP S 392 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASP S 392 " --> pdb=" O THR S 321 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER S 323 " --> pdb=" O VAL S 390 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL S 390 " --> pdb=" O SER S 323 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU S 325 " --> pdb=" O HIS S 388 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 193 through 197 removed outlier: 6.751A pdb=" N THR R 203 " --> pdb=" O VAL R 195 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE R 197 " --> pdb=" O ALA R 201 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA R 201 " --> pdb=" O ILE R 197 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN R 174 " --> pdb=" O ILE R 225 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE R 225 " --> pdb=" O ASN R 174 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 193 through 197 removed outlier: 6.751A pdb=" N THR R 203 " --> pdb=" O VAL R 195 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE R 197 " --> pdb=" O ALA R 201 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA R 201 " --> pdb=" O ILE R 197 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 428 through 432 removed outlier: 6.472A pdb=" N THR S 438 " --> pdb=" O VAL S 430 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL S 432 " --> pdb=" O THR S 436 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR S 436 " --> pdb=" O VAL S 432 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU S 405 " --> pdb=" O VAL S 463 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL S 463 " --> pdb=" O LEU S 405 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LYS S 407 " --> pdb=" O CYS S 461 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY S 459 " --> pdb=" O ALA S 409 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 428 through 432 removed outlier: 6.472A pdb=" N THR S 438 " --> pdb=" O VAL S 430 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL S 432 " --> pdb=" O THR S 436 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR S 436 " --> pdb=" O VAL S 432 " (cutoff:3.500A) 1915 hydrogen bonds defined for protein. 5544 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: 12.47 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8049 1.32 - 1.45: 9632 1.45 - 1.57: 24835 1.57 - 1.70: 48 1.70 - 1.82: 344 Bond restraints: 42908 Sorted by residual: bond pdb=" C2 TPP E 703 " pdb=" S1 TPP E 703 " ideal model delta sigma weight residual 1.675 1.748 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C2 TPP M 703 " pdb=" S1 TPP M 703 " ideal model delta sigma weight residual 1.675 1.747 -0.072 1.00e-02 1.00e+04 5.23e+01 bond pdb=" C2 TPP I 703 " pdb=" S1 TPP I 703 " ideal model delta sigma weight residual 1.675 1.747 -0.072 1.00e-02 1.00e+04 5.15e+01 bond pdb=" C2 TPP Q 703 " pdb=" S1 TPP Q 703 " ideal model delta sigma weight residual 1.675 1.747 -0.072 1.00e-02 1.00e+04 5.14e+01 bond pdb=" C2 TPP D 703 " pdb=" S1 TPP D 703 " ideal model delta sigma weight residual 1.675 1.738 -0.063 1.00e-02 1.00e+04 3.98e+01 ... (remaining 42903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 57261 4.15 - 8.31: 1067 8.31 - 12.46: 71 12.46 - 16.62: 12 16.62 - 20.77: 5 Bond angle restraints: 58416 Sorted by residual: angle pdb=" PA TPP H 703 " pdb=" O3A TPP H 703 " pdb=" PB TPP H 703 " ideal model delta sigma weight residual 139.87 119.10 20.77 1.00e+00 1.00e+00 4.32e+02 angle pdb=" PA TPP L 703 " pdb=" O3A TPP L 703 " pdb=" PB TPP L 703 " ideal model delta sigma weight residual 139.87 119.15 20.72 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA TPP D 703 " pdb=" O3A TPP D 703 " pdb=" PB TPP D 703 " ideal model delta sigma weight residual 139.87 119.16 20.71 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA TPP P 703 " pdb=" O3A TPP P 703 " pdb=" PB TPP P 703 " ideal model delta sigma weight residual 139.87 119.16 20.71 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA TPP I 703 " pdb=" O3A TPP I 703 " pdb=" PB TPP I 703 " ideal model delta sigma weight residual 139.87 123.46 16.41 1.00e+00 1.00e+00 2.69e+02 ... (remaining 58411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 24086 17.64 - 35.27: 1358 35.27 - 52.91: 322 52.91 - 70.54: 115 70.54 - 88.18: 63 Dihedral angle restraints: 25944 sinusoidal: 10104 harmonic: 15840 Sorted by residual: dihedral pdb=" CA HIS K 391 " pdb=" C HIS K 391 " pdb=" N ASP K 392 " pdb=" CA ASP K 392 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA HIS S 391 " pdb=" C HIS S 391 " pdb=" N ASP S 392 " pdb=" CA ASP S 392 " ideal model delta harmonic sigma weight residual 180.00 150.71 29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA HIS G 391 " pdb=" C HIS G 391 " pdb=" N ASP G 392 " pdb=" CA ASP G 392 " ideal model delta harmonic sigma weight residual 180.00 151.55 28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 25941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 6660 0.188 - 0.375: 137 0.375 - 0.563: 2 0.563 - 0.750: 0 0.750 - 0.938: 1 Chirality restraints: 6800 Sorted by residual: chirality pdb=" CB VAL J 138 " pdb=" CA VAL J 138 " pdb=" CG1 VAL J 138 " pdb=" CG2 VAL J 138 " both_signs ideal model delta sigma weight residual False -2.63 -1.69 -0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" CA ASP K 328 " pdb=" N ASP K 328 " pdb=" C ASP K 328 " pdb=" CB ASP K 328 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA ASP S 328 " pdb=" N ASP S 328 " pdb=" C ASP S 328 " pdb=" CB ASP S 328 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 6797 not shown) Planarity restraints: 7516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FAD M 702 " 0.671 2.00e-02 2.50e+03 3.07e-01 4.48e+03 pdb=" C10 FAD M 702 " 0.143 2.00e-02 2.50e+03 pdb=" C2 FAD M 702 " -0.294 2.00e-02 2.50e+03 pdb=" C4 FAD M 702 " -0.018 2.00e-02 2.50e+03 pdb=" C4X FAD M 702 " 0.162 2.00e-02 2.50e+03 pdb=" C5X FAD M 702 " 0.275 2.00e-02 2.50e+03 pdb=" C6 FAD M 702 " 0.199 2.00e-02 2.50e+03 pdb=" C7 FAD M 702 " -0.051 2.00e-02 2.50e+03 pdb=" C7M FAD M 702 " -0.181 2.00e-02 2.50e+03 pdb=" C8 FAD M 702 " -0.234 2.00e-02 2.50e+03 pdb=" C8M FAD M 702 " -0.611 2.00e-02 2.50e+03 pdb=" C9 FAD M 702 " -0.088 2.00e-02 2.50e+03 pdb=" C9A FAD M 702 " 0.195 2.00e-02 2.50e+03 pdb=" N1 FAD M 702 " -0.062 2.00e-02 2.50e+03 pdb=" N10 FAD M 702 " 0.335 2.00e-02 2.50e+03 pdb=" N3 FAD M 702 " -0.234 2.00e-02 2.50e+03 pdb=" N5 FAD M 702 " 0.336 2.00e-02 2.50e+03 pdb=" O2 FAD M 702 " -0.547 2.00e-02 2.50e+03 pdb=" O4 FAD M 702 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD Q 702 " -0.672 2.00e-02 2.50e+03 3.07e-01 4.48e+03 pdb=" C10 FAD Q 702 " -0.144 2.00e-02 2.50e+03 pdb=" C2 FAD Q 702 " 0.293 2.00e-02 2.50e+03 pdb=" C4 FAD Q 702 " 0.018 2.00e-02 2.50e+03 pdb=" C4X FAD Q 702 " -0.162 2.00e-02 2.50e+03 pdb=" C5X FAD Q 702 " -0.275 2.00e-02 2.50e+03 pdb=" C6 FAD Q 702 " -0.198 2.00e-02 2.50e+03 pdb=" C7 FAD Q 702 " 0.052 2.00e-02 2.50e+03 pdb=" C7M FAD Q 702 " 0.180 2.00e-02 2.50e+03 pdb=" C8 FAD Q 702 " 0.234 2.00e-02 2.50e+03 pdb=" C8M FAD Q 702 " 0.610 2.00e-02 2.50e+03 pdb=" C9 FAD Q 702 " 0.088 2.00e-02 2.50e+03 pdb=" C9A FAD Q 702 " -0.195 2.00e-02 2.50e+03 pdb=" N1 FAD Q 702 " 0.062 2.00e-02 2.50e+03 pdb=" N10 FAD Q 702 " -0.334 2.00e-02 2.50e+03 pdb=" N3 FAD Q 702 " 0.234 2.00e-02 2.50e+03 pdb=" N5 FAD Q 702 " -0.337 2.00e-02 2.50e+03 pdb=" O2 FAD Q 702 " 0.547 2.00e-02 2.50e+03 pdb=" O4 FAD Q 702 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD E 702 " -0.671 2.00e-02 2.50e+03 3.07e-01 4.47e+03 pdb=" C10 FAD E 702 " -0.144 2.00e-02 2.50e+03 pdb=" C2 FAD E 702 " 0.293 2.00e-02 2.50e+03 pdb=" C4 FAD E 702 " 0.018 2.00e-02 2.50e+03 pdb=" C4X FAD E 702 " -0.162 2.00e-02 2.50e+03 pdb=" C5X FAD E 702 " -0.276 2.00e-02 2.50e+03 pdb=" C6 FAD E 702 " -0.199 2.00e-02 2.50e+03 pdb=" C7 FAD E 702 " 0.052 2.00e-02 2.50e+03 pdb=" C7M FAD E 702 " 0.180 2.00e-02 2.50e+03 pdb=" C8 FAD E 702 " 0.234 2.00e-02 2.50e+03 pdb=" C8M FAD E 702 " 0.611 2.00e-02 2.50e+03 pdb=" C9 FAD E 702 " 0.087 2.00e-02 2.50e+03 pdb=" C9A FAD E 702 " -0.195 2.00e-02 2.50e+03 pdb=" N1 FAD E 702 " 0.063 2.00e-02 2.50e+03 pdb=" N10 FAD E 702 " -0.335 2.00e-02 2.50e+03 pdb=" N3 FAD E 702 " 0.234 2.00e-02 2.50e+03 pdb=" N5 FAD E 702 " -0.336 2.00e-02 2.50e+03 pdb=" O2 FAD E 702 " 0.547 2.00e-02 2.50e+03 pdb=" O4 FAD E 702 " -0.002 2.00e-02 2.50e+03 ... (remaining 7513 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 160 2.51 - 3.11: 32342 3.11 - 3.71: 64997 3.71 - 4.30: 90422 4.30 - 4.90: 150721 Nonbonded interactions: 338642 Sorted by model distance: nonbonded pdb="MG MG I 701 " pdb=" O1A TPP I 703 " model vdw 1.913 2.170 nonbonded pdb="MG MG Q 701 " pdb=" O1A TPP Q 703 " model vdw 1.914 2.170 nonbonded pdb="MG MG M 701 " pdb=" O1A TPP M 703 " model vdw 1.915 2.170 nonbonded pdb="MG MG E 701 " pdb=" O1A TPP E 703 " model vdw 1.915 2.170 nonbonded pdb="MG MG L 701 " pdb=" O2A TPP L 703 " model vdw 1.921 2.170 ... (remaining 338637 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: 0.09 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 87 through 288 or (resid 289 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 through 312 or (resid 315 a \ nd (name N or name CA or name C or name O or name CB )) or resid 316 or (resid 3 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 318 through \ 369 or (resid 370 and (name N or name CA or name C or name O or name CB )) or r \ esid 371 through 377 or (resid 378 and (name N or name CA or name C or name O or \ name CB )) or resid 379 through 425 or (resid 426 through 432 and (name N or na \ me CA or name C or name O or name CB )) or resid 433 through 571 or (resid 572 t \ hrough 573 and (name N or name CA or name C or name O or name CB )) or resid 574 \ or (resid 575 through 577 and (name N or name CA or name C or