Starting phenix.real_space_refine on Thu Nov 20 23:03:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6evy_3963/11_2025/6evy_3963.cif Found real_map, /net/cci-nas-00/data/ceres_data/6evy_3963/11_2025/6evy_3963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6evy_3963/11_2025/6evy_3963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6evy_3963/11_2025/6evy_3963.map" model { file = "/net/cci-nas-00/data/ceres_data/6evy_3963/11_2025/6evy_3963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6evy_3963/11_2025/6evy_3963.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.046 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 36 5.49 5 Mg 6 5.21 5 S 282 5.16 5 C 25674 2.51 5 N 6978 2.21 5 O 7914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40890 Number of models: 1 Model: "" Number of chains: 24 Chain: "E" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.25, per 1000 atoms: 0.25 Number of scatterers: 40890 At special positions: 0 Unit cell: (119.54, 173.75, 212.67, 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 282 16.00 P 36 15.00 Mg 6 11.99 O 7914 8.00 N 6978 7.00 C 25674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 1.9 seconds 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9576 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 30 sheets defined 48.0% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'E' and resid 10 through 27 removed outlier: 3.893A pdb=" N ILE E 16 " --> pdb=" O ALA E 12 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 81 removed outlier: 4.121A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 129 removed outlier: 3.903A pdb=" N ILE E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP E 127 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.514A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER E 158 " --> pdb=" O MET E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 4.216A pdb=" N ILE E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 189 " --> pdb=" O TYR E 185 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS E 197 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 removed outlier: 4.074A pdb=" N ILE E 209 " --> pdb=" O ASP E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 239 removed outlier: 3.798A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 244 Processing helix chain 'E' and resid 253 through 259 removed outlier: 3.624A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.699A pdb=" N ASN E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.874A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.768A pdb=" N ASN E 329 " --> pdb=" O PRO E 325 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR E 334 " --> pdb=" O ALA E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 401 removed outlier: 3.561A pdb=" N ARG E 390 " --> pdb=" O GLU E 386 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 3.771A pdb=" N GLY E 410 " --> pdb=" O HIS E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 437 removed outlier: 3.711A pdb=" N GLU E 423 " --> pdb=" O SER E 419 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 29 removed outlier: 3.594A pdb=" N ILE F 16 " --> pdb=" O CYS F 12 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY F 17 " --> pdb=" O GLY F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 49 removed outlier: 3.769A pdb=" N VAL F 49 " --> pdb=" O ARG F 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 46 through 49' Processing helix chain 'F' and resid 69 through 79 removed outlier: 4.504A pdb=" N MET F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 108 through 126 removed outlier: 4.457A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 159 removed outlier: 3.604A pdb=" N LEU F 151 " --> pdb=" O MET F 147 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 196 removed outlier: 3.930A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 214 Processing helix chain 'F' and resid 221 through 237 removed outlier: 3.506A pdb=" N HIS F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 240 No H-bonds generated for 'chain 'F' and resid 238 through 240' Processing helix chain 'F' and resid 249 through 258 removed outlier: 3.579A pdb=" N MET F 257 " --> pdb=" O LEU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.583A pdb=" N THR F 290 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN F 292 " --> pdb=" O GLU F 288 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET F 293 " --> pdb=" O LEU F 289 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE F 294 " --> pdb=" O THR F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 337 removed outlier: 3.858A pdb=" N GLN F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN F 337 " --> pdb=" O VAL F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 390 removed outlier: 3.504A pdb=" N MET F 388 " --> pdb=" O GLN F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 400 Processing helix chain 'F' and resid 404 through 427 removed outlier: 4.095A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN F 414 " --> pdb=" O GLU F 410 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP F 427 " --> pdb=" O GLN F 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 27 removed outlier: 3.893A pdb=" N ILE J 16 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 81 removed outlier: 4.121A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 110 through 129 removed outlier: 3.903A pdb=" N ILE J 114 " --> pdb=" O ILE J 110 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASP J 116 " --> pdb=" O LYS J 112 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP J 127 " --> pdb=" O ARG J 123 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 161 removed outlier: 4.513A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU J 155 " --> pdb=" O SER J 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER J 158 " --> pdb=" O MET J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 198 removed outlier: 4.216A pdb=" N ILE J 188 " --> pdb=" O PRO J 184 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU J 189 " --> pdb=" O TYR J 185 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLU J 196 " --> pdb=" O HIS J 192 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N HIS J 197 " --> pdb=" O THR J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 216 removed outlier: 4.074A pdb=" N ILE J 209 " --> pdb=" O ASP J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 239 removed outlier: 3.798A pdb=" N LEU J 227 " --> pdb=" O THR J 223 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 244 Processing helix chain 'J' and resid 253 through 259 removed outlier: 3.624A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 296 removed outlier: 3.700A pdb=" N ASN J 293 " --> pdb=" O ALA J 289 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA J 294 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE J 296 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 301 removed outlier: 3.874A pdb=" N GLN J 301 " --> pdb=" O PRO J 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 336 removed outlier: 3.768A pdb=" N ASN J 329 " --> pdb=" O PRO J 325 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA J 333 " --> pdb=" O ASN J 329 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR J 334 " --> pdb=" O ALA J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 401 removed outlier: 3.561A pdb=" N ARG J 390 " --> pdb=" O GLU J 386 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS J 401 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 410 removed outlier: 3.771A pdb=" N GLY J 410 " --> pdb=" O HIS J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 437 removed outlier: 3.711A pdb=" N GLU J 423 " --> pdb=" O SER J 419 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR J 432 " --> pdb=" O LEU J 428 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU J 433 " --> pdb=" O GLU J 429 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL J 435 " --> pdb=" O ASP J 431 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 27 removed outlier: 3.893A pdb=" N ILE C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 81 removed outlier: 4.121A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 129 removed outlier: 3.903A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.513A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 removed outlier: 4.216A pdb=" N ILE C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU C 196 " --> pdb=" O HIS C 192 