Starting phenix.real_space_refine on Thu Dec 26 03:42:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vz8_21487/12_2024/6vz8_21487.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vz8_21487/12_2024/6vz8_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_21487/12_2024/6vz8_21487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vz8_21487/12_2024/6vz8_21487.map" model { file = "/net/cci-nas-00/data/ceres_data/6vz8_21487/12_2024/6vz8_21487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vz8_21487/12_2024/6vz8_21487.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} 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: {'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} 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: {'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} 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: {'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} 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: 24.22, per 1000 atoms: 0.57 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: 11.48 Conformation dependent library (CDL) restraints added in 5.9 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: 6.46 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: 21.51 Time building geometry restraints manager: 12.99 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: 0.00 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 643 or \ resid 701 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 643 or resid 701 throu \ gh 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 643 or \ resid 701 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 643 or resid 701 throu \ gh 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 643 or \ resid 701 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 643 or resid 701 throu \ gh 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 643 or \ resid 701 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 643 or resid 701 throu \ gh 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: 6.900 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: 0.070 Extract box with map and model: 1.930 Check model and map are aligned: 0.320 Set scattering table: 0.400 Process input model: 99.610 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.510 ------------------------------------------------------------------------------- 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= 0.741 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 : 3.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (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 TRP 0.085 0.014 TRP L 574 HIS 0.017 0.003 HIS M 488 PHE 0.052 0.008 PHE F 107 TYR 0.171 0.014 TYR F 112 ARG 0.094 0.006 ARG Q 373 *********************** 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 : 4.599 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: 0.7175 (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: 0.6972 (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: 0.7643 (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: 0.7100 (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: 0.6218 time to fit residues: 1130.2728 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 : 4.759 ------------------------------------------------------------------------------- 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 462 optimal weight: 2.9990 chunk 415 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 280 optimal weight: 0.6980 chunk 221 optimal weight: 3.9990 chunk 429 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 261 optimal weight: 0.5980 chunk 319 optimal weight: 0.9980 chunk 497 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 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 P 582 ASN Q 128 GLN S 320 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 42908 Z= 0.225 Angle : 0.657 10.012 58416 Z= 0.343 Chirality : 0.046 0.203 6800 Planarity : 0.005 0.054 7516 Dihedral : 8.289 78.263 6362 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.04 % Allowed : 10.77 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.11), residues: 5448 helix: -0.00 (0.10), residues: 2304 sheet: 0.21 (0.14), residues: 1184 loop : -0.26 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 185 HIS 0.008 0.001 HIS E 143 PHE 0.022 0.002 PHE J 223 TYR 0.016 0.002 TYR P 466 ARG 0.008 0.001 ARG S 465 *********************** 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 762 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 675 time to evaluate : 4.674 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: 0.8352 (t) cc_final: 0.8084 (p) REVERT: D 267 TRP cc_start: 0.7466 (m100) cc_final: 0.6634 (m100) REVERT: D 426 LEU cc_start: 0.5845 (mt) cc_final: 0.5619 (tp) REVERT: D 555 ASN cc_start: 0.6050 (m-40) cc_final: 0.4987 (t0) REVERT: D 570 MET cc_start: 0.7466 (tpp) cc_final: 0.6909 (tpt) REVERT: D 572 MET cc_start: 0.4468 (tmm) cc_final: 0.4122 (tmm) REVERT: D 586 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7763 (p) REVERT: D 601 MET cc_start: 0.8956 (mmt) cc_final: 0.8625 (mmt) REVERT: E 227 ASP cc_start: 0.6650 (t0) cc_final: 0.6423 (t0) REVERT: E 347 HIS cc_start: 0.5923 (OUTLIER) cc_final: 0.5297 (t-90) REVERT: E 392 VAL cc_start: 0.7331 (t) cc_final: 0.7126 (p) REVERT: E 449 GLN cc_start: 0.7318 (mm-40) cc_final: 0.6869 (mm-40) REVERT: F 121 LEU cc_start: 0.8991 (tp) cc_final: 0.8719 (tp) REVERT: F 122 ASN cc_start: 0.7729 (t0) cc_final: 0.7101 (m-40) REVERT: F 151 ASN cc_start: 0.9203 (m-40) cc_final: 0.8864 (m110) REVERT: F 185 TRP cc_start: 0.8300 (t60) cc_final: 0.7850 (t60) REVERT: F 214 ILE cc_start: 0.8977 (tp) cc_final: 0.8485 (pt) REVERT: F 224 GLN cc_start: 0.7911 (tp40) cc_final: 0.7566 (tp40) REVERT: G 380 GLN cc_start: 0.8441 (tp-100) cc_final: 0.7866 (tp40) REVERT: G 462 GLU cc_start: 0.7969 (pm20) cc_final: 0.7741 (pm20) REVERT: H 167 THR cc_start: 0.8325 (t) cc_final: 0.8074 (p) REVERT: H 203 THR cc_start: 0.7702 (OUTLIER) cc_final: 0.7421 (p) REVERT: H 223 TYR cc_start: 0.8084 (m-80) cc_final: 0.7816 (m-80) REVERT: H 267 TRP cc_start: 0.7445 (m100) cc_final: 0.6683 (m100) REVERT: H 338 TYR cc_start: 0.7225 (t80) cc_final: 0.7021 (t80) REVERT: H 572 MET cc_start: 0.4341 (ttp) cc_final: 0.3998 (tmm) REVERT: H 586 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7734 (p) REVERT: H 601 MET cc_start: 0.8927 (mmt) cc_final: 0.8599 (mmt) REVERT: H 610 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7409 (pt) REVERT: H 628 MET cc_start: 0.7715 (ttm) cc_final: 0.7003 (ttm) REVERT: I 88 ILE cc_start: 0.8018 (tt) cc_final: 0.7758 (tp) REVERT: I 227 ASP cc_start: 0.6644 (t0) cc_final: 0.5606 (t0) REVERT: I 347 HIS cc_start: 0.5844 (OUTLIER) cc_final: 0.5102 (t-90) REVERT: I 392 VAL cc_start: 0.7415 (t) cc_final: 0.7173 (p) REVERT: I 588 LEU cc_start: 0.6935 (tp) cc_final: 0.6351 (mp) REVERT: J 122 ASN cc_start: 0.7561 (t0) cc_final: 0.7248 (m110) REVERT: J 123 ARG cc_start: 0.7719 (ttm110) cc_final: 0.7442 (ptt90) REVERT: J 180 ARG cc_start: 0.8069 (mtt180) cc_final: 0.7390 (ttm110) REVERT: K 327 ASN cc_start: 0.8746 (t0) cc_final: 0.8068 (t0) REVERT: K 356 GLU cc_start: 0.6443 (pm20) cc_final: 0.6211 (pm20) REVERT: K 371 ASP cc_start: 0.6270 (p0) cc_final: 0.6025 (t0) REVERT: K 380 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7939 (tm-30) REVERT: K 389 GLU cc_start: 0.8014 (pt0) cc_final: 0.7742 (pt0) REVERT: L 105 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7152 (mm-30) REVERT: L 226 MET cc_start: 0.8245 (mmm) cc_final: 0.8011 (mmt) REVERT: L 277 MET cc_start: 0.8078 (mmm) cc_final: 0.7779 (mmm) REVERT: L 338 TYR cc_start: 0.7370 (t80) cc_final: 0.7123 (t80) REVERT: L 422 MET cc_start: 0.4997 (ttt) cc_final: 0.4650 (ttt) REVERT: L 570 MET cc_start: 0.7363 (tpp) cc_final: 