name O or name CB \ )) or resid 578 or (resid 579 through 582 and (name N or name CA or name C or n \ ame O or name CB )) or resid 583 through 584 or (resid 585 and (name N or name C \ A or name C or name O or name CB )) or resid 586 through 616 or (resid 617 and ( \ name N or name CA or name C or name O or name CB )) or resid 618 through 703)) selection = (chain 'E' and (resid 87 through 287 or (resid 288 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 or (resid 292 and (name N o \ r name CA or name C or name O or name CB )) or resid 293 or resid 301 through 30 \ 4 or (resid 305 and (name N or name CA or name C or name O or name CB )) or resi \ d 306 through 312 or resid 315 through 318 or (resid 319 and (name N or name CA \ or name C or name O or name CB )) or resid 320 through 343 or (resid 344 and (na \ me N or name CA or name C or name O or name CB )) or resid 345 through 361 or (r \ esid 362 through 363 and (name N or name CA or name C or name O or name CB )) or \ resid 364 through 428 or (resid 429 through 432 and (name N or name CA or name \ C or name O or name CB )) or resid 433 through 438 or resid 440 through 455 or r \ esid 459 through 535 or (resid 536 and (name N or name CA or name C or name O or \ name CB )) or resid 537 through 593 or resid 597 through 703)) selection = (chain 'H' and (resid 87 through 288 or (resid 289 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 through 312 or (resid 315 a \ nd (name N or name CA or name C or name O or name CB )) or resid 316 or (resid 3 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 318 through \ 369 or (resid 370 and (name N or name CA or name C or name O or name CB )) or r \ esid 371 through 377 or (resid 378 and (name N or name CA or name C or name O or \ name CB )) or resid 379 through 425 or (resid 426 through 432 and (name N or na \ me CA or name C or name O or name CB )) or resid 433 through 571 or (resid 572 t \ hrough 573 and (name N or name CA or name C or name O or name CB )) or resid 574 \ or (resid 575 through 577 and (name N or name CA or name C or name O or name CB \ )) or resid 578 or (resid 579 through 582 and (name N or name CA or name C or n \ ame O or name CB )) or resid 583 through 584 or (resid 585 and (name N or name C \ A or name C or name O or name CB )) or resid 586 through 616 or (resid 617 and ( \ name N or name CA or name C or name O or name CB )) or resid 618 through 703)) selection = (chain 'I' and (resid 87 through 287 or (resid 288 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 or (resid 292 and (name N o \ r name CA or name C or name O or name CB )) or resid 293 or resid 301 through 30 \ 4 or (resid 305 and (name N or name CA or name C or name O or name CB )) or resi \ d 306 through 312 or resid 315 through 318 or (resid 319 and (name N or name CA \ or name C or name O or name CB )) or resid 320 through 343 or (resid 344 and (na \ me N or name CA or name C or name O or name CB )) or resid 345 through 361 or (r \ esid 362 through 363 and (name N or name CA or name C or name O or name CB )) or \ resid 364 through 428 or (resid 429 through 432 and (name N or name CA or name \ C or name O or name CB )) or resid 433 through 438 or resid 440 through 455 or r \ esid 459 through 535 or (resid 536 and (name N or name CA or name C or name O or \ name CB )) or resid 537 through 593 or resid 597 through 703)) selection = (chain 'L' and (resid 87 through 288 or (resid 289 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 through 312 or (resid 315 a \ nd (name N or name CA or name C or name O or name CB )) or resid 316 or (resid 3 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 318 through \ 369 or (resid 370 and (name N or name CA or name C or name O or name CB )) or r \ esid 371 through 377 or (resid 378 and (name N or name CA or name C or name O or \ name CB )) or resid 379 through 425 or (resid 426 through 432 and (name N or na \ me CA or name C or name O or name CB )) or resid 433 through 571 or (resid 572 t \ hrough 573 and (name N or name CA or name C or name O or name CB )) or resid 574 \ or (resid 575 through 577 and (name N or name CA or name C or name O or name CB \ )) or resid 578 or (resid 579 through 582 and (name N or name CA or name C or n \ ame O or name CB )) or resid 583 through 584 or (resid 585 and (name N or name C \ A or name C or name O or name CB )) or resid 586 through 616 or (resid 617 and ( \ name N or name CA or name C or name O or name CB )) or resid 618 through 703)) selection = (chain 'M' and (resid 87 through 287 or (resid 288 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 or (resid 292 and (name N o \ r name CA or name C or name O or name CB )) or resid 293 or resid 301 through 30 \ 4 or (resid 305 and (name N or name CA or name C or name O or name CB )) or resi \ d 306 through 312 or resid 315 through 318 or (resid 319 and (name N or name CA \ or name C or name O or name CB )) or resid 320 through 343 or (resid 344 and (na \ me N or name CA or name C or name O or name CB )) or resid 345 through 361 or (r \ esid 362 through 363 and (name N or name CA or name C or name O or name CB )) or \ resid 364 through 428 or (resid 429 through 432 and (name N or name CA or name \ C or name O or name CB )) or resid 433 through 438 or resid 440 through 455 or r \ esid 459 through 535 or (resid 536 and (name N or name CA or name C or name O or \ name CB )) or resid 537 through 593 or resid 597 through 703)) selection = (chain 'P' and (resid 87 through 288 or (resid 289 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 through 312 or (resid 315 a \ nd (name N or name CA or name C or name O or name CB )) or resid 316 or (resid 3 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 318 through \ 369 or (resid 370 and (name N or name CA or name C or name O or name CB )) or r \ esid 371 through 377 or (resid 378 and (name N or name CA or name C or name O or \ name CB )) or resid 379 through 425 or (resid 426 through 432 and (name N or na \ me CA or name C or name O or name CB )) or resid 433 through 571 or (resid 572 t \ hrough 573 and (name N or name CA or name C or name O or name CB )) or resid 574 \ or (resid 575 through 577 and (name N or name CA or name C or name O or name CB \ )) or resid 578 or (resid 579 through 582 and (name N or name CA or name C or n \ ame O or name CB )) or resid 583 through 584 or (resid 585 and (name N or name C \ A or name C or name O or name CB )) or resid 586 through 616 or (resid 617 and ( \ name N or name CA or name C or name O or name CB )) or resid 618 through 703)) selection = (chain 'Q' and (resid 87 through 287 or (resid 288 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 or (resid 292 and (name N o \ r name CA or name C or name O or name CB )) or resid 293 or resid 301 through 30 \ 4 or (resid 305 and (name N or name CA or name C or name O or name CB )) or resi \ d 306 through 312 or resid 315 through 318 or (resid 319 and (name N or name CA \ or name C or name O or name CB )) or resid 320 through 343 or (resid 344 and (na \ me N or name CA or name C or name O or name CB )) or resid 345 through 361 or (r \ esid 362 through 363 and (name N or name CA or name C or name O or name CB )) or \ resid 364 through 428 or (resid 429 through 432 and (name N or name CA or name \ C or name O or name CB )) or resid 433 through 438 or resid 440 through 455 or r \ esid 459 through 535 or (resid 536 and (name N or name CA or name C or name O or \ name CB )) or resid 537 through 593 or resid 597 through 703)) } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' } 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: 8.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 45.810 Find NCS groups from input model: 1.310 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 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 : 0.011 0.087 42908 Z= 0.628 Angle : 1.537 20.774 58416 Z= 0.977 Chirality : 0.075 0.938 6800 Planarity : 0.016 0.307 7516 Dihedral : 13.536 88.179 15712 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.32 % Favored : 96.51 % Rotamer: Outliers : 0.61 % Allowed : 2.88 % Favored : 96.51 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.10), residues: 5448 helix: -1.91 (0.08), residues: 2276 sheet: 0.01 (0.14), residues: 1196 loop : -0.94 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.094 0.006 ARG Q 373 TYR 0.171 0.014 TYR F 112 PHE 0.052 0.008 PHE F 107 TRP 0.085 0.014 TRP L 574 HIS 0.017 0.003 HIS M 488 Details of bonding type rmsd covalent geometry : bond 0.01117 (42908) covalent geometry : angle 1.53737 (58416) hydrogen bonds : bond 0.19777 ( 1827) hydrogen bonds : angle 7.95510 ( 5544) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 1116 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 167 THR cc_start: 0.8006 (t) cc_final: 0.7728 (p) REVERT: D 426 LEU cc_start: 0.6087 (mt) cc_final: 0.5714 (tp) REVERT: D 555 ASN cc_start: 0.5401 (m-40) cc_final: 0.4618 (t0) REVERT: D 570 MET cc_start: 0.7129 (tpp) cc_final: 0.6641 (tpp) REVERT: D 573 GLN cc_start: 0.4924 (tt0) cc_final: 0.4722 (tm-30) REVERT: D 586 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.6926 (p) REVERT: E 392 VAL cc_start: 0.7094 (t) cc_final: 0.6863 (p) REVERT: E 483 THR cc_start: 0.7785 (p) cc_final: 0.7560 (p) REVERT: F 123 ARG cc_start: 0.7632 (ttm110) cc_final: 0.7174 (ptt180) REVERT: F 221 LYS cc_start: 0.9220 (tttp) cc_final: 0.8892 (ttpt) REVERT: F 222 LYS cc_start: 0.8891 (mttm) cc_final: 0.8644 (mmmt) REVERT: F 224 GLN cc_start: 0.7809 (tp40) cc_final: 0.7380 (tp40) REVERT: G 371 ASP cc_start: 0.6769 (p0) cc_final: 0.6034 (t0) REVERT: G 372 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7549 (pp20) REVERT: G 386 ASP cc_start: 0.8348 (m-30) cc_final: 0.8140 (m-30) REVERT: H 271 MET cc_start: 0.8070 (mtm) cc_final: 0.7858 (mtt) REVERT: H 555 ASN cc_start: 0.5439 (m-40) cc_final: 0.4618 (t0) REVERT: H 570 MET cc_start: 0.7162 (tpp) cc_final: 0.6698 (tpp) REVERT: H 572 MET cc_start: 0.4508 (ttp) cc_final: 0.4243 (tmm) REVERT: H 586 THR cc_start: 0.7746 (OUTLIER) cc_final: 0.6993 (p) REVERT: I 392 VAL cc_start: 0.7141 (t) cc_final: 0.6889 (p) REVERT: I 483 THR cc_start: 0.7782 (p) cc_final: 0.7565 (p) REVERT: J 123 ARG cc_start: 0.7586 (ttm110) cc_final: 0.6971 (ptt180) REVERT: J 221 LYS cc_start: 0.9267 (tttp) cc_final: 0.8928 (ttpt) REVERT: J 222 LYS cc_start: 0.8915 (mttm) cc_final: 0.8678 (mmmt) REVERT: K 371 ASP cc_start: 0.6542 (p0) cc_final: 0.5694 (t0) REVERT: K 372 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7461 (tm-30) REVERT: K 380 GLN cc_start: 0.8351 (tp-100) cc_final: 0.7958 (tm-30) REVERT: K 389 GLU cc_start: 0.7854 (pt0) cc_final: 0.7427 (pt0) REVERT: K 401 ARG cc_start: 0.8117 (mmp-170) cc_final: 0.7661 (mmp80) REVERT: L 223 TYR cc_start: 0.8285 (m-80) cc_final: 0.8050 (m-80) REVERT: L 267 TRP cc_start: 0.7155 (m100) cc_final: 0.6405 (m100) REVERT: L 570 MET cc_start: 0.7276 (tpp) cc_final: 0.6761 (tpp) REVERT: L 572 MET cc_start: 0.4855 (ttp) cc_final: 0.4288 (tmm) REVERT: L 573 GLN cc_start: 0.4632 (tt0) cc_final: 0.4276 (tm-30) REVERT: L 586 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.6746 (p) REVERT: M 495 PHE cc_start: 0.6180 (m-80) cc_final: 0.5827 (m-80) REVERT: M 534 ASP cc_start: 0.7101 (t70) cc_final: 0.6852 (t0) REVERT: M 535 ILE cc_start: 0.6367 (mt) cc_final: 0.6141 (mt) REVERT: M 543 MET cc_start: 0.7743 (mtt) cc_final: 0.6672 (mtt) REVERT: N 123 ARG cc_start: 0.7295 (ttm110) cc_final: 0.6644 (ppt170) REVERT: N 148 LYS cc_start: 0.9246 (ttmm) cc_final: 0.8988 (mttt) REVERT: N 184 MET cc_start: 0.8590 (tpp) cc_final: 0.8076 (tpp) REVERT: N 221 LYS cc_start: 0.9277 (tttp) cc_final: 0.8888 (ttpt) REVERT: N 222 LYS cc_start: 0.8919 (mttm) cc_final: 0.8703 (mmmt) REVERT: O 329 ILE cc_start: 0.7734 (mm) cc_final: 0.7512 (pt) REVERT: O 371 ASP cc_start: 0.6770 (p0) cc_final: 0.5906 (t0) REVERT: O 372 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7519 (tm-30) REVERT: O 386 ASP cc_start: 0.8193 (m-30) cc_final: 0.7835 (m-30) REVERT: O 389 GLU cc_start: 0.7791 (pt0) cc_final: 0.7447 (pt0) REVERT: O 401 ARG cc_start: 0.8041 (mmp-170) cc_final: 0.7627 (mmp80) REVERT: O 447 LYS cc_start: 0.4939 (mmtt) cc_final: 0.4720 (mtpt) REVERT: P 227 ASP cc_start: 0.7055 (t0) cc_final: 0.6833 (p0) REVERT: P 277 MET cc_start: 0.7891 (mtt) cc_final: 0.7656 (mmm) REVERT: P 338 TYR cc_start: 0.6856 (t80) cc_final: 0.6336 (t80) REVERT: P 570 MET cc_start: 0.7230 (tpp) cc_final: 0.6920 (tpp) REVERT: P 572 MET cc_start: 0.4857 (ttp) cc_final: 0.4430 (tmm) REVERT: P 586 THR cc_start: 0.7467 (OUTLIER) cc_final: 0.6661 (p) REVERT: Q 483 THR cc_start: 0.8107 (p) cc_final: 0.7893 (p) REVERT: Q 534 ASP cc_start: 0.7054 (t70) cc_final: 0.6779 (t0) REVERT: Q 535 ILE cc_start: 0.6429 (mt) cc_final: 0.6209 (mt) REVERT: Q 543 MET cc_start: 0.7924 (mtt) cc_final: 0.6880 (mtt) REVERT: R 123 ARG cc_start: 0.7281 (ttm110) cc_final: 0.6731 (ptm160) REVERT: R 148 LYS cc_start: 0.9206 (ttmm) cc_final: 0.8983 (mttt) REVERT: R 154 LYS cc_start: 0.6611 (mttm) cc_final: 0.6391 (ttmm) REVERT: R 191 ARG cc_start: 0.8195 (ttt180) cc_final: 0.7955 (mtp180) REVERT: S 348 GLN cc_start: 0.8501 (mt0) cc_final: 0.8249 (mt0) REVERT: S 371 ASP cc_start: 0.6793 (p0) cc_final: 0.6130 (t0) REVERT: S 372 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7509 (pp20) REVERT: S 389 GLU cc_start: 0.7887 (pt0) cc_final: 0.7241 (pt0) REVERT: S 401 ARG cc_start: 0.8040 (mmp-170) cc_final: 0.7645 (mmp80) outliers start: 26 outliers final: 4 residues processed: 1131 average time/residue: 0.2790 time to fit residues: 505.0377 Evaluate side-chains 619 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 611 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 586 THR Chi-restraints excluded: chain L residue 586 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain P residue 586 THR Chi-restraints excluded: chain R residue 152 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 394 optimal weight: 0.3980 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 0.7980 chunk 523 optimal weight: 0.0000 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 20.0000 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 527 ASN D 582 ASN E 128 GLN E 145 GLN E 449 GLN E 527 ASN G 320 HIS G 452 GLN H 527 ASN H 582 ASN I 128 GLN I 145 GLN I 527 ASN K 320 HIS K 327 ASN L 127 HIS L 527 ASN L 582 ASN M 128 GLN N 141 GLN O 320 HIS P 127 HIS P 527 ASN S 320 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.165283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.128528 restraints weight = 78422.546| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 3.14 r_work: 0.3640 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 42908 Z= 0.155 Angle : 0.660 9.833 58416 Z= 0.346 Chirality : 0.046 0.198 6800 Planarity : 0.005 0.054 7516 Dihedral : 8.293 79.053 6362 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.01 % Allowed : 10.77 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.11), residues: 5448 helix: -0.02 (0.10), residues: 2300 sheet: 0.21 (0.14), residues: 1184 loop : -0.28 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 180 TYR 0.017 0.002 TYR L 466 PHE 0.022 0.002 PHE J 223 TRP 0.019 0.002 TRP R 185 HIS 0.007 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00343 (42908) covalent geometry : angle 0.65969 (58416) hydrogen bonds : bond 0.05250 ( 1827) hydrogen bonds : angle 5.51214 ( 5544) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 668 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 167 THR cc_start: 0.8614 (t) cc_final: 0.8252 (p) REVERT: D 267 TRP cc_start: 0.7541 (m100) cc_final: 0.6817 (m100) REVERT: D 426 LEU cc_start: 0.6143 (mt) cc_final: 0.5854 (tp) REVERT: D 440 TRP cc_start: 0.5008 (t-100) cc_final: 0.4788 (t-100) REVERT: D 555 ASN cc_start: 0.6047 (m-40) cc_final: 0.5162 (t0) REVERT: D 570 MET cc_start: 0.8273 (tpp) cc_final: 0.7551 (tpt) REVERT: D 572 MET cc_start: 0.5114 (tmm) cc_final: 0.4803 (tmm) REVERT: D 601 MET cc_start: 0.9069 (mmt) cc_final: 0.8788 (mmt) REVERT: E 347 HIS cc_start: 0.6586 (OUTLIER) cc_final: 0.5640 (t-90) REVERT: E 449 GLN cc_start: 0.7254 (mm-40) cc_final: 0.6588 (mm-40) REVERT: F 122 ASN cc_start: 0.7931 (t0) cc_final: 0.7561 (m-40) REVERT: F 151 ASN cc_start: 0.8911 (m-40) cc_final: 0.8695 (m110) REVERT: F 185 TRP cc_start: 0.8330 (t60) cc_final: 0.7957 (t60) REVERT: G 380 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8114 (tp40) REVERT: H 167 THR cc_start: 0.8601 (t) cc_final: 0.8258 (p) REVERT: H 203 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7907 (p) REVERT: H 570 MET cc_start: 0.8113 (tpp) cc_final: 0.7543 (tpt) REVERT: H 572 MET cc_start: 0.4836 (ttp) cc_final: 0.4608 (tmm) REVERT: H 601 MET cc_start: 0.9072 (mmt) cc_final: 0.8781 (mmt) REVERT: I 88 ILE cc_start: 0.8065 (tt) cc_final: 0.7806 (tp) REVERT: I 227 ASP cc_start: 0.6127 (t0) cc_final: 0.5235 (t0) REVERT: I 347 HIS cc_start: 0.6725 (OUTLIER) cc_final: 0.5566 (t-90) REVERT: I 588 LEU cc_start: 0.6833 (tp) cc_final: 0.6363 (mp) REVERT: J 180 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7423 (ttm110) REVERT: K 327 ASN cc_start: 0.8988 (t0) cc_final: 0.8472 (t0) REVERT: K 356 GLU cc_start: 0.6646 (pm20) cc_final: 0.6239 (pm20) REVERT: K 371 ASP cc_start: 0.6334 (p0) cc_final: 0.5847 (t0) REVERT: K 372 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7100 (pp20) REVERT: L 105 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7170 (mm-30) REVERT: L 289 LEU cc_start: 0.7911 (mp) cc_final: 0.7710 (mp) REVERT: L 422 MET cc_start: 0.5447 (ttt) cc_final: 0.5204 (ttt) REVERT: L 570 MET cc_start: 0.8169 (tpp) cc_final: 0.7874 (tpt) REVERT: L 572 MET cc_start: 0.4814 (ttp) cc_final: 0.4611 (tmm) REVERT: L 601 MET cc_start: 0.8886 (mmt) cc_final: 0.8644 (mmt) REVERT: M 422 MET cc_start: 0.5790 (mtp) cc_final: 0.5505 (tpp) REVERT: M 495 PHE cc_start: 0.7086 (m-80) cc_final: 0.6861 (m-80) REVERT: N 122 ASN cc_start: 0.7748 (t0) cc_final: 0.7447 (m-40) REVERT: O 356 GLU cc_start: 0.6514 (pm20) cc_final: 0.6116 (pm20) REVERT: O 371 ASP cc_start: 0.6622 (p0) cc_final: 0.6124 (t0) REVERT: O 372 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7148 (pp20) REVERT: P 289 LEU cc_start: 0.7824 (mp) cc_final: 0.7615 (mp) REVERT: P 422 MET cc_start: 0.5275 (ttt) cc_final: 0.5012 (ttt) REVERT: P 570 MET cc_start: 0.8088 (tpp) cc_final: 0.7546 (tpt) REVERT: P 572 MET cc_start: 0.5002 (ttp) cc_final: 0.4691 (tmm) REVERT: Q 322 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8239 (mm-30) REVERT: R 122 ASN cc_start: 0.7984 (t0) cc_final: 0.7435 (m-40) REVERT: S 356 GLU cc_start: 0.6590 (pm20) cc_final: 0.6211 (pm20) REVERT: S 371 ASP cc_start: 0.6664 (p0) cc_final: 0.6185 (t0) REVERT: S 372 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7264 (pp20) outliers start: 86 outliers final: 47 residues processed: 725 average time/residue: 0.2511 time to fit residues: 305.2600 Evaluate side-chains 575 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 522 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 347 HIS Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain G residue 466 THR Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 347 HIS Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain K residue 372 GLU Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 412 CYS Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain O residue 372 GLU Chi-restraints excluded: chain P residue 163 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 433 LEU Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 