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 216 removed outlier: 4.074A pdb=" N ILE C 209 " --> pdb=" O ASP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.798A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 Processing helix chain 'C' and resid 253 through 259 removed outlier: 3.624A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.699A pdb=" N ASN C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 removed outlier: 3.874A pdb=" N GLN C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.769A pdb=" N ASN C 329 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.561A pdb=" N ARG C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.772A pdb=" N GLY C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 437 removed outlier: 3.710A pdb=" N GLU C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 27 removed outlier: 3.893A pdb=" N ILE L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA L 19 " --> pdb=" O GLN L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 81 removed outlier: 4.120A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 110 through 129 removed outlier: 3.904A pdb=" N ILE L 114 " --> pdb=" O ILE L 110 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASP L 116 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU L 117 " --> pdb=" O GLU L 113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP L 127 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 161 removed outlier: 4.513A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU L 155 " --> pdb=" O SER L 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER L 158 " --> pdb=" O MET L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 198 removed outlier: 4.216A pdb=" N ILE L 188 " --> pdb=" O PRO L 184 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU L 189 " --> pdb=" O TYR L 185 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR L 193 " --> pdb=" O LEU L 189 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLU L 196 " --> pdb=" O HIS L 192 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS L 197 " --> pdb=" O THR L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 216 removed outlier: 4.073A pdb=" N ILE L 209 " --> pdb=" O ASP L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 239 removed outlier: 3.798A pdb=" N LEU L 227 " --> pdb=" O THR L 223 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU L 230 " --> pdb=" O ASN L 226 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE L 234 " --> pdb=" O LEU L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 244 Processing helix chain 'L' and resid 253 through 259 removed outlier: 3.623A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 296 removed outlier: 3.700A pdb=" N ASN L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA L 294 " --> pdb=" O GLU L 290 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 301 removed outlier: 3.874A pdb=" N GLN L 301 " --> pdb=" O PRO L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 336 removed outlier: 3.768A pdb=" N ASN L 329 " --> pdb=" O PRO L 325 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA L 333 " --> pdb=" O ASN L 329 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR L 334 " --> pdb=" O ALA L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 401 removed outlier: 3.562A pdb=" N ARG L 390 " --> pdb=" O GLU L 386 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 410 removed outlier: 3.771A pdb=" N GLY L 410 " --> pdb=" O HIS L 406 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 437 removed outlier: 3.711A pdb=" N GLU L 423 " --> pdb=" O SER L 419 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR L 432 " --> pdb=" O LEU L 428 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU L 433 " --> pdb=" O GLU L 429 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL L 435 " --> pdb=" O ASP L 431 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.893A pdb=" N ILE A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 81 removed outlier: 4.120A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 129 removed outlier: 3.903A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.513A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 4.216A pdb=" N ILE A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 4.074A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.799A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.624A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.698A pdb=" N ASN A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.875A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.767A pdb=" N ASN A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.561A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.771A pdb=" N GLY A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 437 removed outlier: 3.710A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 27 removed outlier: 3.893A pdb=" N ILE K 16 " --> pdb=" O ALA K 12 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA K 19 " --> pdb=" O GLN K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 81 removed outlier: 4.120A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 110 through 129 removed outlier: 3.904A pdb=" N ILE K 114 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASP K 116 " --> pdb=" O LYS K 112 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU K 117 " --> pdb=" O GLU K 113 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP K 127 " --> pdb=" O ARG K 123 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 161 removed outlier: 4.513A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER K 158 " --> pdb=" O MET K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 198 removed outlier: 4.215A pdb=" N ILE K 188 " --> pdb=" O PRO K 184 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU K 189 " --> pdb=" O TYR K 185 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU K 196 " --> pdb=" O HIS K 192 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS K 197 " --> pdb=" O THR K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 216 removed outlier: 4.074A pdb=" N ILE K 209 " --> pdb=" O ASP K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 239 removed outlier: 3.798A pdb=" N LEU K 227 " --> pdb=" O THR K 223 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU K 230 " --> pdb=" O ASN K 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE K 234 " --> pdb=" O LEU K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 244 Processing helix chain 'K' and resid 253 through 259 removed outlier: 3.624A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 296 removed outlier: 3.698A pdb=" N ASN K 293 " --> pdb=" O ALA K 289 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA K 294 " --> pdb=" O GLU K 290 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 301 removed outlier: 3.874A pdb=" N GLN K 301 " --> pdb=" O PRO K 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 336 removed outlier: 3.768A pdb=" N ASN K 329 " --> pdb=" O PRO K 325 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA K 333 " --> pdb=" O ASN K 329 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR K 334 " --> pdb=" O ALA K 330 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 401 removed outlier: 3.561A pdb=" N ARG K 390 " --> pdb=" O GLU K 386 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 removed outlier: 3.772A pdb=" N GLY K 410 " --> pdb=" O HIS K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 437 removed outlier: 3.710A pdb=" N GLU K 423 " --> pdb=" O SER K 419 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR K 432 " --> pdb=" O LEU K 428 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU K 433 " --> pdb=" O GLU K 429 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL K 435 " --> pdb=" O ASP K 431 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 29 removed outlier: 3.594A pdb=" N ILE G 16 " --> pdb=" O CYS G 12 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY G 17 " --> pdb=" O GLY G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 49 removed outlier: 3.769A pdb=" N VAL G 49 " --> pdb=" O ARG G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 46 through 49' Processing helix chain 'G' and resid 69 through 79 removed outlier: 4.504A pdb=" N MET G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 106 Processing helix chain 'G' and resid 108 through 126 removed outlier: 4.457A pdb=" N ASP G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP G 118 " --> pdb=" O