0.7132 (tpt) REVERT: L 572 MET cc_start: 0.4604 (ttp) cc_final: 0.4254 (tmm) REVERT: L 586 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7721 (p) REVERT: L 601 MET cc_start: 0.8697 (mmt) cc_final: 0.8424 (mmt) REVERT: M 227 ASP cc_start: 0.6888 (t0) cc_final: 0.5881 (t0) REVERT: M 277 MET cc_start: 0.8158 (mmm) cc_final: 0.7901 (mmt) REVERT: M 422 MET cc_start: 0.5330 (mtp) cc_final: 0.5085 (tpp) REVERT: M 442 ASN cc_start: 0.9298 (t0) cc_final: 0.9086 (p0) REVERT: M 495 PHE cc_start: 0.6024 (m-80) cc_final: 0.5690 (m-80) REVERT: N 122 ASN cc_start: 0.7721 (t0) cc_final: 0.7013 (m-40) REVERT: N 151 ASN cc_start: 0.8941 (m-40) cc_final: 0.8733 (m110) REVERT: O 371 ASP cc_start: 0.6521 (p0) cc_final: 0.6275 (t0) REVERT: P 105 GLU cc_start: 0.7521 (tt0) cc_final: 0.7273 (tt0) REVERT: P 277 MET cc_start: 0.7959 (mtt) cc_final: 0.7754 (mmm) REVERT: P 422 MET cc_start: 0.4962 (ttt) cc_final: 0.4707 (ttt) REVERT: P 513 MET cc_start: 0.7587 (mtp) cc_final: 0.7344 (mtp) REVERT: P 570 MET cc_start: 0.7206 (tpp) cc_final: 0.6792 (tpt) REVERT: P 572 MET cc_start: 0.4800 (ttp) cc_final: 0.4373 (tmm) REVERT: Q 322 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8212 (mm-30) REVERT: R 122 ASN cc_start: 0.7810 (t0) cc_final: 0.7181 (m110) REVERT: R 151 ASN cc_start: 0.8943 (m-40) cc_final: 0.8706 (m110) REVERT: S 356 GLU cc_start: 0.6432 (pm20) cc_final: 0.6230 (pm20) outliers start: 87 outliers final: 46 residues processed: 735 average time/residue: 0.5278 time to fit residues: 651.6367 Evaluate side-chains 586 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 533 time to evaluate : 4.574 ------------------------------------------------------------------------------- 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 586 THR 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 H residue 586 THR Chi-restraints excluded: chain H residue 610 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 412 CYS 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 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 L residue 586 THR 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 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 276 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 414 optimal weight: 3.9990 chunk 338 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 498 optimal weight: 20.0000 chunk 538 optimal weight: 1.9990 chunk 443 optimal weight: 5.9990 chunk 494 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 399 optimal weight: 0.7980 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 127 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 HIS ** J 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 143 HIS N 140 GLN ** N 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 582 ASN Q 128 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 42908 Z= 0.436 Angle : 0.723 9.253 58416 Z= 0.378 Chirality : 0.049 0.191 6800 Planarity : 0.005 0.062 7516 Dihedral : 8.288 80.111 6359 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.82 % Allowed : 11.94 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.11), residues: 5448 helix: -0.14 (0.10), residues: 2316 sheet: 0.17 (0.14), residues: 1192 loop : -0.73 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 440 HIS 0.018 0.002 HIS M 143 PHE 0.022 0.002 PHE E 87 TYR 0.019 0.003 TYR I 154 ARG 0.006 0.001 ARG L 142 *********************** 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 709 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 546 time to evaluate : 5.203 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 105 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7375 (mm-30) REVERT: D 112 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7629 (m) REVERT: D 335 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.6019 (mp) REVERT: D 426 LEU cc_start: 0.5952 (mt) cc_final: 0.5538 (tp) REVERT: D 572 MET cc_start: 0.4413 (tmm) cc_final: 0.4134 (tmm) REVERT: D 601 MET cc_start: 0.8950 (mmt) cc_final: 0.8578 (mmt) REVERT: D 610 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7267 (pt) REVERT: E 392 VAL cc_start: 0.7327 (t) cc_final: 0.7083 (p) REVERT: F 154 LYS cc_start: 0.6958 (mttm) cc_final: 0.6363 (tttt) REVERT: F 214 ILE cc_start: 0.9150 (tp) cc_final: 0.8909 (pt) REVERT: G 348 GLN cc_start: 0.8565 (mp10) cc_final: 0.8167 (mm-40) REVERT: G 400 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8141 (tm-30) REVERT: G 462 GLU cc_start: 0.8103 (pm20) cc_final: 0.7658 (pm20) REVERT: H 105 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7369 (mm-30) REVERT: H 112 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7618 (m) REVERT: H 203 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7646 (p) REVERT: H 335 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.6120 (mp) REVERT: H 422 MET cc_start: 0.4997 (ttm) cc_final: 0.4651 (tpp) REVERT: H 572 MET cc_start: 0.4557 (ttp) cc_final: 0.4155 (tmm) REVERT: I 343 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7573 (pm20) REVERT: I 392 VAL cc_start: 0.7391 (t) cc_final: 0.7123 (p) REVERT: J 123 ARG cc_start: 0.7912 (ttm110) cc_final: 0.7555 (ptt90) REVERT: J 133 CYS cc_start: 0.8365 (m) cc_final: 0.8091 (p) REVERT: J 180 ARG cc_start: 0.8085 (mtt180) cc_final: 0.7854 (mtm-85) REVERT: K 356 GLU cc_start: 0.6526 (pm20) cc_final: 0.6259 (pm20) REVERT: K 371 ASP cc_start: 0.7000 (p0) cc_final: 0.6639 (t0) REVERT: K 380 GLN cc_start: 0.8309 (tp-100) cc_final: 0.7863 (tm-30) REVERT: K 400 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7816 (tm-30) REVERT: K 401 ARG cc_start: 0.8267 (mmp-170) cc_final: 0.7818 (mmp80) REVERT: L 254 VAL cc_start: 0.7257 (OUTLIER) cc_final: 0.6998 (p) REVERT: L 570 MET cc_start: 0.7488 (tpp) cc_final: 0.7176 (tpt) REVERT: L 572 MET cc_start: 0.4640 (ttp) cc_final: 0.4412 (tmm) REVERT: L 586 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8223 (p) REVERT: L 601 MET cc_start: 0.8750 (mmt) cc_final: 0.8431 (mmt) REVERT: M 322 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8080 (mm-30) REVERT: M 442 ASN cc_start: 0.9270 (t0) cc_final: 0.9031 (p0) REVERT: M 495 PHE cc_start: 0.6162 (m-80) cc_final: 0.5795 (m-80) REVERT: M 543 MET cc_start: 0.7903 (mtt) cc_final: 0.7699 (mtt) REVERT: N 217 GLU cc_start: 0.8475 (tt0) cc_final: 0.8045 (pt0) REVERT: O 348 GLN cc_start: 0.8486 (mp10) cc_final: 0.8124 (mm-40) REVERT: O 371 ASP cc_start: 0.7113 (p0) cc_final: 0.6722 (t0) REVERT: P 105 GLU cc_start: 0.7701 (tt0) cc_final: 0.7316 (mm-30) REVERT: P 112 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7675 (m) REVERT: P 254 VAL cc_start: 0.7241 (OUTLIER) cc_final: 0.7020 (p) REVERT: P 422 MET cc_start: 0.5269 (ttt) cc_final: 0.4946 (ttt) REVERT: P 570 MET cc_start: 0.7284 (tpp) cc_final: 0.7038 (tpt) REVERT: P 572 MET cc_start: 0.4784 (ttp) cc_final: 0.4269 (tmm) REVERT: Q 322 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8123 (mm-30) REVERT: Q 543 MET cc_start: 0.7955 (mtt) cc_final: 0.7685 (mtt) REVERT: R 140 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8667 (mm-40) REVERT: R 154 LYS cc_start: 0.6820 (mttm) cc_final: 0.6333 (tttp) REVERT: R 241 MET cc_start: 0.6696 (mmm) cc_final: 0.6408 (mmm) REVERT: S 356 GLU cc_start: 0.6731 (pm20) cc_final: 0.6490 (pm20) REVERT: S 400 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8110 (tm-30) outliers start: 163 outliers final: 92 residues processed: 678 average time/residue: 0.5156 time to fit residues: 594.9943 Evaluate side-chains 583 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 481 time to evaluate : 4.