314 SER Chi-restraints excluded: chain Q residue 372 VAL Chi-restraints excluded: chain Q residue 412 CYS Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 200 HIS Chi-restraints excluded: chain S residue 372 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 414 optimal weight: 7.9990 chunk 313 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 488 optimal weight: 0.5980 chunk 435 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 535 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 543 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 HIS D 626 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 HIS H 626 GLN J 122 ASN M 143 HIS M 600 ASN N 140 GLN N 151 ASN Q 600 ASN R 151 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.159636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.122453 restraints weight = 77532.006| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 3.30 r_work: 0.3566 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 42908 Z= 0.180 Angle : 0.619 8.685 58416 Z= 0.324 Chirality : 0.045 0.185 6800 Planarity : 0.005 0.060 7516 Dihedral : 8.031 75.587 6356 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.09 % Allowed : 11.87 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.11), residues: 5448 helix: 0.25 (0.10), residues: 2300 sheet: 0.32 (0.14), residues: 1192 loop : -0.48 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 416 TYR 0.016 0.002 TYR H 466 PHE 0.019 0.002 PHE E 87 TRP 0.026 0.002 TRP H 440 HIS 0.012 0.001 HIS M 143 Details of bonding type rmsd covalent geometry : bond 0.00421 (42908) covalent geometry : angle 0.61950 (58416) hydrogen bonds : bond 0.04558 ( 1827) hydrogen bonds : angle 5.01289 ( 5544) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 566 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7110 (mm-30) REVERT: D 267 TRP cc_start: 0.7555 (m100) cc_final: 0.6833 (m100) REVERT: D 422 MET cc_start: 0.6029 (OUTLIER) cc_final: 0.5679 (ttm) REVERT: D 570 MET cc_start: 0.8216 (tpp) cc_final: 0.7900 (tpt) REVERT: D 572 MET cc_start: 0.5034 (tmm) cc_final: 0.4636 (tmm) REVERT: E 570 MET cc_start: 0.8142 (tpp) cc_final: 0.7909 (tpp) REVERT: F 185 TRP cc_start: 0.8350 (t60) cc_final: 0.8133 (t60) REVERT: F 214 ILE cc_start: 0.9056 (tp) cc_final: 0.8737 (pt) REVERT: G 348 GLN cc_start: 0.8736 (mp10) cc_final: 0.8493 (mm-40) REVERT: G 380 GLN cc_start: 0.8753 (tp-100) cc_final: 0.8243 (tp40) REVERT: H 203 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.8098 (p) REVERT: H 267 TRP cc_start: 0.7559 (m100) cc_final: 0.6963 (m100) REVERT: H 335 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7151 (mp) REVERT: H 422 MET cc_start: 0.5404 (ttm) cc_final: 0.5021 (tpp) REVERT: H 570 MET cc_start: 0.8132 (tpp) cc_final: 0.7829 (tpt) REVERT: H 572 MET cc_start: 0.4865 (ttp) cc_final: 0.4631 (tmm) REVERT: I 226 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7324 (tpt) REVERT: I 343 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7541 (pm20) REVERT: I 344 LEU cc_start: 0.6945 (mt) cc_final: 0.6337 (mt) REVERT: I 449 GLN cc_start: 0.7313 (mm110) cc_final: 0.6817 (mm-40) REVERT: I 570 MET cc_start: 0.8209 (tpp) cc_final: 0.7995 (tpp) REVERT: I 588 LEU cc_start: 0.7115 (tp) cc_final: 0.6841 (tp) REVERT: K 327 ASN cc_start: 0.8956 (t0) cc_final: 0.8245 (t0) REVERT: K 356 GLU cc_start: 0.6661 (pm20) cc_final: 0.6384 (pm20) REVERT: K 400 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8276 (tm-30) REVERT: K 401 ARG cc_start: 0.8693 (mmp-170) cc_final: 0.8393 (mmp80) REVERT: L 105 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7367 (mm-30) REVERT: L 254 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8331 (p) REVERT: L 422 MET cc_start: 0.5630 (ttt) cc_final: 0.5244 (ttt) REVERT: L 570 MET cc_start: 0.8324 (tpp) cc_final: 0.7944 (tpt) REVERT: L 601 MET cc_start: 0.8899 (mmt) cc_final: 0.8650 (mmt) REVERT: M 322 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8126 (mm-30) REVERT: M 495 PHE cc_start: 0.7118 (m-80) cc_final: 0.6880 (m-80) REVERT: N 140 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8624 (mm-40) REVERT: O 348 GLN cc_start: 0.8636 (mp10) cc_final: 0.8355 (mm-40) REVERT: O 356 GLU cc_start: 0.6624 (pm20) cc_final: 0.6384 (pm20) REVERT: P 105 GLU cc_start: 0.7362 (tt0) cc_final: 0.6834 (mm-30) REVERT: P 254 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8394 (p) REVERT: P 289 LEU cc_start: 0.7990 (mp) cc_final: 0.7738 (mt) REVERT: P 422 MET cc_start: 0.5615 (ttt) cc_final: 0.5212 (ttt) REVERT: P 570 MET cc_start: 0.8214 (tpp) cc_final: 0.7491 (tpt) REVERT: P 572 MET cc_start: 0.5022 (ttp) cc_final: 0.4657 (tmm) REVERT: P 601 MET cc_start: 0.8964 (mmt) cc_final: 0.8689 (mmt) REVERT: Q 322 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8101 (mm-30) REVERT: S 356 GLU cc_start: 0.6748 (pm20) cc_final: 0.6542 (pm20) outliers start: 132 outliers final: 77 residues processed: 665 average time/residue: 0.2272 time to fit residues: 259.8034 Evaluate side-chains 580 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 497 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain G residue 466 THR Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 226 MET Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain I residue 412 CYS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 314 SER Chi-restraints excluded: chain M residue 344 LEU Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 412 CYS Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain O residue 383 LYS Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain P residue 163 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 254 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 433 LEU Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 229 GLU Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 314 SER Chi-restraints excluded: chain Q residue 372 VAL Chi-restraints excluded: chain Q residue 412 CYS Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 200 HIS Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 383 LYS Chi-restraints excluded: chain S residue 466 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 150 optimal weight: 2.9990 chunk 416 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 449 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 482 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 GLN N 141 GLN N 151 ASN R 151 ASN S 348 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.157994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.120323 restraints weight = 77849.546| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.01 r_work: 0.3519 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 42908 Z= 0.148 Angle : 0.574 8.073 58416 Z= 0.298 Chirality : 0.044 0.238 6800 Planarity : 0.004 0.060 7516 Dihedral : 7.896 85.583 6356 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.88 % Allowed : 13.39 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.11), residues: 5448 helix: 0.49 (0.10), residues: 2276 sheet: 0.35 (0.14), residues: 1208 loop : -0.56 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 416 TYR 0.015 0.002 TYR E 154 PHE 0.020 0.001 PHE N 223 TRP 0.017 0.002 TRP D 440 HIS 0.007 0.001 HIS Q 143 Details of bonding type rmsd covalent geometry : bond 0.00346 (42908) covalent geometry : angle 0.57364 (58416) hydrogen bonds : bond 0.04000 ( 1827) hydrogen bonds : angle 4.79596 ( 5544) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 518 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7065 (mm-30) REVERT: D 267 TRP cc_start: 0.7529 (m100) cc_final: 0.6875 (m100) REVERT: D 570 MET cc_start: 0.8316 (tpp) cc_final: 0.7883 (tpt) REVERT: D 572 MET cc_start: 0.4803 (tmm) cc_final: 0.4411 (tmm) REVERT: D 601 MET cc_start: 0.9017 (mmt) cc_final: 0.8713 (mmt) REVERT: E 570 MET cc_start: 0.8195 (tpp) cc_final: 0.7901 (tpp) REVERT: G 348 GLN cc_start: 0.8698 (mp10) cc_final: 0.8469 (mm-40) REVERT: G 380 GLN cc_start: 0.8689 (tp-100) cc_final: 0.8284 (tp40) REVERT: H 203 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8114 (p) REVERT: H 267 TRP cc_start: 0.7576 (m100) cc_final: 0.6958 (m100) REVERT: H 335 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6992 (mp) REVERT: H 570 MET cc_start: 0.8229 (tpp) cc_final: 0.7828 (tpt) REVERT: I 343 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7699 (pm20) REVERT: I 344 LEU cc_start: 0.6998 (mt) cc_final: 0.6306 (mt) REVERT: I 570 MET cc_start: 0.8206 (tpp) cc_final: 0.7964 (tpp) REVERT: J 156 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7636 (mt-10) REVERT: J 180 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7658 (mtm-85) REVERT: K 356 GLU cc_start: 0.6791 (pm20) cc_final: 0.6516 (pm20) REVERT: L 267 TRP cc_start: 0.7444 (m100) cc_final: 0.6611 (m100) REVERT: L 570 MET cc_start: 0.8376 (tpp) cc_final: 0.7941 (tpt) REVERT: L 572 MET cc_start: 0.4934 (tmm) cc_final: 0.4660 (tmm) REVERT: L 601 MET cc_start: 0.8890 (mmt) cc_final: 0.8607 (mmt) REVERT: M 322 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8164 (mm-30) REVERT: M 495 PHE cc_start: 0.7053 (m-80) cc_final: 0.6820 (m-80) REVERT: N 156 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: N 241 MET cc_start: 0.6915 (mmm) cc_final: 0.6315 (mmm) REVERT: O 348 GLN cc_start: 0.8634 (mp10) cc_final: 0.8387 (mm-40) REVERT: O 356 GLU cc_start: 0.6666 (pm20) cc_final: 0.6453 (pm20) REVERT: O 371 ASP cc_start: 0.7122 (p0) cc_final: 0.6851 (t0) REVERT: P 105 GLU cc_start: 0.7419 (tt0) cc_final: 0.6878 (mm-30) REVERT: P 289 LEU cc_start: 0.8057 (mp) cc_final: 0.7849 (mt) REVERT: P 422 MET cc_start: 0.5816 (ttt) cc_final: 0.5436 (ttt) REVERT: P 570 MET cc_start: 0.8026 (tpp) cc_final: 0.7669 (tpt) REVERT: P 572 MET cc_start: 0.5108 (ttp) cc_final: 0.4806 (tmm) REVERT: P 586 