ASP G 114 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 159 removed outlier: 3.604A pdb=" N LEU G 151 " --> pdb=" O MET G 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU G 157 " --> pdb=" O SER G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 196 removed outlier: 3.930A pdb=" N GLN G 191 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU G 194 " --> pdb=" O HIS G 190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR G 196 " --> pdb=" O LEU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 214 Processing helix chain 'G' and resid 221 through 237 removed outlier: 3.506A pdb=" N HIS G 227 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL G 229 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR G 237 " --> pdb=" O MET G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 240 No H-bonds generated for 'chain 'G' and resid 238 through 240' Processing helix chain 'G' and resid 249 through 258 removed outlier: 3.579A pdb=" N MET G 257 " --> pdb=" O LEU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 294 removed outlier: 3.583A pdb=" N THR G 290 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN G 292 " --> pdb=" O GLU G 288 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET G 293 " --> pdb=" O LEU G 289 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE G 294 " --> pdb=" O THR G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 337 removed outlier: 3.858A pdb=" N GLN G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN G 334 " --> pdb=" O MET G 330 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN G 337 " --> pdb=" O VAL G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 390 removed outlier: 3.504A pdb=" N MET G 388 " --> pdb=" O GLN G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 400 Processing helix chain 'G' and resid 404 through 427 removed outlier: 4.095A pdb=" N PHE G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN G 414 " --> pdb=" O GLU G 410 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP G 427 " --> pdb=" O GLN G 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 removed outlier: 3.595A pdb=" N ILE D 16 " --> pdb=" O CYS D 12 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY D 17 " --> pdb=" O GLY D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 49 removed outlier: 3.770A pdb=" N VAL D 49 " --> pdb=" O ARG D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 46 through 49' Processing helix chain 'D' and resid 69 through 79 removed outlier: 4.504A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 108 through 126 removed outlier: 4.457A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 159 removed outlier: 3.604A pdb=" N LEU D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.930A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 214 Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.506A pdb=" N HIS D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 249 through 258 removed outlier: 3.579A pdb=" N MET D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.583A pdb=" N THR D 290 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN D 292 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.858A pdb=" N GLN D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN D 337 " --> pdb=" O VAL D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 390 removed outlier: 3.504A pdb=" N MET D 388 " --> pdb=" O GLN D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 404 through 427 removed outlier: 4.096A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 414 " --> pdb=" O GLU D 410 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 removed outlier: 3.594A pdb=" N ILE I 16 " --> pdb=" O CYS I 12 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY I 17 " --> pdb=" O GLY I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 49 removed outlier: 3.769A pdb=" N VAL I 49 " --> pdb=" O ARG I 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 46 through 49' Processing helix chain 'I' and resid 69 through 79 removed outlier: 4.505A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 126 removed outlier: 4.456A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP I 118 " --> pdb=" O ASP I 114 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL I 119 " --> pdb=" O SER I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 159 removed outlier: 3.604A pdb=" N LEU I 151 " --> pdb=" O MET I 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 152 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU I 157 " --> pdb=" O SER I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 196 removed outlier: 3.931A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR I 196 " --> pdb=" O LEU I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.506A pdb=" N HIS I 227 " --> pdb=" O GLY I 223 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU I 228 " --> pdb=" O ASP I 224 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL I 229 " --> pdb=" O LEU I 225 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 240 No H-bonds generated for 'chain 'I' and resid 238 through 240' Processing helix chain 'I' and resid 249 through 258 removed outlier: 3.579A pdb=" N MET I 257 " --> pdb=" O LEU I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 294 removed outlier: 3.583A pdb=" N THR I 290 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN I 292 " --> pdb=" O GLU I 288 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET I 293 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE I 294 " --> pdb=" O THR I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 322 through 337 removed outlier: 3.858A pdb=" N GLN I 329 " --> pdb=" O GLU I 325 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN I 334 " --> pdb=" O MET I 330 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN I 337 " --> pdb=" O VAL I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 390 removed outlier: 3.505A pdb=" N MET I 388 " --> pdb=" O GLN I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 400 Processing helix chain 'I' and resid 404 through 427 removed outlier: 4.095A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN I 414 " --> pdb=" O GLU I 410 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP I 427 " --> pdb=" O GLN I 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.594A pdb=" N ILE B 16 " --> pdb=" O CYS B 12 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.770A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 69 through 79 removed outlier: 4.505A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 126 removed outlier: 4.456A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 159 removed outlier: 3.604A pdb=" N LEU B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.931A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.506A pdb=" N HIS B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 249 through 258 removed outlier: 3.580A pdb=" N MET B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.583A pdb=" N THR B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.858A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.504A pdb=" N MET B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 427 removed outlier: 4.096A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN B 414 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 29 removed outlier: 3.594A pdb=" N ILE H 16 " --> pdb=" O CYS H 12 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY H 17 " --> pdb=" O GLY H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 49 removed outlier: 3.769A pdb=" N VAL H 49 " --> pdb=" O ARG H 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 46 through 49' Processing helix chain 'H' and resid 69 through 79 removed outlier: 4.504A pdb=" N MET H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 108 through 126 removed outlier: 4.457A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP H 118 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 159 removed outlier: 3.604A pdb=" N LEU H 151 " --> pdb=" O MET H 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE H 152 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU H 157 " --> pdb=" O SER H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 196 removed outlier: 3.931A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU H 194 " --> pdb=" O HIS H 190 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR H 196 " --> pdb=" O LEU H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 214 