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 163 ILE 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 335 LEU Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 610 ILE Chi-restraints excluded: chain E residue 167 THR 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 178 GLU Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain G residue 466 THR Chi-restraints excluded: chain H residue 112 VAL 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 I residue 167 THR 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 I residue 524 SER Chi-restraints excluded: chain J residue 88 THR 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 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 433 LEU Chi-restraints excluded: chain L residue 491 TRP Chi-restraints excluded: chain L residue 586 THR Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 201 ILE 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 558 VAL 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 164 VAL Chi-restraints excluded: chain N residue 176 HIS Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain O residue 438 THR Chi-restraints excluded: chain P residue 112 VAL 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 167 THR 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 S residue 357 THR Chi-restraints excluded: chain S residue 383 LYS Chi-restraints excluded: chain S residue 417 ASP Chi-restraints excluded: chain S residue 438 THR 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 492 optimal weight: 9.9990 chunk 374 optimal weight: 7.9990 chunk 258 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 237 optimal weight: 7.9990 chunk 334 optimal weight: 2.9990 chunk 500 optimal weight: 4.9990 chunk 529 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 474 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 582 ASN E 128 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 582 ASN I 128 GLN ** J 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 449 GLN S 348 GLN S 395 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 42908 Z= 0.221 Angle : 0.576 9.744 58416 Z= 0.298 Chirality : 0.044 0.194 6800 Planarity : 0.004 0.061 7516 Dihedral : 7.987 88.811 6357 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.67 % Allowed : 13.67 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.11), residues: 5448 helix: 0.38 (0.10), residues: 2284 sheet: 0.20 (0.15), residues: 1188 loop : -0.64 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 440 HIS 0.006 0.001 HIS G 391 PHE 0.023 0.001 PHE L 91 TYR 0.014 0.002 TYR M 154 ARG 0.007 0.000 ARG O 416 *********************** 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 655 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 541 time to evaluate : 4.893 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: 0.8109 (mt-10) cc_final: 0.7138 (mm-30) REVERT: D 267 TRP cc_start: 0.7495 (m100) cc_final: 0.6831 (m100) REVERT: D 335 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5768 (mp) REVERT: D 570 MET cc_start: 0.7303 (tpt) cc_final: 0.7072 (tpt) REVERT: D 572 MET cc_start: 0.4331 (tmm) cc_final: 0.4088 (tmm) REVERT: D 610 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7361 (pt) REVERT: E 277 MET cc_start: 0.8194 (mmm) cc_final: 0.7978 (mmm) REVERT: E 392 VAL cc_start: 0.7325 (t) cc_final: 0.7060 (p) REVERT: G 348 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8144 (mm-40) REVERT: G 376 LYS cc_start: 0.9034 (tmmt) cc_final: 0.8711 (tmtt) REVERT: G 380 GLN cc_start: 0.8409 (tp-100) cc_final: 0.8063 (tp40) REVERT: G 400 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8162 (tm-30) REVERT: H 105 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7123 (mm-30) REVERT: H 203 THR cc_start: 0.7955 (OUTLIER) cc_final: 0.7688 (p) REVERT: H 267 TRP cc_start: 0.7463 (m100) cc_final: 0.6760 (m100) REVERT: H 335 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5921 (mp) REVERT: H 570 MET cc_start: 0.7367 (tpt) cc_final: 0.7117 (tpt) REVERT: H 572 MET cc_start: 0.4448 (ttp) cc_final: 0.4063 (tmm) REVERT: I 227 ASP cc_start: 0.7239 (t0) cc_final: 0.7004 (t0) REVERT: I 277 MET cc_start: 0.8173 (mmm) cc_final: 0.7677 (mmm) REVERT: I 343 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7845 (pm20) REVERT: I 392 VAL cc_start: 0.7318 (t) cc_final: 0.7042 (p) REVERT: J 123 ARG cc_start: 0.7890 (ttm110) cc_final: 0.7589 (ptt90) REVERT: J 133 CYS cc_start: 0.8371 (m) cc_final: 0.7972 (p) REVERT: J 156 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7183 (mt-10) REVERT: J 182 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8000 (pm20) REVERT: J 217 GLU cc_start: 0.8405 (tt0) cc_final: 0.7822 (pt0) REVERT: J 241 MET cc_start: 0.7000 (mmm) cc_final: 0.6737 (mmm) REVERT: K 380 GLN cc_start: 0.8142 (tp-100) cc_final: 0.7869 (tm-30) REVERT: K 400 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8079 (tm-30) REVERT: L 105 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7379 (mm-30) REVERT: L 570 MET cc_start: 0.7569 (tpp) cc_final: 0.7229 (tpt) REVERT: L 572 MET cc_start: 0.4717 (ttp) cc_final: 0.4447 (tmm) REVERT: M 322 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8154 (mm-30) REVERT: M 429 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7739 (mpp80) REVERT: M 495 PHE cc_start: 0.6070 (m-80) cc_final: 0.5748 (m-80) REVERT: N 156 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7022 (mt-10) REVERT: N 241 MET cc_start: 0.6689 (mmm) cc_final: 0.6287 (mmm) REVERT: O 348 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8129 (mm-40) REVERT: P 91 PHE cc_start: 0.7051 (m-80) cc_final: 0.6795 (m-10) REVERT: P 105 GLU cc_start: 0.7757 (tt0) cc_final: 0.7339 (mm-30) REVERT: P 227 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.6859 (p0) REVERT: P 280 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.7036 (mtp) REVERT: P 572 MET cc_start: 0.4756 (ttp) cc_final: 0.4529 (tmm) REVERT: P 586 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8105 (p) REVERT: Q 322 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8074 (mm-30) REVERT: Q 495 PHE cc_start: 0.6027 (m-80) cc_final: 0.5703 (m-80) REVERT: R 154 LYS cc_start: 0.6745 (mttm) cc_final: 0.6208 (tttt) REVERT: R 165 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8218 (tm-30) REVERT: S 400 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8105 (tm-30) outliers start: 114 outliers final: 65 residues processed: 618 average time/residue: 0.5244 time to fit residues: 547.6414 Evaluate side-chains 560 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 482 time to evaluate : 4.989 ------------------------------------------------------------------------------- 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 335 LEU Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 604 PHE Chi-restraints excluded: chain D residue 610 ILE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 304 LEU 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 178 GLU Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET 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 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 524 SER Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 156 GLU 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 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 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 139 LEU Chi-restraints excluded: chain N residue 156 GLU Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 200 HIS Chi-restraints excluded: chain O residue 348 GLN Chi-restraints excluded: chain O residue 383 LYS 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 227 ASP Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 280 MET Chi-restraints excluded: chain P residue 586 THR Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 254 VAL 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 165 GLU 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 441 optimal weight: 0.0270 chunk 300 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 394 optimal