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8502 (p) REVERT: P 620 ASP cc_start: 0.6316 (t0) cc_final: 0.6078 (t0) REVERT: Q 322 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8123 (mm-30) REVERT: R 241 MET cc_start: 0.6958 (mmm) cc_final: 0.6658 (mmm) outliers start: 123 outliers final: 75 residues processed: 612 average time/residue: 0.2239 time to fit residues: 236.0888 Evaluate side-chains 558 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 478 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 604 PHE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain G residue 466 THR Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 604 PHE Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain I residue 412 CYS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 156 GLU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain K residue 383 LYS Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 344 LEU Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 412 CYS Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 550 THR Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 156 GLU Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain O residue 383 LYS Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 433 LEU Chi-restraints excluded: chain P residue 586 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 372 VAL Chi-restraints excluded: chain Q residue 412 CYS Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 200 HIS Chi-restraints excluded: chain S residue 383 LYS Chi-restraints excluded: chain S residue 417 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 236 optimal weight: 8.9990 chunk 484 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 307 optimal weight: 10.0000 chunk 321 optimal weight: 8.9990 chunk 345 optimal weight: 0.7980 chunk 465 optimal weight: 1.9990 chunk 333 optimal weight: 1.9990 chunk 412 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 487 GLN H 582 ASN I 128 GLN J 113 ASN ** J 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 379 GLN P 128 GLN Q 593 GLN S 348 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.153699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.115534 restraints weight = 77607.571| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.35 r_work: 0.3444 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 42908 Z= 0.264 Angle : 0.677 8.414 58416 Z= 0.351 Chirality : 0.048 0.214 6800 Planarity : 0.005 0.064 7516 Dihedral : 8.210 88.889 6356 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.65 % Allowed : 13.81 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.11), residues: 5448 helix: 0.08 (0.10), residues: 2352 sheet: 0.03 (0.15), residues: 1180 loop : -0.85 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG O 416 TYR 0.026 0.002 TYR E 154 PHE 0.017 0.002 PHE E 604 TRP 0.015 0.002 TRP E 504 HIS 0.011 0.002 HIS N 176 Details of bonding type rmsd covalent geometry : bond 0.00643 (42908) covalent geometry : angle 0.67744 (58416) hydrogen bonds : bond 0.05038 ( 1827) hydrogen bonds : angle 5.03687 ( 5544) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 490 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7583 (mm-30) REVERT: D 277 MET cc_start: 0.8347 (mtp) cc_final: 0.8125 (mmm) REVERT: D 426 LEU cc_start: 0.6332 (mt) cc_final: 0.5989 (tp) REVERT: D 570 MET cc_start: 0.8364 (tpp) cc_final: 0.8059 (tpt) REVERT: D 572 MET cc_start: 0.4894 (tmm) cc_final: 0.4658 (tmm) REVERT: D 601 MET cc_start: 0.9094 (mmt) cc_final: 0.8786 (mmt) REVERT: E 449 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6771 (mm-40) REVERT: E 534 ASP cc_start: 0.7402 (t70) cc_final: 0.7082 (t0) REVERT: E 570 MET cc_start: 0.8244 (tpp) cc_final: 0.7943 (tpp) REVERT: F 133 CYS cc_start: 0.8499 (m) cc_final: 0.8277 (p) REVERT: F 154 LYS cc_start: 0.7844 (mttm) cc_final: 0.7423 (tttt) REVERT: G 348 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8484 (mm-40) REVERT: G 380 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8334 (tp40) REVERT: G 420 ASP cc_start: 0.8558 (m-30) cc_final: 0.7838 (m-30) REVERT: H 203 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8265 (p) REVERT: H 277 MET cc_start: 0.8372 (mtp) cc_final: 0.7768 (mmm) REVERT: H 335 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7156 (mp) REVERT: H 570 MET cc_start: 0.8309 (tpp) cc_final: 0.8016 (tpt) REVERT: H 572 MET cc_start: 0.4833 (tmm) cc_final: 0.4456 (tmm) REVERT: I 277 MET cc_start: 0.8281 (mmm) cc_final: 0.7970 (mmm) REVERT: I 442 ASN cc_start: 0.8927 (p0) cc_final: 0.8698 (p0) REVERT: I 534 ASP cc_start: 0.7431 (t70) cc_final: 0.7100 (t0) REVERT: I 570 MET cc_start: 0.8276 (tpp) cc_final: 0.8029 (tpp) REVERT: J 140 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8542 (mm-40) REVERT: J 178 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8650 (tm-30) REVERT: K 356 GLU cc_start: 0.6901 (pm20) cc_final: 0.6691 (pm20) REVERT: L 254 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8330 (p) REVERT: L 280 MET cc_start: 0.7702 (mtp) cc_final: 0.7008 (mpp) REVERT: L 572 MET cc_start: 0.4796 (tmm) cc_final: 0.4475 (tmm) REVERT: M 322 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8087 (mm-30) REVERT: M 495 PHE cc_start: 0.7354 (m-80) cc_final: 0.7116 (m-80) REVERT: N 156 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: N 241 MET cc_start: 0.7073 (mmm) cc_final: 0.5878 (mmm) REVERT: O 348 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8436 (mm-40) REVERT: O 356 GLU cc_start: 0.6908 (pm20) cc_final: 0.6692 (pm20) REVERT: P 91 PHE cc_start: 0.7264 (m-80) cc_final: 0.7060 (m-10) REVERT: P 105 GLU cc_start: 0.7445 (tt0) cc_final: 0.7204 (tt0) REVERT: P 254 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8374 (p) REVERT: P 280 MET cc_start: 0.7699 (mtp) cc_final: 0.7112 (mpp) REVERT: P 422 MET cc_start: 0.6011 (ttt) cc_final: 0.5663 (ttt) REVERT: P 570 MET cc_start: 0.8269 (tpp) cc_final: 0.7893 (tpt) REVERT: Q 322 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8031 (mm-30) outliers start: 156 outliers final: 113 residues processed: 608 average time/residue: 0.2323 time to fit residues: 241.2682 Evaluate side-chains 576 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 455 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 597 ILE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 379 GLN Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain G residue 466 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 597 ILE Chi-restraints excluded: chain H residue 604 PHE Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain I residue 412 CYS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain I residue 550 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 133 CYS Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 178 GLU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain K residue 383 LYS Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain K residue 438 THR Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 412 CYS Chi-restraints excluded: chain L residue 491 TRP Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 181 ASP Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 344 LEU Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 412 CYS Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 527 ASN Chi-restraints excluded: chain M residue 550 THR Chi-restraints excluded: chain M residue 558 VAL Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 156 GLU Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain O residue 348 GLN Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain O residue 438 THR Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 ASP Chi-restraints excluded: chain P residue 254 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 433 LEU Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain Q residue 167 THR Chi-restraints excluded: chain Q residue 181 ASP Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 229 GLU Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 314 SER Chi-restraints excluded: chain Q residue 344 LEU Chi-restraints excluded: chain Q residue 372 VAL Chi-restraints excluded: chain Q residue 412 CYS Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 550 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 417 ASP Chi-restraints excluded: chain S residue 438 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 499 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 215 optimal weight: 20.0000 chunk 442 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 463 optimal weight: 6.9990 chunk 328 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 chunk 522 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 GLN F 174 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 449 GLN O 379 GLN S 348 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.154393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.116392 restraints weight = 77846.862| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.03 r_work: 0.3472 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 42908 Z= 0.202 Angle : 0.622 9.727 58416 Z= 0.320 Chirality : 0.045 0.190 6800 Planarity : 0.005 0.064 7516 Dihedral : 8.119 87.933 6356 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.46 % Allowed : 14.75 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.11), residues: 5448 helix: 0.28 (0.10), residues: 2320 sheet: -0.04 (0.15), residues: 1184 loop : -0.87 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG O 416 TYR 0.020 0.002 TYR E 154 PHE 0.014 0.001 PHE P 240 TRP 0.013 0.002 TRP I 504 HIS 0.007 0.001 HIS Q 143 Details of bonding type rmsd covalent geometry : bond 0.00487 (42908) covalent geometry : angle 0.62226 (58416) hydrogen bonds : bond 0.04436 ( 1827) hydrogen bonds : angle 4.85598 ( 