Processing helix chain 'H' and resid 221 through 237 removed outlier: 3.507A pdb=" N HIS H 227 " --> pdb=" O GLY H 223 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU H 228 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL H 229 " --> pdb=" O LEU H 225 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 240 No H-bonds generated for 'chain 'H' and resid 238 through 240' Processing helix chain 'H' and resid 249 through 258 removed outlier: 3.579A pdb=" N MET H 257 " --> pdb=" O LEU H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 294 removed outlier: 3.583A pdb=" N THR H 290 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN H 292 " --> pdb=" O GLU H 288 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET H 293 " --> pdb=" O LEU H 289 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE H 294 " --> pdb=" O THR H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 337 removed outlier: 3.857A pdb=" N GLN H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN H 334 " --> pdb=" O MET H 330 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN H 337 " --> pdb=" O VAL H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 390 removed outlier: 3.505A pdb=" N MET H 388 " --> pdb=" O GLN H 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 400 Processing helix chain 'H' and resid 404 through 427 removed outlier: 4.095A pdb=" N PHE H 408 " --> pdb=" O ASP H 404 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN H 414 " --> pdb=" O GLU H 410 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP H 427 " --> pdb=" O GLN H 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 92 through 93 removed outlier: 8.238A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 53 through 55 removed outlier: 3.735A pdb=" N VAL E 62 " --> pdb=" O SER E 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 269 through 273 Processing sheet with id=AA4, first strand: chain 'F' and resid 90 through 92 removed outlier: 7.855A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N PHE F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU F 135 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N MET F 164 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N TYR F 200 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR F 166 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA F 271 " --> pdb=" O ALA F 365 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR F 312 " --> pdb=" O ASN F 370 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N LYS F 350 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL F 313 " --> pdb=" O LYS F 350 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ALA F 352 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALA F 315 " --> pdb=" O ALA F 352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.809A pdb=" N LYS F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 92 through 93 removed outlier: 8.239A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE J 135 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N PHE J 169 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL J 137 " --> pdb=" O PHE J 169 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE J 171 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS J 166 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE J 202 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER J 170 " --> pdb=" O VAL J 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 53 through 55 removed outlier: 3.735A pdb=" N VAL J 62 " --> pdb=" O SER J 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 269 through 273 Processing sheet with id=AA9, first strand: chain 'C' and resid 92 through 93 removed outlier: 8.238A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.734A pdb=" N VAL C 62 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 269 through 273 Processing sheet with id=AB3, first strand: chain 'L' and resid 92 through 93 removed outlier: 8.238A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE L 135 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N PHE L 169 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL L 137 " --> pdb=" O PHE L 169 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE L 171 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 53 through 55 removed outlier: 3.735A pdb=" N VAL L 62 " --> pdb=" O SER L 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 269 through 273 Processing sheet with id=AB6, first strand: chain 'A' and resid 92 through 93 removed outlier: 8.238A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.736A pdb=" N VAL A 62 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 269 through 273 Processing sheet with id=AB9, first strand: chain 'K' and resid 92 through 93 removed outlier: 8.238A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE K 135 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N PHE K 169 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL K 137 " --> pdb=" O PHE K 169 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE K 171 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 53 through 55 removed outlier: 3.735A pdb=" N VAL K 62 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 269 through 273 Processing sheet with id=AC3, first strand: chain 'G' and resid 90 through 92 removed outlier: 7.856A pdb=" N VAL G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU G 65 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN G 131 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN G 165 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE G 133 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N PHE G 167 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU G 135 " --> pdb=" O PHE G 167 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N MET G 164 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N TYR G 200 " --> pdb=" O MET G 164 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR G 166 " --> pdb=" O TYR G 200 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR G 199 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N PHE G 265 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER G 371 " --> pdb=" O PHE G 265 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA G 271 " --> pdb=" O ALA G 365 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR G 312 " --> pdb=" O ASN G 370 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N LYS G 350 " --> pdb=" O LEU G 311 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL G 313 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ALA G 352 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA G 315 " --> pdb=" O ALA G 352 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.810A pdb=" N LYS G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 90 through 92 removed outlier: 7.855A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA D 271 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR D 312 " --> pdb=" O ASN D 370 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N LYS D 350 " --> pdb=" O LEU D 311 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL D 313 " --> pdb=" O LYS D 350 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ALA D 352 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA D 315 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.809A pdb=" N LYS D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 90 through 92 removed outlier: 7.856A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN I 131 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN I 165 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE I 133 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N MET I 164 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA I 271 " --> pdb=" O ALA I 365 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR I 312 " --> pdb=" O ASN I 370 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N LYS I 350 " --> pdb=" O LEU I 311 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL I 313 " --> pdb=" O LYS I 350 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ALA I 352 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA I 315 " --> pdb=" O ALA I 352 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 51 through 54 removed outlier: 3.809A pdb=" N LYS I 58 " --> pdb=" O ALA I 54 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.855A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA B 271 