weight: 0.7980 chunk 218 optimal weight: 10.0000 chunk 452 optimal weight: 5.9990 chunk 366 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 270 optimal weight: 2.9990 chunk 475 optimal weight: 0.9990 chunk 133 optimal weight: 0.0170 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 487 GLN J 113 ASN J 141 GLN N 140 GLN ** N 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.4405 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= 0.155 Angle : 0.534 9.012 58416 Z= 0.274 Chirality : 0.043 0.187 6800 Planarity : 0.004 0.061 7516 Dihedral : 7.789 88.676 6356 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.60 % Allowed : 14.75 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.11), residues: 5448 helix: 0.73 (0.11), residues: 2284 sheet: 0.37 (0.15), residues: 1136 loop : -0.57 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 185 HIS 0.005 0.001 HIS J 176 PHE 0.020 0.001 PHE L 91 TYR 0.012 0.001 TYR D 356 ARG 0.013 0.000 ARG O 416 *********************** 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 651 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 540 time to evaluate : 5.173 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: 0.8039 (mt-10) cc_final: 0.7058 (mm-30) REVERT: D 267 TRP cc_start: 0.7465 (m100) cc_final: 0.6816 (m100) REVERT: D 335 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.5661 (mp) REVERT: D 570 MET cc_start: 0.7304 (tpt) cc_final: 0.7038 (tpt) REVERT: E 392 VAL cc_start: 0.7341 (t) cc_final: 0.7033 (p) REVERT: F 182 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: G 348 GLN cc_start: 0.8623 (mp10) cc_final: 0.8218 (mm-40) REVERT: G 376 LYS cc_start: 0.9054 (tmmt) cc_final: 0.8762 (tmtt) REVERT: G 380 GLN cc_start: 0.8318 (tp-100) cc_final: 0.8084 (tp40) REVERT: G 400 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8124 (tm-30) REVERT: H 105 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7121 (mm-30) REVERT: H 203 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7627 (p) REVERT: H 267 TRP cc_start: 0.7473 (m100) cc_final: 0.6796 (m100) REVERT: H 335 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5708 (mp) REVERT: H 570 MET cc_start: 0.7396 (tpt) cc_final: 0.7099 (tpt) REVERT: H 572 MET cc_start: 0.4414 (ttp) cc_final: 0.4058 (tmm) REVERT: I 343 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7843 (pm20) REVERT: I 392 VAL cc_start: 0.7346 (t) cc_final: 0.7057 (p) REVERT: J 123 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7576 (ptt90) REVERT: J 156 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: J 241 MET cc_start: 0.7074 (mmm) cc_final: 0.5626 (mmm) REVERT: K 348 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8438 (mm-40) REVERT: K 400 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8060 (tm-30) REVERT: K 462 GLU cc_start: 0.8172 (pt0) cc_final: 0.7905 (pt0) REVERT: L 570 MET cc_start: 0.7572 (tpp) cc_final: 0.7226 (tpt) REVERT: L 572 MET cc_start: 0.4649 (ttp) cc_final: 0.4250 (tmm) REVERT: M 322 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8050 (mm-30) REVERT: M 429 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7621 (mpp80) REVERT: M 442 ASN cc_start: 0.9273 (t0) cc_final: 0.9049 (p0) REVERT: M 495 PHE cc_start: 0.6037 (m-80) cc_final: 0.5716 (m-80) REVERT: N 156 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7019 (mt-10) REVERT: N 217 GLU cc_start: 0.8495 (tt0) cc_final: 0.8072 (tm-30) REVERT: N 241 MET cc_start: 0.6850 (mmm) cc_final: 0.5390 (mmm) REVERT: O 348 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8177 (mm-40) REVERT: O 389 GLU cc_start: 0.8074 (pt0) cc_final: 0.7742 (pt0) REVERT: O 435 HIS cc_start: 0.5735 (m170) cc_final: 0.5305 (m-70) REVERT: O 462 GLU cc_start: 0.8385 (pt0) cc_final: 0.8175 (pt0) REVERT: P 91 PHE cc_start: 0.7008 (m-80) cc_final: 0.6748 (m-10) REVERT: P 105 GLU cc_start: 0.7791 (tt0) cc_final: 0.7239 (mm-30) REVERT: P 227 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.6893 (p0) REVERT: P 570 MET cc_start: 0.7240 (tpt) cc_final: 0.6707 (tpp) REVERT: Q 322 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8053 (mm-30) REVERT: Q 495 PHE cc_start: 0.5958 (m-80) cc_final: 0.5647 (m-80) REVERT: R 154 LYS cc_start: 0.6886 (mttm) cc_final: 0.6302 (tttt) REVERT: R 165 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8247 (tm-30) REVERT: R 241 MET cc_start: 0.7023 (mmm) cc_final: 0.6816 (mmm) REVERT: S 348 GLN cc_start: 0.8446 (mt0) cc_final: 0.8176 (mt0) REVERT: S 389 GLU cc_start: 0.8050 (pt0) cc_final: 0.7711 (pt0) REVERT: S 400 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8016 (tm-30) outliers start: 111 outliers final: 66 residues processed: 622 average time/residue: 0.5143 time to fit residues: 542.0513 Evaluate side-chains 564 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 489 time to evaluate : 4.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 604 PHE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 163 ILE 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 471 LEU Chi-restraints excluded: chain E residue 616 THR 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 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 424 ILE Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 556 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 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 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 88 ILE 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 471 LEU 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 156 GLU 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 383 LYS Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 227 ASP 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 193 THR Chi-restraints excluded: chain Q residue 264 ILE 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 164 VAL Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 200 HIS Chi-restraints excluded: chain S residue 462 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 178 optimal weight: 0.0470 chunk 477 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 310 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 530 optimal weight: 0.9980 chunk 440 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 278 optimal weight: 3.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 GLN F 141 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 582 ASN I 128 GLN N 140 GLN ** N 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 GLN S 348 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.4676 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= 0.279 Angle : 0.593 10.021 58416 Z= 0.305 Chirality : 0.044 0.197 6800 Planarity : 0.005 0.067 7516 Dihedral : 7.935 86.683 6355 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.00 % Allowed : 14.86 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.11), residues: 5448 helix: 0.59 (0.11), residues: 2308 sheet: 0.19 (0.15), residues: 1188 loop : -0.67 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 440 HIS 0.008 0.001 HIS Q 143 PHE 0.013 0.001 PHE D 495 TYR 0.017 0.002 TYR I 154 ARG 0.014 0.000 ARG K 416 *********************** 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 632 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 504 time to evaluate : 4.829 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: 0.8107 (mt-10) cc_final: 0.7132 (mm-30) REVERT: D 267 TRP cc_start: 0.7562 (m100) cc_final: 0.6811 (m100) REVERT: D 335 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5744 (mp) REVERT: D 570 MET cc_start: 0.7427 (tpt) cc_final: 0.7148 (tpp) REVERT: E 392 VAL cc_start: 0.7272 (t) cc_final: 0.6985 (p) REVERT: E 449 GLN cc_start: 0.7342 (mm-40) cc_final: 0.6953 (mm-40) REVERT: F 140 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8670 (mm-40) REVERT: G 