5544) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 488 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7183 (mm-30) REVERT: D 267 TRP cc_start: 0.7653 (m100) cc_final: 0.6930 (m100) REVERT: D 277 MET cc_start: 0.8379 (mtp) cc_final: 0.8173 (mmm) REVERT: D 335 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7151 (mp) REVERT: D 570 MET cc_start: 0.8387 (tpp) cc_final: 0.8067 (tpt) REVERT: D 572 MET cc_start: 0.4893 (tmm) cc_final: 0.4657 (tmm) REVERT: D 601 MET cc_start: 0.9077 (mmt) cc_final: 0.8779 (mmt) REVERT: E 449 GLN cc_start: 0.7186 (mm-40) cc_final: 0.6715 (mm-40) REVERT: E 570 MET cc_start: 0.8294 (tpp) cc_final: 0.8006 (tpp) REVERT: F 133 CYS cc_start: 0.8484 (m) cc_final: 0.8242 (p) REVERT: G 348 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8460 (mm-40) REVERT: G 380 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8328 (tp40) REVERT: H 203 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8388 (p) REVERT: H 335 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7024 (mp) REVERT: H 570 MET cc_start: 0.8371 (tpp) cc_final: 0.8066 (tpt) REVERT: H 572 MET cc_start: 0.4824 (tmm) cc_final: 0.4596 (tmm) REVERT: I 277 MET cc_start: 0.8287 (mmm) cc_final: 0.7902 (mmm) REVERT: I 442 ASN cc_start: 0.8898 (p0) cc_final: 0.8659 (p0) REVERT: I 570 MET cc_start: 0.8313 (tpp) cc_final: 0.8069 (tpp) REVERT: J 140 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8574 (mm-40) REVERT: J 180 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7518 (mtm-85) REVERT: J 182 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8272 (pm20) REVERT: K 356 GLU cc_start: 0.6938 (pm20) cc_final: 0.6734 (pm20) REVERT: K 416 ARG cc_start: 0.8556 (mmm160) cc_final: 0.8331 (mmm160) REVERT: L 254 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8330 (p) REVERT: L 280 MET cc_start: 0.7735 (mtp) cc_final: 0.7532 (mtp) REVERT: L 601 MET cc_start: 0.8810 (mmt) cc_final: 0.8463 (mmt) REVERT: M 322 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7985 (mm-30) REVERT: M 429 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7449 (mpp80) REVERT: M 495 PHE cc_start: 0.7352 (m-80) cc_final: 0.7126 (m-80) REVERT: M 623 GLU cc_start: 0.7516 (pp20) cc_final: 0.7266 (pp20) REVERT: N 156 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: O 348 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8419 (mm-40) REVERT: O 416 ARG cc_start: 0.8639 (mmm160) cc_final: 0.8313 (mmm160) REVERT: P 91 PHE cc_start: 0.7157 (m-80) cc_final: 0.6938 (m-10) REVERT: P 105 GLU cc_start: 0.7497 (tt0) cc_final: 0.7224 (mm-30) REVERT: P 254 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8409 (p) REVERT: P 280 MET cc_start: 0.7663 (mtp) cc_final: 0.7452 (mtp) REVERT: P 335 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7294 (mp) REVERT: P 570 MET cc_start: 0.8273 (tpp) cc_final: 0.7928 (tpt) outliers start: 148 outliers final: 110 residues processed: 597 average time/residue: 0.2339 time to fit residues: 237.7584 Evaluate side-chains 578 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 458 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain D residue 597 ILE Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 379 GLN Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain G residue 466 THR Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 124 MET Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 604 PHE Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain I residue 412 CYS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 133 CYS Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 182 GLU Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain K residue 383 LYS Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain K residue 438 THR Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 491 TRP Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 181 ASP Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 314 SER Chi-restraints excluded: chain M residue 344 LEU Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 412 CYS Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 527 ASN Chi-restraints excluded: chain M residue 550 THR Chi-restraints excluded: chain M residue 558 VAL Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 156 GLU Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 200 HIS Chi-restraints excluded: chain O residue 348 GLN Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain O residue 438 THR Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 254 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 433 LEU Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain Q residue 181 ASP Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 314 SER Chi-restraints excluded: chain Q residue 344 LEU Chi-restraints excluded: chain Q residue 372 VAL Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 527 ASN Chi-restraints excluded: chain Q residue 550 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 200 HIS Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 438 THR Chi-restraints excluded: chain S residue 462 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 76 optimal weight: 6.9990 chunk 360 optimal weight: 0.4980 chunk 299 optimal weight: 8.9990 chunk 301 optimal weight: 10.0000 chunk 265 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 469 optimal weight: 0.7980 chunk 389 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 379 GLN R 87 HIS S 348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.155529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.117679 restraints weight = 77310.151| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.37 r_work: 0.3481 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 42908 Z= 0.151 Angle : 0.584 9.145 58416 Z= 0.299 Chirality : 0.044 0.190 6800 Planarity : 0.004 0.067 7516 Dihedral : 7.938 87.109 6356 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.16 % Allowed : 15.15 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.11), residues: 5448 helix: 0.56 (0.11), residues: 2292 sheet: 0.02 (0.15), residues: 1188 loop : -0.78 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG S 416 TYR 0.016 0.002 TYR E 154 PHE 0.015 0.001 PHE P 240 TRP 0.011 0.001 TRP N 185 HIS 0.005 0.001 HIS I 143 Details of bonding type rmsd covalent geometry : bond 0.00360 (42908) covalent geometry : angle 0.58433 (58416) hydrogen bonds : bond 0.03917 ( 1827) hydrogen bonds : angle 4.66448 ( 5544) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 492 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7149 (mm-30) REVERT: D 267 TRP cc_start: 0.7647 (m100) cc_final: 0.6953 (m100) REVERT: D 277 MET cc_start: 0.8530 (mtp) cc_final: 0.7958 (mmm) REVERT: D 280 MET cc_start: 0.7637 (mtp) cc_final: 0.7128 (mpp) REVERT: D 335 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7053 (mp) REVERT: D 570 MET cc_start: 0.8368 (tpp) cc_final: 0.8127 (tpt) REVERT: D 572 MET cc_start: 0.4820 (tmm) cc_final: 0.4595 (tmm) REVERT: E 103 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7455 (tt) REVERT: E 449 GLN cc_start: 0.7192 (mm-40) cc_final: 0.6731 (mm-40) REVERT: E 570 MET cc_start: 0.8216 (tpp) cc_final: 0.7921 (tpp) REVERT: F 127 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8983 (tt) REVERT: F 140 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8549 (mm-40) REVERT: F 182 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8587 (pm20) REVERT: F 241 MET cc_start: 0.7376 (mmm) cc_final: 0.5805 (mmm) REVERT: G 348 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8499 (mm-40) REVERT: G 380 GLN cc_start: 0.8634 (tp-100) cc_final: 0.8314 (tp40) REVERT: G 404 MET cc_start: 0.8551 (ttt) cc_final: 0.8319 (ttt) REVERT: H 267 TRP cc_start: 0.7659 (m100) cc_final: 0.6960 (m100) REVERT: H 277 MET cc_start: 0.8417 (mtp) cc_final: 0.8016 (mmm) REVERT: H 335 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6881 (mp) REVERT: H 570 MET cc_start: 0.8356 (tpp) cc_final: 0.8140 (tpt) REVERT: H 572 MET cc_start: 0.4698 (tmm) cc_final: 0.4480 (tmm) REVERT: I 277 MET cc_start: 0.8377 (mmm) cc_final: 0.7963 (mmm) REVERT: I 442 ASN cc_start: 0.8953 (p0) cc_final: 0.8710 (p0) REVERT: I 570 MET cc_start: 0.8302 (tpp) cc_final: 0.8071 (tpp) REVERT: J 127 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9003 (tt) REVERT: J 140 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8661 (mm-40) REVERT: K 404 MET cc_start: 0.8560 (ttt) cc_final: 0.8309 (ttt) REVERT: L 105 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7433 (mt-10) REVERT: L 254 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8369 (p) REVERT: L 267 TRP cc_start: 0.7476 (m100) cc_final: 0.6714 (m100) REVERT: L 280 MET cc_start: 0.7782 (mtp) cc_final: 0.7547 (mtp) REVERT: L 601 MET cc_start: 0.8834 (mmt) cc_final: 0.8523 (mmt) REVERT: M 429 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7578 (mpp80) REVERT: M 495 PHE cc_start: 0.7273 (m-80) cc_final: 0.7044 (m-80) REVERT: M 623 GLU cc_start: 0.7428 (pp20) cc_final: 0.7149 (pp20) REVERT: N 156 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: O 348 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8458 (mm-40) REVERT: P 91 PHE cc_start: 0.7180 (m-80) cc_final: 0.6954 (m-10) REVERT: P 105 GLU cc_start: 0.7537 (tt0) cc_final: 0.7238 (mm-30) REVERT: P 280 MET cc_start: 0.7625 (mtp) cc_final: 0.7395 (mtp) REVERT: P 422 MET cc_start: 0.5853 (ttt) cc_final: 0.5634 (ttt) REVERT: P 570 MET cc_start: 0.8292 (tpp) cc_final: 0.7938 (tpt) REVERT: P 572 MET cc_start: 0.5249 (tmm) cc_final: 0.4983 (tmm) REVERT: R 156 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7524 (mt-10) outliers start: 135 outliers final: 97 residues processed: 593 average time/residue: 0.2430 time to fit residues: 244.6651 Evaluate side-chains 562 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 