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.810A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 90 through 92 removed outlier: 7.856A pdb=" N VAL H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU H 65 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN H 131 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ASN H 165 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE H 133 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N PHE H 167 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU H 135 " --> pdb=" O PHE H 167 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N MET H 164 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N TYR H 200 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR H 166 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR H 199 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE H 265 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER H 371 " --> pdb=" O PHE H 265 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA H 271 " --> pdb=" O ALA H 365 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR H 312 " --> pdb=" O ASN H 370 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N LYS H 350 " --> pdb=" O LEU H 311 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL H 313 " --> pdb=" O LYS H 350 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ALA H 352 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA H 315 " --> pdb=" O ALA H 352 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 51 through 54 removed outlier: 3.809A pdb=" N LYS H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) 1566 hydrogen bonds defined for protein. 4644 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: 8.50 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 13782 1.36 - 1.49: 10952 1.49 - 1.63: 16648 1.63 - 1.76: 0 1.76 - 1.90: 438 Bond restraints: 41820 Sorted by residual: bond pdb=" PG GSP G 501 " pdb=" S1G GSP G 501 " ideal model delta sigma weight residual 1.700 1.900 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" PG GSP F 501 " pdb=" S1G GSP F 501 " ideal model delta sigma weight residual 1.700 1.899 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" PG GSP H 501 " pdb=" S1G GSP H 501 " ideal model delta sigma weight residual 1.700 1.899 -0.199 2.00e-02 2.50e+03 9.92e+01 bond pdb=" PG GSP I 501 " pdb=" S1G GSP I 501 " ideal model delta sigma weight residual 1.700 1.899 -0.199 2.00e-02 2.50e+03 9.89e+01 bond pdb=" PG GSP B 501 " pdb=" S1G GSP B 501 " ideal model delta sigma weight residual 1.700 1.899 -0.199 2.00e-02 2.50e+03 9.89e+01 ... (remaining 41815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 56013 2.81 - 5.63: 641 5.63 - 8.44: 127 8.44 - 11.26: 39 11.26 - 14.07: 6 Bond angle restraints: 56826 Sorted by residual: angle pdb=" O2G GSP D 501 " pdb=" PG GSP D 501 " pdb=" O3G GSP D 501 " ideal model delta sigma weight residual 109.50 95.43 14.07 3.00e+00 1.11e-01 2.20e+01 angle pdb=" O2G GSP B 501 " pdb=" PG GSP B 501 " pdb=" O3G GSP B 501 " ideal model delta sigma weight residual 109.50 95.53 13.97 3.00e+00 1.11e-01 2.17e+01 angle pdb=" O2G GSP H 501 " pdb=" PG GSP H 501 " pdb=" O3G GSP H 501 " ideal model delta sigma weight residual 109.50 95.58 13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" O2G GSP I 501 " pdb=" PG GSP I 501 " pdb=" O3G GSP I 501 " ideal model delta sigma weight residual 109.50 95.61 13.89 3.00e+00 1.11e-01 2.15e+01 angle pdb=" O2G GSP F 501 " pdb=" PG GSP F 501 " pdb=" O3G GSP F 501 " ideal model delta sigma weight residual 109.50 95.63 13.87 3.00e+00 1.11e-01 2.14e+01 ... (remaining 56821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.39: 24623 32.39 - 64.78: 184 64.78 - 97.18: 31 97.18 - 129.57: 15 129.57 - 161.96: 17 Dihedral angle restraints: 24870 sinusoidal: 9942 harmonic: 14928 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -128.77 -161.96 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -130.88 -159.85 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C4' GTP K 501 " pdb=" C5' GTP K 501 " pdb=" O5' GTP K 501 " pdb=" PA GTP K 501 " ideal model delta sinusoidal sigma weight residual 260.87 104.42 156.45 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 24867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4516 0.051 - 0.103: 1374 0.103 - 0.154: 267 0.154 - 0.206: 47 0.206 - 0.257: 12 Chirality restraints: 6216 Sorted by residual: chirality pdb=" C2' GSP H 501 " pdb=" C1' GSP H 501 " pdb=" C3' GSP H 501 " pdb=" O2' GSP H 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C2' GSP B 501 " pdb=" C1' GSP B 501 " pdb=" C3' GSP B 501 " pdb=" O2' GSP B 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.72 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C2' GSP D 501 " pdb=" C1' GSP D 501 " pdb=" C3' GSP D 501 " pdb=" O2' GSP D 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.71 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 6213 not shown) Planarity restraints: 7398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP A 501 " 0.080 2.00e-02 2.50e+03 3.18e-02 3.04e+01 pdb=" C2 GTP A 501 " -0.009 2.00e-02 2.50e+03 pdb=" C4 GTP A 501 " -0.029 2.00e-02 2.50e+03 pdb=" C5 GTP A 501 " -0.016 2.00e-02 2.50e+03 pdb=" C6 GTP A 501 " 0.015 2.00e-02 2.50e+03 pdb=" C8 GTP A 501 " -0.023 2.00e-02 2.50e+03 pdb=" N1 GTP A 501 " 0.019 2.00e-02 2.50e+03 pdb=" N2 GTP A 501 " -0.002 2.00e-02 2.50e+03 pdb=" N3 GTP A 501 " -0.036 2.00e-02 2.50e+03 pdb=" N7 GTP A 501 " -0.019 2.00e-02 2.50e+03 pdb=" N9 GTP A 501 " -0.017 2.00e-02 2.50e+03 pdb=" O6 GTP A 501 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GSP I 501 " -0.063 2.00e-02 2.50e+03 2.60e-02 2.03e+01 pdb=" C2 GSP I 501 " 0.007 2.00e-02 2.50e+03 pdb=" C4 GSP I 501 " 0.022 2.00e-02 2.50e+03 pdb=" C5 GSP I 501 " 0.017 2.00e-02 2.50e+03 pdb=" C6 GSP I 501 " -0.008 2.00e-02 2.50e+03 pdb=" C8 GSP I 501 " 0.016 2.00e-02 2.50e+03 pdb=" N1 GSP I 501 " -0.013 2.00e-02 2.50e+03 pdb=" N2 GSP I 501 " 0.003 2.00e-02 2.50e+03 pdb=" N3 GSP I 501 " 0.027 2.00e-02 2.50e+03 pdb=" N7 GSP I 501 " 0.022 2.00e-02 2.50e+03 pdb=" N9 GSP I 501 " 0.008 2.00e-02 2.50e+03 pdb=" O6 GSP I 501 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP L 501 " -0.059 2.00e-02 2.50e+03 2.43e-02 1.78e+01 pdb=" C2 GTP L 501 " 0.002 2.00e-02 2.50e+03 pdb=" C4 GTP L 501 " 0.019 2.00e-02 2.50e+03 pdb=" C5 GTP L 501 " 0.008 2.00e-02 2.50e+03 pdb=" C6 GTP L 501 " -0.020 2.00e-02 2.50e+03 pdb=" C8 GTP L 501 " 0.023 2.00e-02 2.50e+03 pdb=" N1 GTP L 501 " -0.026 2.00e-02 2.50e+03 pdb=" N2 GTP L 501 " 0.016 2.00e-02 2.50e+03 pdb=" N3 GTP L 501 " 0.025 2.00e-02 2.50e+03 pdb=" N7 GTP L 501 " 0.016 2.00e-02 2.50e+03 pdb=" N9 GTP L 501 " 0.013 2.00e-02 2.50e+03 pdb=" O6 GTP L 501 " -0.016 2.00e-02 2.50e+03 ... (remaining 7395 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 388 2.62 - 3.19: 34553 3.19 - 3.76: 61548 3.76 - 4.33: 86261 4.33 - 4.90: 140626 Nonbonded interactions: 323376 Sorted by model distance: nonbonded pdb=" O3G GTP L 501 " pdb="MG MG L 502 " model vdw 2.046 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 2.054 2.170 nonbonded pdb=" O2G GTP J 501 " pdb="MG MG J 502 " model vdw 2.057 2.170 nonbonded pdb=" O2B GTP J 501 " pdb="MG MG J 502 " model vdw 2.061 2.170 nonbonded pdb=" O2B GTP L 501 " pdb="MG MG L 502 " model vdw 2.069 2.170 ... (remaining 323371 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: 0.15 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'C' selection = chain 'L' selection = chain 'A' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'D' selection = chain 'I' selection = chain 'B' selection = chain 'H' } 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 group one per residue 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.080 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 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 : 0.006 0.200 41820 Z= 0.294 Angle : 0.907 14.069 56826 Z= 0.482 Chirality : 0.051 0.257 6216 Planarity : 0.007 0.064 7398 Dihedral : 11.403 161.960 15294 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.08), residues: 5130 helix: -3.93 (0.05), residues: 2064 sheet: -1.47 (0.17), residues: 804 loop : -2.55 (0.10), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 390 TYR 0.022 0.002 TYR K 224 PHE 0.015 0.002 PHE A 49 TRP 0.027 0.002 TRP G 101 HIS 0.010 0.002 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00625 (41820) covalent geometry : angle 0.90717 (56826) hydrogen bonds : bond 0.32115 ( 1566) hydrogen bonds : angle 9.22964 ( 