348 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8188 (mm-40) REVERT: G 376 LYS cc_start: 0.9116 (tmmt) cc_final: 0.8841 (tmtt) REVERT: G 400 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8069 (tm-30) REVERT: H 203 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7793 (p) REVERT: H 267 TRP cc_start: 0.7558 (m100) cc_final: 0.6772 (m100) REVERT: H 335 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5769 (mp) REVERT: H 572 MET cc_start: 0.4677 (ttp) cc_final: 0.4408 (tmm) REVERT: I 343 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7926 (pm20) REVERT: I 392 VAL cc_start: 0.7331 (t) cc_final: 0.7057 (p) REVERT: J 123 ARG cc_start: 0.7836 (ttm110) cc_final: 0.7518 (ptt90) REVERT: J 156 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: K 348 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8440 (mm-40) REVERT: K 400 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7957 (tm-30) REVERT: K 462 GLU cc_start: 0.8211 (pt0) cc_final: 0.7819 (pt0) REVERT: L 254 VAL cc_start: 0.7296 (OUTLIER) cc_final: 0.7071 (p) REVERT: L 570 MET cc_start: 0.7622 (tpp) cc_final: 0.7406 (tpt) REVERT: L 572 MET cc_start: 0.4772 (ttp) cc_final: 0.4337 (tmm) REVERT: L 620 ASP cc_start: 0.6778 (t0) cc_final: 0.6573 (t0) REVERT: M 322 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8016 (mm-30) REVERT: M 429 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7596 (mpp80) REVERT: M 495 PHE cc_start: 0.6247 (m-80) cc_final: 0.5913 (m-80) REVERT: N 156 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7048 (mt-10) REVERT: O 348 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8196 (mm-40) REVERT: O 416 ARG cc_start: 0.8713 (mmm160) cc_final: 0.8279 (mmm160) REVERT: O 456 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8590 (mm-30) REVERT: P 91 PHE cc_start: 0.7086 (m-80) cc_final: 0.6813 (m-10) REVERT: P 105 GLU cc_start: 0.7785 (tt0) cc_final: 0.7323 (mm-30) REVERT: P 227 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7054 (p0) REVERT: P 254 VAL cc_start: 0.7372 (OUTLIER) cc_final: 0.7166 (p) REVERT: P 570 MET cc_start: 0.6821 (tpt) cc_final: 0.6531 (tpt) REVERT: Q 495 PHE cc_start: 0.6122 (m-80) cc_final: 0.5773 (m-80) REVERT: R 154 LYS cc_start: 0.6960 (mttm) cc_final: 0.6311 (tttt) REVERT: R 165 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: S 400 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7978 (tm-30) outliers start: 128 outliers final: 94 residues processed: 601 average time/residue: 0.5099 time to fit residues: 519.4244 Evaluate side-chains 574 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 469 time to evaluate : 5.087 ------------------------------------------------------------------------------- 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 E residue 88 ILE 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 471 LEU Chi-restraints excluded: chain F residue 88 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 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 417 ASP Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain H residue 88 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 556 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 271 MET 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 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 189 THR Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain K residue 383 LYS Chi-restraints excluded: chain L residue 88 ILE 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 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 314 SER Chi-restraints excluded: chain M residue 344 LEU Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 527 ASN 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 156 GLU Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 348 GLN Chi-restraints excluded: chain O residue 383 LYS Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 227 ASP 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 88 ILE Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 344 LEU Chi-restraints excluded: chain Q residue 412 CYS 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 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 165 GLU Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain S residue 349 SER 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 511 optimal weight: 8.9990 chunk 59 optimal weight: 0.5980 chunk 302 optimal weight: 20.0000 chunk 387 optimal weight: 0.9990 chunk 299 optimal weight: 8.9990 chunk 446 optimal weight: 10.0000 chunk 296 optimal weight: 0.0970 chunk 528 optimal weight: 0.8980 chunk 330 optimal weight: 4.9990 chunk 322 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 487 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 140 GLN ** N 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 42908 Z= 0.205 Angle : 0.556 12.786 58416 Z= 0.284 Chirality : 0.043 0.185 6800 Planarity : 0.004 0.060 7516 Dihedral : 7.815 89.708 6355 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.41 % Allowed : 16.10 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 5448 helix: 0.81 (0.11), residues: 2284 sheet: 0.25 (0.15), residues: 1164 loop : -0.67 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 267 HIS 0.006 0.001 HIS R 176 PHE 0.027 0.001 PHE N 223 TYR 0.014 0.001 TYR M 154 ARG 0.017 0.000 ARG G 416 *********************** 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 593 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 490 time to evaluate : 4.969 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: 0.8131 (mt-10) cc_final: 0.7117 (mm-30) REVERT: D 267 TRP cc_start: 0.7539 (m100) cc_final: 0.6833 (m100) REVERT: D 277 MET cc_start: 0.8435 (mtp) cc_final: 0.7888 (mmm) REVERT: D 335 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5667 (mp) REVERT: E 392 VAL cc_start: 0.7277 (t) cc_final: 0.6991 (p) REVERT: E 449 GLN cc_start: 0.7386 (mm-40) cc_final: 0.7039 (mm-40) REVERT: F 140 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8686 (mm-40) REVERT: F 241 MET cc_start: 0.7264 (mmm) cc_final: 0.5455 (mmm) REVERT: G 348 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8217 (mm-40) REVERT: G 376 LYS cc_start: 0.9059 (tmmt) cc_final: 0.8809 (tmtt) REVERT: G 400 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8068 (tm-30) REVERT: H 203 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7822 (p) REVERT: H 267 TRP cc_start: 0.7534 (m100) cc_final: 0.6776 (m100) REVERT: H 335 LEU cc_start: 0.6089 (OUTLIER) cc_final: 0.5665 (mp) REVERT: H 572 MET cc_start: 0.4642 (ttp) cc_final: 0.4352 (tmm) REVERT: I 343 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7941 (pm20) REVERT: I 392 VAL cc_start: 0.7296 (t) cc_final: 0.7003 (p) REVERT: J 123 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7561 (ptt90) REVERT: J 156 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: K 348 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8437 (mm-40) REVERT: K 400 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7972 (tm-30) REVERT: K 462 GLU cc_start: 0.8204 (pt0) cc_final: 0.7832 (pt0) REVERT: L 570 MET cc_start: 0.7630 (tpp) cc_final: 0.7426 (tpt) REVERT: L 572 MET cc_start: 0.4691 (ttp) cc_final: 0.4448 (tmm) REVERT: L 620 ASP cc_start: 0.6739 (t0) cc_final: 0.6528 (t0) REVERT: M 429 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7534 (mpp80) REVERT: M 495 PHE cc_start: 0.6216 (m-80) cc_final: 0.5888 (m-80) REVERT: N 140 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8613 (mm110) REVERT: N 156 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: O 348 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8204 (mm-40) REVERT: O 416 ARG cc_start: 0.8686 (mmm160) cc_final: 0.8328 (mmm160) REVERT: O 456 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8531 (mm-30) REVERT: P 91 