454 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 604 PHE Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 379 GLN Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 604 PHE Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain I residue 412 CYS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 491 TRP Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 314 SER Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 412 CYS Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 527 ASN Chi-restraints excluded: chain M residue 550 THR Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 156 GLU Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 200 HIS Chi-restraints excluded: chain O residue 348 GLN Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 433 LEU Chi-restraints excluded: chain Q residue 181 ASP Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 230 ASP Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 280 MET Chi-restraints excluded: chain Q residue 314 SER Chi-restraints excluded: chain Q residue 372 VAL Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 550 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 156 GLU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 200 HIS Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 438 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 458 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 402 optimal weight: 1.9990 chunk 434 optimal weight: 0.9990 chunk 491 optimal weight: 30.0000 chunk 464 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 427 optimal weight: 0.8980 chunk 432 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 141 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 379 GLN Q 442 ASN S 348 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.156644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.119371 restraints weight = 77506.997| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.41 r_work: 0.3503 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 42908 Z= 0.121 Angle : 0.566 9.240 58416 Z= 0.288 Chirality : 0.043 0.191 6800 Planarity : 0.004 0.059 7516 Dihedral : 7.764 81.501 6355 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.76 % Allowed : 15.99 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.11), residues: 5448 helix: 0.75 (0.11), residues: 2300 sheet: 0.19 (0.15), residues: 1144 loop : -0.75 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 416 TYR 0.012 0.001 TYR I 154 PHE 0.015 0.001 PHE L 240 TRP 0.012 0.001 TRP N 185 HIS 0.005 0.001 HIS R 176 Details of bonding type rmsd covalent geometry : bond 0.00281 (42908) covalent geometry : angle 0.56607 (58416) hydrogen bonds : bond 0.03481 ( 1827) hydrogen bonds : angle 4.49551 ( 5544) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 490 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 267 TRP cc_start: 0.7608 (m100) cc_final: 0.6939 (m100) REVERT: D 277 MET cc_start: 0.8523 (mtp) cc_final: 0.7809 (mmm) REVERT: D 280 MET cc_start: 0.7663 (mtp) cc_final: 0.7109 (mpp) REVERT: D 335 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6851 (mp) REVERT: D 572 MET cc_start: 0.4658 (tmm) cc_final: 0.4425 (tmm) REVERT: D 604 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.6755 (t80) REVERT: E 103 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7406 (tt) REVERT: E 267 TRP cc_start: 0.8279 (m100) cc_final: 0.7882 (m100) REVERT: E 442 ASN cc_start: 0.9104 (t0) cc_final: 0.8875 (p0) REVERT: E 449 GLN cc_start: 0.7156 (mm-40) cc_final: 0.6687 (mm-40) REVERT: E 570 MET cc_start: 0.8247 (tpp) cc_final: 0.7952 (tpp) REVERT: G 348 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8500 (mm-40) REVERT: G 380 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8254 (tp40) REVERT: H 267 TRP cc_start: 0.7613 (m100) cc_final: 0.6974 (m100) REVERT: H 335 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6807 (mp) REVERT: H 572 MET cc_start: 0.4579 (tmm) cc_final: 0.4369 (tmm) REVERT: I 277 MET cc_start: 0.8420 (mmm) cc_final: 0.8034 (mmm) REVERT: I 442 ASN cc_start: 0.8925 (p0) cc_final: 0.8677 (p0) REVERT: I 570 MET cc_start: 0.8215 (tpp) cc_final: 0.7996 (tpp) REVERT: J 127 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8977 (tt) REVERT: J 182 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8363 (pm20) REVERT: K 404 MET cc_start: 0.8581 (ttt) cc_final: 0.8355 (ttt) REVERT: L 267 TRP cc_start: 0.7449 (m100) cc_final: 0.6758 (m100) REVERT: L 601 MET cc_start: 0.8823 (mmt) cc_final: 0.8538 (mmt) REVERT: M 103 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7627 (tt) REVERT: M 429 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7624 (mpp80) REVERT: M 495 PHE cc_start: 0.7207 (m-80) cc_final: 0.6979 (m-80) REVERT: M 623 GLU cc_start: 0.7397 (pp20) cc_final: 0.7116 (pp20) REVERT: N 156 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: N 185 TRP cc_start: 0.8431 (t60) cc_final: 0.7787 (t60) REVERT: N 217 GLU cc_start: 0.8516 (tt0) cc_final: 0.8127 (pt0) REVERT: O 348 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8445 (mm-40) REVERT: P 91 PHE cc_start: 0.7190 (m-80) cc_final: 0.6988 (m-10) REVERT: P 105 GLU cc_start: 0.7529 (tt0) cc_final: 0.7200 (mm-30) REVERT: P 280 MET cc_start: 0.7609 (mtp) cc_final: 0.7395 (mtp) REVERT: P 335 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7147 (mp) REVERT: P 422 MET cc_start: 0.5902 (ttt) cc_final: 0.5702 (ttt) REVERT: P 570 MET cc_start: 0.8322 (tpp) cc_final: 0.7334 (tpt) REVERT: P 572 MET cc_start: 0.5196 (tmm) cc_final: 0.4943 (tmm) REVERT: Q 442 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8718 (p0) REVERT: R 156 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: S 404 MET cc_start: 0.8500 (ttt) cc_final: 0.8279 (ttt) outliers start: 118 outliers final: 84 residues processed: 580 average time/residue: 0.2422 time to fit residues: 239.3397 Evaluate side-chains 554 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 457 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 604 PHE Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 230 ASP Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 604 PHE Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 412 CYS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 182 GLU Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain K residue 383 LYS Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 491 TRP Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 314 SER Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 550 THR Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 156 GLU Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 200 HIS Chi-restraints excluded: chain O residue 348 GLN Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 433 LEU Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain Q residue 181 ASP Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 229 GLU Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 314 SER Chi-restraints excluded: chain Q residue 344 LEU Chi-restraints excluded: chain Q residue 442 ASN Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 550 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 156 GLU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 200 HIS Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 417 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 226 optimal weight: 5.9990 chunk 403 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 332 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 247 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 516 optimal weight: 6.9990 chunk 475 optimal weight: 0.0980 chunk 285 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 442 ASN S 348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.155511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.117925 restraints weight = 77510.480| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.06 r_work: 0.3498 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 42908 Z= 0.159 Angle : 0.597 9.074 58416 Z= 0.305 Chirality : 0.044 0.232 6800 Planarity : 0.005 0.090 7516 Dihedral : 7.759 84.931 6352 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.65 % Allowed : 16.22 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.11), residues: 5448 helix: 0.66 (0.11), residues: 2316 sheet: 0.11 (0.15), residues: 1164 loop : -0.79 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG S 416 TYR 0.016 0.002 TYR E 154 PHE 0.012 0.001 PHE P 240 TRP 0.028 0.002 TRP N 185 HIS 0.007 0.001 HIS M 143 Details of bonding type rmsd covalent geometry : bond 0.00383 (42908) covalent geometry : angle 0.59686 (58416) hydrogen bonds : bond 0.03852 ( 1827) hydrogen bonds : angle 4.54000 ( 5544) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 469 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 267 TRP cc_start: 0.7643 (m100) cc_final: 0.6965 (m100) REVERT: D 277 MET cc_start: 0.8517 (mtp) cc_final: 0.7677 (mmm) REVERT: D 280 MET cc_start: 0.7601 (mtp) cc_final: 0.6945 (mpp) REVERT: D 335 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6864 (mp) REVERT: D 570 MET cc_start: 0.8288 (tpt) cc_final: 0.7998 (tpt) REVERT: D 572 MET cc_start: 0.4656 (tmm) cc_final: 0.4424 (tmm) REVERT: D 604 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.6763 (t80) REVERT: E 103 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7471 (tt) REVERT: E 267 TRP cc_start: 0.8264 (m100) cc_final: 0.7851 (m100) REVERT: E 449 GLN cc_start: 0.7140 (mm-40) cc_final: 0.6675 (mm-40) REVERT: E 570 MET cc_start: 0.8279 (tpp) cc_final: 0.7977 (tpp) REVERT: F 133 CYS cc_start: 0.8513 (m) cc_final: 0.8235 (p) REVERT: G 380 GLN cc_start: 0.8614 (tp-100) cc_final: 0.8330 (tm-30) REVERT: H 267 TRP cc_start: 0.7674 (m100) cc_final: 0.6979 (m100) REVERT: H 280 MET cc_start: 0.7724 (mtp) cc_final: 0.7085 (mpp) REVERT: H 335 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6798 (mp) REVERT: H 572 MET cc_start: 0.4546 (tmm) cc_final: 0.4342 (tmm) REVERT: I 267 TRP cc_start: 0.8274 (m100) cc_final: 0.7881 (m100) REVERT: I 277 MET cc_start: 0.8401 (mmm) cc_final: 0.8044 (mmm) REVERT: I 570 MET cc_start: 0.8284 (tpp) cc_final: 0.8056 (tpp) REVERT: J 182 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8393 (pm20) REVERT: K 404 MET cc_start: 0.8573 (ttt) cc_final: 0.8351 (ttt) REVERT: L 267 TRP cc_start: 0.7516 (m100) cc_final: 0.6754 (m100) REVERT: L 280 MET cc_start: 0.7646 (mtp) cc_final: 0.6932 (mpp) REVERT: L 578 PHE cc_start: 0.7204 (m-80) cc_final: 0.6865 (m-10) REVERT: L 601 MET cc_start: 0.8849 (mmt) cc_final: 0.8523 (mmt) REVERT: M 103 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7643 (tt) REVERT: M 429 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7587 (mpp80) REVERT: M 495 PHE cc_start: 0.7287 (m-80) cc_final: 0.7058 (m-80) REVERT: N 156 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: O 348 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8442 (mm-40) REVERT: P 91 PHE cc_start: 0.7214 (m-80) cc_final: 0.6965 (m-10) REVERT: P 105 GLU cc_start: 0.7509 (tt0) cc_final: 0.7240 (mm-30) REVERT: P 335 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7111 (mp) REVERT: P 570 MET cc_start: 0.7971 (tpp) cc_final: 0.7625 (tpt) REVERT: R 217 GLU cc_start: 0.8469 (tt0) cc_final: 0.8123 (pt0) outliers start: 113 outliers final: 92 residues processed: 558 average time/residue: 0.2313 time to fit residues: 222.1632 Evaluate side-chains 547 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 446 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 604 PHE Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 604 PHE Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain I residue 412 CYS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 133 CYS Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 182 GLU Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain K residue 383 LYS Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 491 TRP Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 314 SER Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 412 CYS Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 550 THR Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 156 GLU Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain O residue 348 GLN Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 433 LEU Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain Q residue 181 ASP Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 229 GLU Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 280 MET Chi-restraints excluded: chain Q residue 314 SER Chi-restraints excluded: chain Q residue 344 LEU Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 550 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 200 HIS Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 383 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 272 optimal weight: 0.8980 chunk 529 optimal weight: 7.9990 chunk 428 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 330 optimal weight: 7.9990 chunk 457 optimal weight: 0.9990 chunk 413 optimal weight: 0.9990 chunk 418 optimal weight: 0.9980 chunk 506 optimal weight: 0.0020 chunk 356 optimal weight: 10.0000 chunk 276 optimal weight: 0.7980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 442 ASN S 348 GLN ** S 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.157359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.120366 restraints weight = 77314.244| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.46 r_work: 0.3516 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 42908 Z= 0.114 Angle : 0.572 13.280 58416 Z= 0.291 Chirality : 0.043 0.187 6800 Planarity : 0.004 0.072 7516 Dihedral : 7.599 89.078 6352 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.99 % Allowed : 16.83 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.11), residues: 5448 helix: 0.86 (0.11), residues: 2312 sheet: 0.22 (0.15), residues: 1164 loop : -0.72 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG I 429 TYR 0.014 0.001 TYR H 356 PHE 0.013 0.001 PHE P 240 TRP 0.021 0.001 TRP N 185 HIS 0.005 0.001 HIS F 176 Details of bonding type rmsd covalent geometry : bond 0.00266 (42908) covalent geometry : angle 0.57246 (58416) hydrogen bonds : bond 0.03276 ( 1827) hydrogen bonds : angle 4.37875 ( 5544) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 490 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7130 (mm-30) REVERT: D 267 TRP cc_start: 0.7596 (m100) cc_final: 0.6987 (m100) REVERT: D 277 MET cc_start: 0.8540 (mtp) cc_final: 0.7733 (mmm) REVERT: D 280 MET cc_start: 0.7570 (mtp) cc_final: 0.6950 (mpp) REVERT: D 570 MET cc_start: 0.8285 (tpt) cc_final: 0.7986 (tpt) REVERT: D 572 MET cc_start: 0.4551 (tmm) cc_final: 0.4324 (tmm) REVERT: D 604 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.6786 (t80) REVERT: E 103 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7419 (tt) REVERT: E 267 TRP cc_start: 0.8257 (m100) cc_final: 0.7874 (m100) REVERT: E 442 ASN cc_start: 0.9095 (t0) cc_final: 0.8861 (p0) REVERT: E 449 GLN cc_start: 0.7148 (mm-40) cc_final: 0.6690 (mm-40) REVERT: E 570 MET cc_start: 0.8212 (tpp) cc_final: 0.7974 (tpt) REVERT: F 133 CYS cc_start: 0.8504 (m) cc_final: 0.8137 (p) REVERT: G 416 ARG cc_start: 0.8355 (mmm160) cc_final: 0.7985 (mmm160) REVERT: H 267 TRP cc_start: 0.7634 (m100) cc_final: 0.7010 (m100) REVERT: H 280 MET cc_start: 0.7715 (mtp) cc_final: 0.7037 (mpp) REVERT: H 335 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6639 (mp) REVERT: H 572 MET cc_start: 0.4468 (tmm) cc_final: 0.4263 (tmm) REVERT: I 277 MET cc_start: 0.8449 (mmm) cc_final: 0.8125 (mmm) REVERT: I 570 MET cc_start: 0.8264 (tpp) cc_final: 0.8045 (tpp) REVERT: J 182 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8416 (pm20) REVERT: K 404 MET cc_start: 0.8572 (ttt) cc_final: 0.8363 (ttt) REVERT: L 267 TRP cc_start: 0.7490 (m100) cc_final: 0.6797 (m100) REVERT: L 280 MET cc_start: 0.7576 (mtp) cc_final: 0.6864 (mpp) REVERT: L 578 PHE cc_start: 0.7228 (m-80) cc_final: 0.6867 (m-10) REVERT: M 103 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7612 (tt) REVERT: M 429 ARG cc_start: 0.8195 (ttm-80) cc_final: 0.7627 (mpp80) REVERT: M 440 TRP cc_start: 0.4860 (t-100) cc_final: 0.4595 (t-100) REVERT: M 495 PHE cc_start: 0.7221 (m-80) cc_final: 0.6993 (m-80) REVERT: N 185 TRP cc_start: 0.8539 (t60) cc_final: 0.8321 (t60) REVERT: O 348 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8436 (mm-40) REVERT: O 456 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8631 (mm-30) REVERT: P 105 GLU cc_start: 0.7536 (tt0) cc_final: 0.7250 (tt0) REVERT: P 335 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7048 (mp) REVERT: P 570 MET cc_start: 0.8089 (tpp) cc_final: 0.7712 (tpt) REVERT: R 184 MET cc_start: 0.8547 (ttp) cc_final: 0.8247 (ttp) REVERT: R 217 GLU cc_start: 0.8508 (tt0) cc_final: 0.8177 (pt0) REVERT: S 400 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8249 (tm-30) outliers start: 85 outliers final: 75 residues processed: 553 average time/residue: 0.2300 time to fit residues: 218.3135 Evaluate side-chains 545 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 463 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 604 PHE Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 604 PHE Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 412 CYS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 182 GLU Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 314 SER Chi-restraints excluded: chain M residue 411 VAL Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 550 THR Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 158 ILE Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain O residue 348 GLN Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 229 GLU Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 314 SER Chi-restraints excluded: chain Q residue 344 LEU Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 550 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 200 HIS Chi-restraints excluded: chain S residue 383 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 274 optimal weight: 10.0000 chunk 545 optimal weight: 0.9990 chunk 149 optimal weight: 0.0020 chunk 116 optimal weight: 1.9990 chunk 462 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 510 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 295 optimal weight: 0.0040 chunk 336 optimal weight: 0.9990 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 393 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.158042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.121025 restraints weight = 77878.962| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.46 r_work: 0.3532 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 42908 Z= 0.107 Angle : 0.563 10.429 58416 Z= 0.286 Chirality : 0.043 0.216 6800 Planarity : 0.004 0.067 7516 Dihedral : 7.439 85.131 6352 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.90 % Allowed : 17.06 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.11), residues: 5448 helix: 0.97 (0.11), residues: 2340 sheet: 0.30 (0.15), residues: 1160 loop : -0.65 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG S 416 TYR 0.016 0.001 TYR H 338 PHE 0.032 0.001 PHE P 91 TRP 0.030 0.001 TRP P 440 HIS 0.005 0.001 HIS F 176 Details of bonding type rmsd covalent geometry : bond 0.00247 (42908) covalent geometry : angle 0.56338 (58416) hydrogen bonds : bond 0.03101 ( 1827) hydrogen bonds : angle 4.28654 ( 5544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11367.81 seconds wall clock time: 195 minutes 6.79 seconds (11706.79 seconds total)