4644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1848 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1848 time to evaluate : 1.683 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: E 2 ARG cc_start: 0.8487 (mtm180) cc_final: 0.8127 (ptt-90) REVERT: E 18 ASN cc_start: 0.9299 (m-40) cc_final: 0.9048 (t0) REVERT: E 21 TRP cc_start: 0.9606 (m100) cc_final: 0.9132 (m100) REVERT: E 85 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8008 (tp-100) REVERT: E 88 HIS cc_start: 0.7454 (t-170) cc_final: 0.6592 (m-70) REVERT: E 121 ARG cc_start: 0.8045 (mmm160) cc_final: 0.7664 (tpt170) REVERT: E 127 ASP cc_start: 0.9015 (m-30) cc_final: 0.8644 (m-30) REVERT: E 129 CYS cc_start: 0.7683 (m) cc_final: 0.7156 (p) REVERT: E 160 ASP cc_start: 0.8915 (t70) cc_final: 0.8155 (t0) REVERT: E 163 LYS cc_start: 0.8683 (mtpp) cc_final: 0.8137 (mmtt) REVERT: E 202 PHE cc_start: 0.8759 (m-80) cc_final: 0.8336 (m-10) REVERT: E 217 LEU cc_start: 0.9055 (mt) cc_final: 0.8515 (mt) REVERT: E 305 CYS cc_start: 0.8649 (m) cc_final: 0.8402 (m) REVERT: E 343 PHE cc_start: 0.8578 (m-80) cc_final: 0.8376 (m-10) REVERT: E 345 ASP cc_start: 0.8228 (t70) cc_final: 0.7858 (t0) REVERT: E 355 ILE cc_start: 0.9062 (mp) cc_final: 0.8343 (mt) REVERT: E 367 ASP cc_start: 0.8779 (p0) cc_final: 0.8563 (p0) REVERT: E 368 LEU cc_start: 0.9329 (mp) cc_final: 0.9105 (mp) REVERT: E 376 CYS cc_start: 0.8981 (t) cc_final: 0.8067 (t) REVERT: E 425 MET cc_start: 0.9366 (tpp) cc_final: 0.9115 (tpp) REVERT: E 431 ASP cc_start: 0.8664 (m-30) cc_final: 0.8330 (t0) REVERT: F 14 ASN cc_start: 0.9228 (m-40) cc_final: 0.8869 (m-40) REVERT: F 21 TRP cc_start: 0.9348 (m100) cc_final: 0.8958 (m100) REVERT: F 51 TYR cc_start: 0.8966 (m-80) cc_final: 0.8630 (m-80) REVERT: F 86 ARG cc_start: 0.7045 (mtp180) cc_final: 0.5221 (mmm160) REVERT: F 91 VAL cc_start: 0.9521 (t) cc_final: 0.9289 (p) REVERT: F 100 ASN cc_start: 0.8856 (t0) cc_final: 0.8611 (t0) REVERT: F 107 THR cc_start: 0.9136 (m) cc_final: 0.8713 (m) REVERT: F 152 ILE cc_start: 0.9397 (mt) cc_final: 0.9013 (mm) REVERT: F 163 ILE cc_start: 0.8981 (pp) cc_final: 0.8735 (mt) REVERT: F 164 MET cc_start: 0.8464 (tpt) cc_final: 0.8161 (tpt) REVERT: F 239 CYS cc_start: 0.8506 (m) cc_final: 0.8252 (t) REVERT: F 265 PHE cc_start: 0.9243 (m-80) cc_final: 0.8674 (m-10) REVERT: F 276 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8297 (mmp80) REVERT: F 297 LYS cc_start: 0.8743 (ptpt) cc_final: 0.7672 (mppt) REVERT: F 300 MET cc_start: 0.8517 (mtt) cc_final: 0.8274 (mtm) REVERT: F 340 TYR cc_start: 0.8674 (m-80) cc_final: 0.8458 (m-80) REVERT: F 355 ASP cc_start: 0.8276 (m-30) cc_final: 0.7564 (m-30) REVERT: F 367 PHE cc_start: 0.9149 (t80) cc_final: 0.8890 (t80) REVERT: F 377 LEU cc_start: 0.8114 (tp) cc_final: 0.7882 (tp) REVERT: F 406 MET cc_start: 0.8695 (tpp) cc_final: 0.8103 (mpp) REVERT: F 427 ASP cc_start: 0.7995 (m-30) cc_final: 0.7433 (t70) REVERT: J 2 ARG cc_start: 0.8502 (mtm180) cc_final: 0.8205 (ptt-90) REVERT: J 18 ASN cc_start: 0.9310 (m-40) cc_final: 0.9027 (t0) REVERT: J 21 TRP cc_start: 0.9621 (m100) cc_final: 0.9146 (m100) REVERT: J 85 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8077 (tp40) REVERT: J 88 HIS cc_start: 0.7785 (t-170) cc_final: 0.6730 (m-70) REVERT: J 121 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7652 (tpt170) REVERT: J 127 ASP cc_start: 0.8950 (m-30) cc_final: 0.8569 (m-30) REVERT: J 129 CYS cc_start: 0.7818 (m) cc_final: 0.7548 (p) REVERT: J 160 ASP cc_start: 0.8986 (t70) cc_final: 0.7475 (t70) REVERT: J 163 LYS cc_start: 0.8712 (mtpp) cc_final: 0.8173 (mptt) REVERT: J 202 PHE cc_start: 0.8757 (m-80) cc_final: 0.8420 (m-10) REVERT: J 210 TYR cc_start: 0.8782 (m-80) cc_final: 0.8392 (m-80) REVERT: J 217 LEU cc_start: 0.9064 (mt) cc_final: 0.8554 (mt) REVERT: J 221 ARG cc_start: 0.8657 (mtt90) cc_final: 0.8398 (mmt90) REVERT: J 234 ILE cc_start: 0.8941 (mt) cc_final: 0.8580 (mm) REVERT: J 235 VAL cc_start: 0.8850 (t) cc_final: 0.8555 (t) REVERT: J 256 GLN cc_start: 0.8906 (pt0) cc_final: 0.8658 (tm-30) REVERT: J 271 THR cc_start: 0.9053 (m) cc_final: 0.8774 (p) REVERT: J 297 GLU cc_start: 0.9013 (tt0) cc_final: 0.8788 (tm-30) REVERT: J 304 LYS cc_start: 0.9204 (tppt) cc_final: 0.8950 (mmmt) REVERT: J 305 CYS cc_start: 0.8425 (m) cc_final: 0.7928 (m) REVERT: J 332 ILE cc_start: 0.9592 (mt) cc_final: 0.9325 (pt) REVERT: J 343 PHE cc_start: 0.8649 (m-80) cc_final: 0.8398 (m-10) REVERT: J 345 ASP cc_start: 0.8505 (t70) cc_final: 0.7974 (t0) REVERT: J 355 ILE cc_start: 0.9171 (mp) cc_final: 0.8554 (mm) REVERT: J 357 TYR cc_start: 0.7328 (m-80) cc_final: 0.7082 (m-10) REVERT: J 367 ASP cc_start: 0.8879 (p0) cc_final: 0.8635 (p0) REVERT: J 380 ASN cc_start: 0.9109 (t0) cc_final: 0.8570 (t0) REVERT: J 425 MET cc_start: 0.9436 (tpp) cc_final: 0.9168 (tpp) REVERT: C 2 ARG cc_start: 0.8535 (mtm180) cc_final: 0.8126 (ptt-90) REVERT: C 25 CYS cc_start: 0.8655 (m) cc_final: 0.8131 (m) REVERT: C 85 GLN cc_start: 0.8808 (mm-40) cc_final: 0.7833 (mm-40) REVERT: C 91 GLN cc_start: 0.8460 (mt0) cc_final: 0.8254 (mt0) REVERT: C 157 LEU cc_start: 0.9627 (mt) cc_final: 0.9295 (mt) REVERT: C 160 ASP cc_start: 0.8975 (t70) cc_final: 0.8085 (t70) REVERT: C 163 LYS cc_start: 0.8476 (mtpp) cc_final: 0.8156 (mptt) REVERT: C 205 ASP cc_start: 0.8651 (t0) cc_final: 0.8352 (t70) REVERT: C 210 TYR cc_start: 0.8274 (m-80) cc_final: 0.7817 (m-80) REVERT: C 211 ASP cc_start: 0.8567 (t0) cc_final: 0.7828 (t70) REVERT: C 220 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7552 (tp30) REVERT: C 256 GLN cc_start: 0.8813 (pt0) cc_final: 0.8560 (pt0) REVERT: C 266 HIS cc_start: 0.9128 (p-80) cc_final: 0.8871 (p90) REVERT: C 305 CYS cc_start: 0.8685 (m) cc_final: 0.8438 (m) REVERT: C 357 TYR cc_start: 0.7193 (m-80) cc_final: 0.6378 (m-80) REVERT: C 376 CYS cc_start: 0.9076 (t) cc_final: 0.8317 (t) REVERT: C 380 ASN cc_start: 0.8698 (t0) cc_final: 0.7754 (t0) REVERT: C 401 LYS cc_start: 0.9243 (mmtt) cc_final: 0.9027 (mmmm) REVERT: C 425 MET cc_start: 0.9174 (tpp) cc_final: 0.8942 (tpp) REVERT: L 2 ARG cc_start: 0.8402 (mtm180) cc_final: 0.8035 (ptt-90) REVERT: L 18 ASN cc_start: 0.9162 (m-40) cc_final: 0.8889 (t0) REVERT: L 25 CYS cc_start: 0.8621 (m) cc_final: 0.8083 (m) REVERT: L 85 GLN cc_start: 0.8822 (mm-40) cc_final: 0.7865 (mm-40) REVERT: L 91 GLN cc_start: 0.8485 (mt0) cc_final: 0.8144 (mt0) REVERT: L 121 ARG cc_start: 0.8338 (mmm160) cc_final: 0.7933 (mmm160) REVERT: L 145 THR cc_start: 0.8837 (m) cc_final: 0.8443 (m) REVERT: L 160 ASP cc_start: 0.8879 (t70) cc_final: 0.7522 (m-30) REVERT: L 163 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8196 (mptt) REVERT: L 183 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8553 (pt0) REVERT: L 209 ILE cc_start: 0.9420 (mt) cc_final: 0.9131 (mm) REVERT: L 210 TYR cc_start: 0.8511 (m-80) cc_final: 0.8045 (m-80) REVERT: L 211 ASP cc_start: 0.8783 (t0) cc_final: 0.7769 (t70) REVERT: L 215 ARG cc_start: 0.8495 (ttp-110) cc_final: 0.8289 (mtm180) REVERT: L 230 LEU cc_start: 0.9051 (mp) cc_final: 0.8779 (tt) REVERT: L 253 THR cc_start: 0.8892 (m) cc_final: 0.8670 (t) REVERT: L 256 GLN cc_start: 0.8591 (pt0) cc_final: 0.7794 (tm-30) REVERT: L 266 HIS cc_start: 0.9095 (p-80) cc_final: 0.8534 (p90) REVERT: L 302 MET cc_start: 0.8961 (mtt) cc_final: 0.8170 (mtt) REVERT: L 308 ARG cc_start: 0.9030 (mtm180) cc_final: 0.8807 (mtm-85) REVERT: L 345 ASP cc_start: 0.8575 (t70) cc_final: 0.8366 (t0) REVERT: L 355 ILE cc_start: 0.9078 (mp) cc_final: 0.8721 (mp) REVERT: L 357 TYR cc_start: 0.7181 (m-80) cc_final: 0.6564 (m-80) REVERT: L 376 CYS cc_start: 0.9196 (t) cc_final: 0.8283 (t) REVERT: L 378 LEU cc_start: 0.8693 (mt) cc_final: 0.8459 (mp) REVERT: L 380 ASN cc_start: 0.9006 (t0) cc_final: 0.7884 (t0) REVERT: L 430 LYS cc_start: 0.8603 (ptmm) cc_final: 0.8261 (mmmt) REVERT: A 21 TRP cc_start: 0.9489 (m100) cc_final: 0.8956 (m100) REVERT: A 85 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8030 (mm-40) REVERT: A 129 CYS cc_start: 0.8049 (m) cc_final: 0.7569 (p) REVERT: A 160 ASP cc_start: 0.8894 (t70) cc_final: 0.8264 (t70) REVERT: A 163 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8188 (mptt) REVERT: A 177 VAL cc_start: 0.8854 (t) cc_final: 0.8343 (p) REVERT: A 202 PHE cc_start: 0.8695 (m-80) cc_final: 0.8240 (m-10) REVERT: A 205 ASP cc_start: 0.8660 (t0) cc_final: 0.8369 (t70) REVERT: A 210 TYR cc_start: 0.8863 (m-80) cc_final: 0.8234 (m-80) REVERT: A 211 ASP cc_start: 0.8682 (t0) cc_final: 0.7830 (t70) REVERT: A 217 LEU cc_start: 