PHE cc_start: 0.7015 (m-80) cc_final: 0.6771 (m-10) REVERT: P 105 GLU cc_start: 0.7872 (tt0) cc_final: 0.7342 (mm-30) REVERT: P 227 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.6914 (p0) REVERT: Q 495 PHE cc_start: 0.6111 (m-80) cc_final: 0.5807 (m-80) REVERT: R 154 LYS cc_start: 0.6945 (mttm) cc_final: 0.6308 (tttt) REVERT: R 165 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: S 348 GLN cc_start: 0.8425 (mt0) cc_final: 0.8213 (mt0) REVERT: S 400 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7978 (tm-30) REVERT: S 462 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7916 (pt0) outliers start: 103 outliers final: 80 residues processed: 565 average time/residue: 0.5086 time to fit residues: 489.5902 Evaluate side-chains 560 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 470 time to evaluate : 5.286 ------------------------------------------------------------------------------- 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 230 ASP 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 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 471 LEU Chi-restraints excluded: chain E residue 513 MET 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 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 424 ILE Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 604 PHE Chi-restraints excluded: chain I residue 88 ILE 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 271 MET 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 524 SER Chi-restraints excluded: chain I residue 550 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 156 GLU Chi-restraints excluded: chain J residue 164 VAL 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 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 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 254 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 314 SER 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 127 LEU 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 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 227 ASP 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 88 ILE Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 264 ILE 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 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 165 GLU Chi-restraints excluded: chain R residue 200 HIS Chi-restraints excluded: chain S residue 462 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 326 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 315 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 103 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 chunk 335 optimal weight: 2.9990 chunk 359 optimal weight: 6.9990 chunk 261 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 415 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** J 141 GLN M 449 GLN ** N 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 442 ASN Q 600 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 42908 Z= 0.186 Angle : 0.552 12.556 58416 Z= 0.280 Chirality : 0.043 0.181 6800 Planarity : 0.004 0.062 7516 Dihedral : 7.712 88.110 6355 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.46 % Allowed : 16.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.11), residues: 5448 helix: 0.92 (0.11), residues: 2308 sheet: 0.30 (0.15), residues: 1144 loop : -0.70 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 185 HIS 0.005 0.001 HIS R 176 PHE 0.014 0.001 PHE R 223 TYR 0.012 0.001 TYR M 154 ARG 0.014 0.000 ARG G 416 *********************** 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 602 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 497 time to evaluate : 4.937 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: 0.8079 (mt-10) cc_final: 0.7068 (mm-30) REVERT: D 227 ASP cc_start: 0.7171 (t70) cc_final: 0.6640 (p0) REVERT: D 267 TRP cc_start: 0.7503 (m100) cc_final: 0.6811 (m100) REVERT: D 335 LEU cc_start: 0.5919 (OUTLIER) cc_final: 0.5536 (mp) REVERT: E 267 TRP cc_start: 0.8367 (m100) cc_final: 0.7868 (m100) REVERT: E 392 VAL cc_start: 0.7279 (t) cc_final: 0.6990 (p) REVERT: E 442 ASN cc_start: 0.9187 (t0) cc_final: 0.8940 (p0) REVERT: E 449 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6993 (mm-40) REVERT: F 140 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8661 (mm-40) REVERT: G 348 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8239 (mm-40) REVERT: G 376 LYS cc_start: 0.9060 (tmmt) cc_final: 0.8850 (tmtt) REVERT: G 380 GLN cc_start: 0.8336 (tp40) cc_final: 0.8125 (tm-30) REVERT: G 400 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8064 (tm-30) REVERT: H 203 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7802 (p) REVERT: H 227 ASP cc_start: 0.7013 (t0) cc_final: 0.6640 (p0) REVERT: H 267 TRP cc_start: 0.7506 (m100) cc_final: 0.6763 (m100) REVERT: H 335 LEU cc_start: 0.6002 (OUTLIER) cc_final: 0.5528 (mp) REVERT: H 426 LEU cc_start: 0.6025 (mt) cc_final: 0.5711 (tp) REVERT: H 572 MET cc_start: 0.4706 (ttp) cc_final: 0.4356 (tmm) REVERT: I 343 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7945 (pm20) REVERT: I 392 VAL cc_start: 0.7400 (t) cc_final: 0.7122 (p) REVERT: I 513 MET cc_start: 0.8681 (ptm) cc_final: 0.8466 (ptp) REVERT: J 123 ARG cc_start: 0.7884 (ttm110) cc_final: 0.7578 (ptt90) REVERT: J 156 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: K 348 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8436 (mm-40) REVERT: K 400 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7980 (tm-30) REVERT: K 416 ARG cc_start: 0.8633 (mmm160) cc_final: 0.8176 (mmm160) REVERT: K 462 GLU cc_start: 0.8196 (pt0) cc_final: 0.7843 (pt0) REVERT: L 570 MET cc_start: 0.7715 (tpp) cc_final: 0.7488 (tpt) REVERT: L 572 MET cc_start: 0.4730 (ttp) cc_final: 0.4433 (tmm) REVERT: L 620 ASP cc_start: 0.6842 (t0) cc_final: 0.6600 (t0) REVERT: M 429 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7553 (mpp80) REVERT: M 495 PHE cc_start: 0.6118 (m-80) cc_final: 0.5795 (m-80) REVERT: N 156 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7081 (mt-10) REVERT: N 185 TRP cc_start: 0.8483 (t60) cc_final: 0.7767 (t60) REVERT: N 217 GLU cc_start: 0.8539 (tt0) cc_final: 0.8121 (tm-30) REVERT: O 348 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8224 (mm-40) REVERT: O 416 ARG cc_start: 0.8707 (mmm160) cc_final: 0.8500 (mmm160) REVERT: P 91 PHE cc_start: 0.7055 (m-80) cc_final: 0.6775 (m-10) REVERT: P 105 GLU cc_start: 0.7857 (tt0) cc_final: 0.7352 (mm-30) REVERT: P 227 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.6982 (p0) REVERT: P 280 MET cc_start: 0.7494 (mtp) cc_final: 0.7102 (mtp) REVERT: Q 495 PHE cc_start: 0.6098 (m-80) cc_final: 0.5788 (m-80) REVERT: R 154 LYS cc_start: 0.6937 (mttm) cc_final: 0.6278 (tttt) REVERT: R 165 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8319 (tm-30) REVERT: R 182 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8712 (pt0) REVERT: R 191 ARG cc_start: 0.8783 (ttm-80) cc_final: 0.8433 (ttt180) REVERT: S 348 GLN cc_start: 0.8424 (mt0) cc_final: 0.8185 (mt0) REVERT: S 400 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7967 (tm-30) REVERT: S 462 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7846 (pt0) outliers start: 105 outliers final: 81 residues processed: 573 average time/residue: 0.5158 time to fit residues: 501.0624 Evaluate side-chains 570 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 478 time to evaluate : 6.029 ------------------------------------------------------------------------------- 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 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 E residue 513 MET 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 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 424 ILE Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 604 PHE Chi-restraints excluded: chain I residue 88 ILE 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 I residue 524 SER 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 127 LEU 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 J residue 229 VAL Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain K residue 349 SER 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 228 VAL Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain M residue 88 ILE 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 471 LEU 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 156 GLU Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 182 GLU Chi-restraints excluded: chain N residue 200 HIS Chi-restraints excluded: chain O residue 348 GLN Chi-restraints excluded: chain O residue 379 GLN Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 227 ASP Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 ASP 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 193 THR Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 280 MET 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 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 182 GLU Chi-restraints excluded: chain R residue 200 HIS Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 462 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 480 optimal weight: 0.8980 chunk 506 optimal weight: 0.0670 chunk 461 optimal weight: 7.9990 chunk 492 optimal weight: 0.4980 chunk 505 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 chunk 386 optimal weight: 0.9980 chunk 151 optimal weight: 0.0870 chunk 444 optimal weight: 3.9990 chunk 465 optimal weight: 3.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- 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 M 600 ASN ** N 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 42908 Z= 0.155 Angle : 0.549 11.872 58416 Z= 0.277 Chirality : 0.043 0.249 6800 Planarity : 0.004 0.054 7516 Dihedral : 7.589 87.159 6355 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.87 % Allowed : 16.92 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.11), residues: 5448 helix: 1.03 (0.11), residues: 2312 sheet: 0.39 (0.15), residues: 1128 loop : -0.59 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP N 185 HIS 0.005 0.001 HIS R 176 PHE 0.020 0.001 PHE R 223 TYR 0.011 0.001 TYR P 356 ARG 0.018 0.000 ARG E 429 *********************** 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 586 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 506 time to evaluate : 5.621 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 105 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7001 (mm-30) REVERT: D 227 ASP cc_start: 0.7141 (t70) cc_final: 0.6688 (p0) REVERT: D 267 TRP cc_start: 0.7508 (m100) cc_final: 0.6837 (m100) REVERT: D 280 MET cc_start: 0.7741 (mtm) cc_final: 0.7538 (mtm) REVERT: D 335 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5506 (mp) REVERT: D 570 MET cc_start: 0.7302 (tpt) cc_final: 0.6575 (tpt) REVERT: E 103 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7530 (tt) REVERT: E 267 TRP cc_start: 0.8335 (m100) cc_final: 0.7847 (m100) REVERT: E 392 VAL cc_start: 0.7348 (t) cc_final: 0.7070 (p) REVERT: E 442 ASN cc_start: 0.9183 (t0) cc_final: 0.8942 (p0) REVERT: E 449 GLN cc_start: 0.7359 (mm-40) cc_final: 0.7045 (mm-40) REVERT: F 140 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8687 (mm-40) REVERT: G 348 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8253 (mm-40) REVERT: G 400 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8028 (tm-30) REVERT: H 203 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7775 (p) REVERT: H 227 ASP cc_start: 0.6927 (t0) cc_final: 0.6548 (p0) REVERT: H 267 TRP cc_start: 0.7500 (m100) cc_final: 0.6793 (m100) REVERT: H 277 MET cc_start: 0.8313 (mtp) cc_final: 0.7719 (mmm) REVERT: H 335 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5327 (mp) REVERT: H 570 MET cc_start: 0.7402 (tpt) cc_final: 0.6806 (tpt) REVERT: H 572 MET cc_start: 0.4672 (ttp) cc_final: 0.4319 (tmm) REVERT: I 343 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7909 (pm20) REVERT: I 392 VAL cc_start: 0.7415 (t) cc_final: 0.7135 (p) REVERT: J 123 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7576 (ptt90) REVERT: J 156 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: K 400 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7974 (tm-30) REVERT: K 416 ARG cc_start: 0.8622 (mmm160) cc_final: 0.8270 (mmm160) REVERT: K 462 GLU cc_start: 0.8148 (pt0) cc_final: 0.7840 (pt0) REVERT: L 280 MET cc_start: 0.7485 (mtp) cc_final: 0.7063 (mtp) REVERT: L 570 MET cc_start: 0.7678 (tpp) cc_final: 0.7451 (tpt) REVERT: L 572 MET cc_start: 0.4682 (ttp) cc_final: 0.4364 (tmm) REVERT: L 620 ASP cc_start: 0.6832 (t0) cc_final: 0.6602 (t0) REVERT: M 429 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7560 (mpp80) REVERT: M 442 ASN cc_start: 0.9278 (t0) cc_final: 0.9016 (p0) REVERT: M 495 PHE cc_start: 0.6068 (m-80) cc_final: 0.5743 (m-80) REVERT: N 140 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8566 (mm-40) REVERT: N 156 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7067 (mt-10) REVERT: N 185 TRP cc_start: 0.8321 (t60) cc_final: 0.7760 (t60) REVERT: N 217 GLU cc_start: 0.8572 (tt0) cc_final: 0.8150 (tm-30) REVERT: O 348 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8242 (mm-40) REVERT: O 456 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8498 (mm-30) REVERT: P 105 GLU cc_start: 0.7866 (tt0) cc_final: 0.7362 (mm-30) REVERT: P 227 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.6979 (p0) REVERT: P 280 MET cc_start: 0.7485 (mtp) cc_final: 0.7049 (mtp) REVERT: P 570 MET cc_start: 0.7013 (tpp) cc_final: 0.6764 (tpp) REVERT: Q 268 GLU cc_start: 0.7503 (pp20) cc_final: 0.7302 (pp20) REVERT: Q 495 PHE cc_start: 0.6060 (m-80) cc_final: 0.5750 (m-80) REVERT: R 154 LYS cc_start: 0.6890 (mttm) cc_final: 0.6242 (tttt) REVERT: R 165 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: R 191 ARG cc_start: 0.8767 (ttm-80) cc_final: 0.8363 (ttp-170) REVERT: S 348 GLN cc_start: 0.8437 (mt0) cc_final: 0.8208 (mt0) REVERT: S 400 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7941 (tm-30) REVERT: S 420 ASP cc_start: 0.8579 (m-30) cc_final: 0.7623 (m-30) REVERT: S 462 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7748 (pt0) outliers start: 80 outliers final: 60 residues processed: 562 average time/residue: 0.5289 time to fit residues: 502.2567 Evaluate side-chains 549 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 478 time to evaluate : 5.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ILE 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 254 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 471 LEU 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 178 GLU Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 604 PHE 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 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 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 349 SER Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain M residue 88 ILE 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 471 LEU Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL 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 P residue 167 THR Chi-restraints excluded: chain P residue 227 ASP 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 88 ILE Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 264 ILE 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 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 200 HIS Chi-restraints excluded: chain S residue 462 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 490 optimal weight: 9.9990 chunk 323 optimal weight: 8.9990 chunk 520 optimal weight: 1.9990 chunk 