0.9091 (mt) cc_final: 0.8821 (mt) REVERT: A 345 ASP cc_start: 0.8252 (t70) cc_final: 0.7828 (t0) REVERT: A 376 CYS cc_start: 0.8880 (t) cc_final: 0.8438 (t) REVERT: A 402 ARG cc_start: 0.7964 (mmt-90) cc_final: 0.7752 (mmt180) REVERT: A 415 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7585 (tm-30) REVERT: A 425 MET cc_start: 0.9334 (tpp) cc_final: 0.8971 (tpt) REVERT: K 2 ARG cc_start: 0.8737 (mtm180) cc_final: 0.8003 (ptt-90) REVERT: K 18 ASN cc_start: 0.9141 (m-40) cc_final: 0.8816 (t0) REVERT: K 21 TRP cc_start: 0.9547 (m100) cc_final: 0.9027 (m100) REVERT: K 85 GLN cc_start: 0.8678 (mm-40) cc_final: 0.7789 (tp-100) REVERT: K 125 LEU cc_start: 0.9341 (mt) cc_final: 0.9111 (mt) REVERT: K 129 CYS cc_start: 0.7951 (m) cc_final: 0.7645 (p) REVERT: K 152 LEU cc_start: 0.9328 (tp) cc_final: 0.8977 (tp) REVERT: K 157 LEU cc_start: 0.9397 (mt) cc_final: 0.9107 (mt) REVERT: K 160 ASP cc_start: 0.8863 (t70) cc_final: 0.8211 (t0) REVERT: K 163 LYS cc_start: 0.8735 (mtpp) cc_final: 0.8356 (mptt) REVERT: K 172 TYR cc_start: 0.8570 (t80) cc_final: 0.8323 (t80) REVERT: K 177 VAL cc_start: 0.8647 (t) cc_final: 0.8208 (p) REVERT: K 202 PHE cc_start: 0.8663 (m-80) cc_final: 0.8057 (m-10) REVERT: K 205 ASP cc_start: 0.8356 (t0) cc_final: 0.8013 (t70) REVERT: K 210 TYR cc_start: 0.8957 (m-80) cc_final: 0.8391 (m-80) REVERT: K 211 ASP cc_start: 0.8871 (t0) cc_final: 0.8517 (t70) REVERT: K 227 LEU cc_start: 0.9403 (mp) cc_final: 0.9179 (mp) REVERT: K 256 GLN cc_start: 0.8760 (pt0) cc_final: 0.8077 (tm-30) REVERT: K 345 ASP cc_start: 0.8412 (t70) cc_final: 0.8134 (t0) REVERT: K 355 ILE cc_start: 0.8930 (mp) cc_final: 0.8590 (mp) REVERT: K 357 TYR cc_start: 0.6723 (m-80) cc_final: 0.6351 (m-80) REVERT: K 376 CYS cc_start: 0.9117 (t) cc_final: 0.8764 (t) REVERT: K 380 ASN cc_start: 0.9055 (t0) cc_final: 0.7885 (t0) REVERT: K 425 MET cc_start: 0.9374 (tpp) cc_final: 0.8949 (tpt) REVERT: K 430 LYS cc_start: 0.8713 (ptmm) cc_final: 0.8436 (tmtt) REVERT: G 14 ASN cc_start: 0.9194 (m-40) cc_final: 0.8671 (m-40) REVERT: G 21 TRP cc_start: 0.9363 (m100) cc_final: 0.8634 (m100) REVERT: G 51 TYR cc_start: 0.8850 (m-80) cc_final: 0.8646 (m-80) REVERT: G 81 PHE cc_start: 0.7427 (m-80) cc_final: 0.7163 (m-80) REVERT: G 86 ARG cc_start: 0.7118 (mtp180) cc_final: 0.5333 (mmm160) REVERT: G 91 VAL cc_start: 0.9515 (t) cc_final: 0.9221 (p) REVERT: G 115 SER cc_start: 0.9596 (m) cc_final: 0.9318 (p) REVERT: G 152 ILE cc_start: 0.9331 (mt) cc_final: 0.9074 (mm) REVERT: G 195 ASN cc_start: 0.8177 (m-40) cc_final: 0.7705 (m-40) REVERT: G 257 MET cc_start: 0.8865 (mmp) cc_final: 0.8615 (mmp) REVERT: G 265 PHE cc_start: 0.9302 (m-80) cc_final: 0.9093 (m-10) REVERT: G 297 LYS cc_start: 0.8655 (ptpt) cc_final: 0.7552 (mppt) REVERT: G 300 MET cc_start: 0.8547 (mtt) cc_final: 0.8297 (mtm) REVERT: G 306 ARG cc_start: 0.8844 (mtt90) cc_final: 0.8630 (mtt180) REVERT: G 312 THR cc_start: 0.9078 (p) cc_final: 0.8756 (p) REVERT: G 322 SER cc_start: 0.9043 (m) cc_final: 0.8723 (m) REVERT: G 355 ASP cc_start: 0.8222 (m-30) cc_final: 0.7732 (m-30) REVERT: G 367 PHE cc_start: 0.9144 (t80) cc_final: 0.8866 (t80) REVERT: G 377 LEU cc_start: 0.8064 (tp) cc_final: 0.7768 (tp) REVERT: G 406 MET cc_start: 0.8623 (tpp) cc_final: 0.8177 (mpp) REVERT: G 423 GLN cc_start: 0.9015 (tp-100) cc_final: 0.8733 (tp40) REVERT: G 427 ASP cc_start: 0.8030 (m-30) cc_final: 0.7527 (t70) REVERT: D 6 HIS cc_start: 0.9229 (t70) cc_final: 0.9014 (t-90) REVERT: D 14 ASN cc_start: 0.9242 (m-40) cc_final: 0.8761 (m-40) REVERT: D 64 ILE cc_start: 0.9289 (mt) cc_final: 0.9060 (mt) REVERT: D 100 ASN cc_start: 0.8959 (t0) cc_final: 0.8677 (t0) REVERT: D 103 LYS cc_start: 0.9448 (mttt) cc_final: 0.9023 (mttt) REVERT: D 107 THR cc_start: 0.9086 (m) cc_final: 0.8651 (m) REVERT: D 130 LEU cc_start: 0.9047 (tp) cc_final: 0.8634 (tt) REVERT: D 152 ILE cc_start: 0.9434 (mt) cc_final: 0.9222 (mm) REVERT: D 163 ILE cc_start: 0.9135 (pp) cc_final: 0.8684 (mt) REVERT: D 164 MET cc_start: 0.8770 (tpt) cc_final: 0.8460 (tpt) REVERT: D 195 ASN cc_start: 0.8178 (m-40) cc_final: 0.7391 (m-40) REVERT: D 199 THR cc_start: 0.8739 (m) cc_final: 0.8169 (p) REVERT: D 205 GLU cc_start: 0.8379 (tp30) cc_final: 0.8072 (tp30) REVERT: D 207 LEU cc_start: 0.9492 (mp) cc_final: 0.9004 (tp) REVERT: D 239 CYS cc_start: 0.8223 (m) cc_final: 0.7800 (t) REVERT: D 247 ASN cc_start: 0.8530 (m-40) cc_final: 0.7906 (m-40) REVERT: D 276 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.7971 (mmp80) REVERT: D 293 MET cc_start: 0.7893 (mtm) cc_final: 0.7637 (mtt) REVERT: D 306 ARG cc_start: 0.8845 (mtt90) cc_final: 0.8348 (ttm110) REVERT: D 312 THR cc_start: 0.9156 (p) cc_final: 0.8824 (t) REVERT: D 313 VAL cc_start: 0.9197 (t) cc_final: 0.8653 (m) REVERT: D 323 MET cc_start: 0.8578 (mmm) cc_final: 0.7909 (mmm) REVERT: D 324 LYS cc_start: 0.9201 (tttm) cc_final: 0.8553 (tttp) REVERT: D 327 ASP cc_start: 0.8887 (m-30) cc_final: 0.8480 (p0) REVERT: D 349 VAL cc_start: 0.9418 (t) cc_final: 0.9162 (t) REVERT: D 377 LEU cc_start: 0.8415 (tp) cc_final: 0.7959 (tp) REVERT: D 379 LYS cc_start: 0.9133 (mtpt) cc_final: 0.8693 (ttmm) REVERT: D 397 TRP cc_start: 0.8535 (m100) cc_final: 0.8254 (m100) REVERT: D 406 MET cc_start: 0.8363 (tpp) cc_final: 0.7983 (mpp) REVERT: D 427 ASP cc_start: 0.7805 (m-30) cc_final: 0.7317 (t70) REVERT: I 14 ASN cc_start: 0.9191 (m-40) cc_final: 0.8614 (m-40) REVERT: I 52 ASN cc_start: 0.9142 (m-40) cc_final: 0.8839 (m-40) REVERT: I 73 MET cc_start: 0.8812 (mmt) cc_final: 0.8569 (mmm) REVERT: I 74 ASP cc_start: 0.8541 (t70) cc_final: 0.8273 (t70) REVERT: I 103 LYS cc_start: 0.9363 (mttt) cc_final: 0.9012 (mttt) REVERT: I 107 THR cc_start: 0.9046 (m) cc_final: 0.8747 (m) REVERT: I 130 LEU cc_start: 0.9222 (tp) cc_final: 0.8884 (tt) REVERT: I 143 THR cc_start: 0.9327 (m) cc_final: 0.9052 (p) REVERT: I 163 ILE cc_start: 0.9078 (pp) cc_final: 0.8838 (mt) REVERT: I 170 VAL cc_start: 0.9145 (t) cc_final: 0.8869 (m) REVERT: I 187 LEU cc_start: 0.9336 (mt) cc_final: 0.9112 (mp) REVERT: I 195 ASN cc_start: 0.8383 (m-40) cc_final: 0.7792 (m-40) REVERT: I 199 THR cc_start: 0.8736 (m) cc_final: 0.8238 (p) REVERT: I 205 GLU cc_start: 0.8363 (tp30) cc_final: 0.7571 (tp30) REVERT: I 207 LEU cc_start: 0.9403 (mp) cc_final: 0.8851 (tp) REVERT: I 247 ASN cc_start: 0.8787 (m-40) cc_final: 0.7888 (m-40) REVERT: I 276 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.7891 (mmp80) REVERT: I 300 MET cc_start: 0.8215 (mtt) cc_final: 0.7942 (mtm) REVERT: I 306 ARG cc_start: 0.8889 (mtt90) cc_final: 0.8585 (mpt180) REVERT: I 312 THR cc_start: 0.9187 (p) cc_final: 0.8863 (t) REVERT: I 313 VAL cc_start: 0.9220 (t) cc_final: 0.8804 (m) REVERT: I 323 MET cc_start: 0.8427 (mmm) cc_final: 0.7742 (mmm) REVERT: I 324 LYS cc_start: 0.9146 (tttm) cc_final: 0.8518 (tttp) REVERT: I 327 ASP cc_start: 0.8741 (m-30) cc_final: 0.8429 (p0) REVERT: I 340 TYR cc_start: 0.8770 (m-80) cc_final: 0.8415 (m-10) REVERT: I 349 VAL cc_start: 0.9433 (t) cc_final: 0.9151 (t) REVERT: I 363 MET cc_start: 0.8862 (ptp) cc_final: 0.8640 (pmm) REVERT: I 377 LEU cc_start: 0.8256 (tp) cc_final: 0.7897 (tp) REVERT: I 379 LYS cc_start: 0.9160 (mtpt) cc_final: 0.8892 (ttmm) REVERT: I 397 TRP cc_start: 0.8473 (m100) cc_final: 0.7968 (m-10) REVERT: I 406 MET cc_start: 0.8541 (tpp) cc_final: 0.8142 (mpp) REVERT: I 415 MET cc_start: 0.9166 (ttm) cc_final: 0.8740 (ttp) REVERT: I 427 ASP cc_start: 0.7654 (m-30) cc_final: 0.7421 (t70) REVERT: B 14 ASN cc_start: 0.9127 (m-40) cc_final: 0.8788 (m-40) REVERT: B 37 HIS cc_start: 0.7636 (m90) cc_final: 0.7264 (m90) REVERT: B 65 LEU cc_start: 0.9014 (mp) cc_final: 0.8684 (mp) REVERT: B 91 VAL cc_start: 0.9675 (t) cc_final: 0.9471 (p) REVERT: B 107 THR cc_start: 0.9175 (m) cc_final: 0.8657 (m) REVERT: B 130 LEU cc_start: 0.8814 (tp) cc_final: 0.8475 (tt) REVERT: B 203 ASP cc_start: 0.8036 (m-30) cc_final: 0.7832 (t0) REVERT: B 257 MET cc_start: 0.8842 (mmp) cc_final: 0.8212 (mmm) REVERT: B 297 LYS cc_start: 0.8836 (ptpt) cc_final: 0.7381 (mppt) REVERT: B 306 ARG cc_start: 0.8796 (mtt90) cc_final: 0.8305 (mpp80) REVERT: B 312 THR cc_start: 0.8927 (p) cc_final: 0.8476 (t) REVERT: B 313 VAL cc_start: 0.9110 (t) cc_final: 0.8789 (m) REVERT: B 343 GLU cc_start: 0.8420 (tp30) cc_final: 0.8171 (tp30) REVERT: B 397 TRP cc_start: 0.8745 (m100) cc_final: 0.8499 (m100) REVERT: B 406 MET cc_start: 0.8557 (tpp) cc_final: 0.8150 (tpp) REVERT: B 427 ASP cc_start: 0.8134 (m-30) cc_final: 0.7591 (t70) REVERT: H 4 ILE