317 optimal weight: 0.7980 chunk 246 optimal weight: 0.7980 chunk 361 optimal weight: 2.9990 chunk 545 optimal weight: 0.9980 chunk 502 optimal weight: 1.9990 chunk 434 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 335 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 113 ASN F 141 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 GLN ** N 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 452 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 42908 Z= 0.186 Angle : 0.563 11.274 58416 Z= 0.285 Chirality : 0.043 0.226 6800 Planarity : 0.004 0.057 7516 Dihedral : 7.563 89.698 6355 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.94 % Allowed : 17.13 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.11), residues: 5448 helix: 1.01 (0.11), residues: 2320 sheet: 0.42 (0.15), residues: 1136 loop : -0.62 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP P 440 HIS 0.004 0.001 HIS F 176 PHE 0.032 0.001 PHE P 91 TYR 0.012 0.001 TYR E 356 ARG 0.015 0.000 ARG I 429 ********************** 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 572 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 489 time to evaluate : 4.429 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 105 GLU cc_start: 0.8061 (mt-10) cc_final: 0.6964 (mm-30) REVERT: D 267 TRP cc_start: 0.7533 (m100) cc_final: 0.6833 (m100) REVERT: D 280 MET cc_start: 0.7763 (mtm) cc_final: 0.7412 (mtm) REVERT: D 335 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5457 (mp) REVERT: E 103 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7528 (tt) REVERT: E 267 TRP cc_start: 0.8338 (m100) cc_final: 0.7847 (m100) REVERT: E 392 VAL cc_start: 0.7391 (t) cc_final: 0.7102 (p) REVERT: E 449 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6986 (mm-40) REVERT: F 140 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8719 (mm-40) REVERT: G 348 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8265 (mm-40) REVERT: G 400 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8049 (tm-30) REVERT: G 416 ARG cc_start: 0.8542 (mmm160) cc_final: 0.8236 (mmm160) REVERT: H 203 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7786 (p) REVERT: H 227 ASP cc_start: 0.7008 (t0) cc_final: 0.6632 (p0) REVERT: H 267 TRP cc_start: 0.7529 (m100) cc_final: 0.6783 (m100) REVERT: H 277 MET cc_start: 0.8350 (mtp) cc_final: 0.7752 (mmm) REVERT: H 335 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5438 (mp) REVERT: H 572 MET cc_start: 0.4699 (ttp) cc_final: 0.4410 (tmm) REVERT: I 267 TRP cc_start: 0.8331 (m100) cc_final: 0.7879 (m100) REVERT: I 343 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7901 (pm20) REVERT: I 392 VAL cc_start: 0.7409 (t) cc_final: 0.7115 (p) REVERT: I 604 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7146 (t80) REVERT: J 123 ARG cc_start: 0.7894 (ttm110) cc_final: 0.7611 (ptt90) REVERT: J 156 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: K 327 ASN cc_start: 0.8379 (t0) cc_final: 0.7072 (t0) REVERT: K 400 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7971 (tm-30) REVERT: K 416 ARG cc_start: 0.8724 (mmm160) cc_final: 0.8334 (mmm160) REVERT: K 420 ASP cc_start: 0.8475 (m-30) cc_final: 0.7334 (m-30) REVERT: K 462 GLU cc_start: 0.8158 (pt0) cc_final: 0.7822 (pt0) REVERT: L 280 MET cc_start: 0.7510 (mtp) cc_final: 0.7077 (mtp) REVERT: L 570 MET cc_start: 0.7693 (tpp) cc_final: 0.7413 (tpt) REVERT: L 572 MET cc_start: 0.4663 (ttp) cc_final: 0.4371 (tmm) REVERT: L 620 ASP cc_start: 0.6844 (t0) cc_final: 0.6585 (t0) REVERT: M 429 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7567 (mpp80) REVERT: M 442 ASN cc_start: 0.9275 (t0) cc_final: 0.9015 (p0) REVERT: M 495 PHE cc_start: 0.6104 (m-80) cc_final: 0.5777 (m-80) REVERT: N 140 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8569 (mm-40) REVERT: N 156 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7074 (mt-10) REVERT: N 217 GLU cc_start: 0.8578 (tt0) cc_final: 0.8152 (tm-30) REVERT: O 348 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8235 (mm-40) REVERT: O 420 ASP cc_start: 0.8521 (m-30) cc_final: 0.7574 (m-30) REVERT: P 105 GLU cc_start: 0.7859 (tt0) cc_final: 0.7363 (mm-30) REVERT: P 227 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7075 (p0) REVERT: P 280 MET cc_start: 0.7518 (mtp) cc_final: 0.7081 (mtp) REVERT: Q 495 PHE cc_start: 0.6091 (m-80) cc_final: 0.5781 (m-80) REVERT: R 154 LYS cc_start: 0.6921 (mttm) cc_final: 0.6252 (tttt) REVERT: R 165 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8297 (tm-30) REVERT: R 184 MET cc_start: 0.8125 (ttp) cc_final: 0.7744 (ttp) REVERT: R 191 ARG cc_start: 0.8811 (ttm-80) cc_final: 0.8390 (ttp-170) REVERT: S 348 GLN cc_start: 0.8427 (mt0) cc_final: 0.8192 (mt0) REVERT: S 400 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7943 (tm-30) REVERT: S 462 GLU cc_start: 0.8087 (pt0) cc_final: 0.7704 (pt0) outliers start: 83 outliers final: 67 residues processed: 546 average time/residue: 0.5418 time to fit residues: 501.1399 Evaluate side-chains 546 residues out of total 4628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 468 time to evaluate : 5.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ILE 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 254 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 113 ASN 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 178 GLU Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 604 PHE 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 I residue 524 SER Chi-restraints excluded: chain I residue 550 THR Chi-restraints excluded: chain I residue 604 PHE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 156 GLU Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain K residue 349 SER Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 433 LEU Chi-restraints excluded: chain M residue 88 ILE 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 471 LEU Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL 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 N residue 200 HIS Chi-restraints excluded: chain O residue 348 GLN Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 227 ASP 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 88 ILE Chi-restraints excluded: chain Q residue 193 THR Chi-restraints excluded: chain Q residue 264 ILE 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 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain S residue 452 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 266 optimal weight: 3.9990 chunk 345 optimal weight: 6.9990 chunk 463 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 400 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 435 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 447 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** K 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.157838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.120629 restraints weight = 77425.509| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 3.40 r_work: 0.3526 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.368 42908 Z= 0.244 Angle : 0.669 59.197 58416 Z= 0.367 Chirality : 0.049 1.916 6800 Planarity : 0.004 0.145 7516 Dihedral : 7.576 89.719 6355 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.22 % Favored : 97.76 % Rotamer: Outliers : 2.06 % Allowed : 17.06 % Favored : 80.88 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.11), residues: 5448 helix: 1.00 (0.11), residues: 2336 sheet: 0.44 (0.15), residues: 1128 loop : -0.61 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP P 440 HIS 0.006 0.001 HIS R 176 PHE 0.026 0.001 PHE L 578 TYR 0.020 0.001 TYR M 338 ARG 0.011 0.000 ARG I 429 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10933.62 seconds wall clock time: 198 minutes 45.48 seconds (11925.48 seconds total)