cc_start: 0.9581 (mt) cc_final: 0.9376 (mm) REVERT: H 14 ASN cc_start: 0.9150 (m-40) cc_final: 0.8616 (m-40) REVERT: H 21 TRP cc_start: 0.9418 (m100) cc_final: 0.9180 (m100) REVERT: H 91 VAL cc_start: 0.9706 (t) cc_final: 0.9464 (p) REVERT: H 107 THR cc_start: 0.9209 (m) cc_final: 0.8733 (m) REVERT: H 115 SER cc_start: 0.9674 (m) cc_final: 0.9431 (p) REVERT: H 130 LEU cc_start: 0.9071 (tp) cc_final: 0.8681 (tt) REVERT: H 152 ILE cc_start: 0.9355 (mt) cc_final: 0.9094 (mm) REVERT: H 155 ILE cc_start: 0.9566 (mt) cc_final: 0.9029 (mt) REVERT: H 178 THR cc_start: 0.8693 (m) cc_final: 0.8408 (m) REVERT: H 257 MET cc_start: 0.8889 (mmp) cc_final: 0.8315 (mmm) REVERT: H 297 LYS cc_start: 0.8687 (ptpt) cc_final: 0.7382 (mppt) REVERT: H 306 ARG cc_start: 0.8820 (mtt90) cc_final: 0.8354 (mpp80) REVERT: H 312 THR cc_start: 0.8898 (p) cc_final: 0.8485 (t) REVERT: H 313 VAL cc_start: 0.9238 (t) cc_final: 0.8946 (m) REVERT: H 349 VAL cc_start: 0.9413 (t) cc_final: 0.9198 (t) REVERT: H 379 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8630 (ttmm) REVERT: H 392 LYS cc_start: 0.9003 (mtmt) cc_final: 0.8786 (mtmm) REVERT: H 397 TRP cc_start: 0.8688 (m100) cc_final: 0.8239 (m-10) REVERT: H 406 MET cc_start: 0.8570 (tpp) cc_final: 0.8032 (tpp) REVERT: H 427 ASP cc_start: 0.8078 (m-30) cc_final: 0.7616 (t70) outliers start: 0 outliers final: 0 residues processed: 1848 average time/residue: 0.2621 time to fit residues: 786.3423 Evaluate side-chains 1111 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1111 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 494 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN F 131 GLN F 190 HIS F 226 ASN ** F 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 HIS F 396 HIS J 15 GLN ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 HIS ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 192 HIS ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 ASN C 15 GLN ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 107 HIS C 128 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN L 15 GLN ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 HIS L 128 GLN ** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 192 HIS L 197 HIS L 356 ASN A 15 GLN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS A 128 GLN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN A 356 ASN K 15 GLN ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 HIS ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN K 192 HIS ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN G 131 GLN G 190 HIS G 226 ASN ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 396 HIS D 131 GLN D 190 HIS D 226 ASN ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN I 190 HIS I 226 ASN I 247 ASN ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 396 HIS B 131 GLN B 190 HIS B 226 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 HIS H 131 GLN H 190 HIS H 226 ASN ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 396 HIS Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.093747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.083076 restraints weight = 94117.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.085828 restraints weight = 51708.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.087694 restraints weight = 32105.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.089013 restraints weight = 21629.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.089947 restraints weight = 15397.155| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 41820 Z= 0.217 Angle : 0.662 12.135 56826 Z= 0.347 Chirality : 0.046 0.180 6216 Planarity : 0.005 0.050 7398 Dihedral : 11.344 166.652 5778 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.02 % Allowed : 2.60 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.10), residues: 5130 helix: -1.50 (0.09), residues: 2250 sheet: -0.32 (0.19), residues: 690 loop : -2.02 (0.11), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 121 TYR 0.023 0.002 TYR E 224 PHE 0.022 0.002 PHE F 341 TRP 0.017 0.002 TRP L 21 HIS 0.006 0.001 HIS L 283 Details of bonding type rmsd covalent geometry : bond 0.00476 (41820) covalent geometry : angle 0.66167 (56826) hydrogen bonds : bond 0.05901 ( 1566) hydrogen bonds : angle 5.34746 ( 4644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1309 time to evaluate : 1.568 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: E 2 ARG cc_start: 0.8617 (mtm180) cc_final: 0.8109 (ptt-90) REVERT: E 21 TRP cc_start: 0.9515 (m100) cc_final: 0.9107 (m100) REVERT: E 36 MET cc_start: 0.8844 (ptm) cc_final: 0.8516 (ptm) REVERT: E 85 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8056 (tp40) REVERT: E 102 ASN cc_start: 0.8417 (t0) cc_final: 0.7720 (t0) REVERT: E 121 ARG cc_start: 0.7614 (mmm160) cc_final: 0.7271 (tpt170) REVERT: E 127 ASP cc_start: 0.9090 (m-30) cc_final: 0.8784 (m-30) REVERT: E 132 LEU cc_start: 0.7989 (tt) cc_final: 0.7782 (tt) REVERT: E 152 LEU cc_start: 0.9234 (tp) cc_final: 0.8807 (tp) REVERT: E 163 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8006 (mmtt) REVERT: E 202 PHE cc_start: 0.9145 (m-80) cc_final: 0.8393 (m-10) REVERT: E 203 MET cc_start: 0.9171 (mmp) cc_final: 0.8844 (mmp) REVERT: E 230 LEU cc_start: 0.9093 (mp) cc_final: 0.8826 (tt) REVERT: E 235 VAL cc_start: 0.8866 (t) cc_final: 0.8584 (t) REVERT: E 266 HIS cc_start: 0.8990 (p90) cc_final: 0.8695 (p90) REVERT: E 302 MET cc_start: 0.8883 (mtp) cc_final: 0.8565 (mtp) REVERT: E 313 MET cc_start: 0.7573 (ptp) cc_final: 0.7301 (ptp) REVERT: E 355 ILE cc_start: 0.8877 (mp) cc_final: 0.8662 (mt) REVERT: E 367 ASP cc_start: 0.8714 (p0) cc_final: 0.8184 (p0) REVERT: E 368 LEU cc_start: 0.9327 (mp) cc_final: 0.9061 (mp) REVERT: E 377 MET cc_start: 0.8300 (ttp) cc_final: 0.7296 (ttp) REVERT: E 380 ASN cc_start: 0.8849 (t0) cc_final: 0.8215 (t0) REVERT: F 14 ASN cc_start: 0.9253 (m-40) cc_final: 0.8931 (m-40) REVERT: F 21 TRP cc_start: 0.9347 (m100) cc_final: 0.8652 (m100) REVERT: F 45 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8090 (mt-10) REVERT: F 51 TYR cc_start: 0.8578 (m-80) cc_final: 0.8359 (m-80) REVERT: F 91 VAL cc_start: 0.9557 (t) cc_final: 0.9341 (p) REVERT: F 203 ASP cc_start: 0.8279 (t0) cc_final: 0.7375 (m-30) REVERT: F 205 GLU cc_start: 0.8269 (tp30) cc_final: 0.7653 (tp30) REVERT: F 300 MET cc_start: 0.8384 (mtt) cc_final: 0.8028 (mtm) REVERT: F 320 ARG cc_start: 0.7613 (mmt180) cc_final: 0.6932 (mpt180) REVERT: F 367 PHE cc_start: 0.8998 (t80) cc_final: 0.8757 (t80) REVERT: F 375 GLN cc_start: 0.8592 (pp30) cc_final: 0.8210 (pp30) REVERT: F 427 ASP cc_start: 0.8053 (m-30) cc_final: 0.7613 (t70) REVERT: J 2 ARG cc_start: 0.8573 (mtm180) cc_final: 0.8083 (ptt-90) REVERT: J 18 ASN cc_start: 0.9130 (m-40) cc_final: 0.8909 (t0) REVERT: J 21 TRP cc_start: 0.9534 (m100) cc_final: 0.9104 (m100) REVERT: J 24 TYR cc_start: 0.8817 (m-10) cc_final: 0.8471 (m-80) REVERT: J 36 MET cc_start: 0.8736 (ptm) cc_final: 0.8292 (ptm) REVERT: J 85 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8045 (tp40) REVERT: J 127 ASP cc_start: 0.8844 (m-30) cc_final: 0.8621 (m-30) REVERT: J 152 LEU cc_start: 0.9238 (tp) cc_final: 0.8861 (tp) REVERT: J 163 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8037 (mmtt) REVERT: J 172 TYR cc_start: 0.8601 (t80) cc_final: 0.8340 (t80) REVERT: J 183 GLU cc_start: 0.8238 (pt0) cc_final: 0.8030 (pt0) REVERT: J 202 PHE cc_start: 0.9011 (m-80) cc_final: 0.8045 (m-10) REVERT: J 203 MET cc_start: 0.9162 (mmp) cc_final: 0.8889 (mmp) REVERT: J 230 LEU cc_start: 0.9059 (mp) cc_final: 0.8787 (tt) REVERT: J 256 GLN cc_start: 0.8987 (pt0) cc_final: 0.8414 (tm-30) REVERT: J 266 HIS cc_start: 0.8906 (p90) cc_final: 0.8671 (p90) REVERT: J 271 THR cc_start: 0.9153 (m) cc_final: 0.8766 (p) REVERT: J 302 MET cc_start: 0.8812 (mtm) cc_final: 0.8269 (mtm) REVERT: J 343 PHE cc_start: 0.8610 (m-80) cc_final: 0.8397 (m-10) REVERT: J 345 ASP cc_start: 0.8509 (t70) cc_final: 0.8273 (t0) REVERT: J 367 ASP cc_start: 0.8711 (p0) cc_final: 0.8335 (p0) REVERT: J 382 THR cc_start: 0.9312 (p) cc_final: 0.8876 (p) REVERT: J 398 MET cc_start: 0.9080 (mmm) cc_final: 0.8747 (mmt) REVERT: C 85 GLN cc_start: 0.8561 (mm-40) cc_final: 0.7668 (mm-40) REVERT: C 88 HIS cc_start: 0.7981 (t-90) cc_final: 0.7438 (t-170) REVERT: C 90 GLU cc_start: 0.8909 (tp30) cc_final: 0.8444 (tp30) REVERT: C 102 ASN cc_start: 0.8753 (t0) cc_final: 0.8403 (t0) REVERT: C 152 LEU cc_start: 0.9411 (tp) cc_final: 0.9144 (tp) REVERT: C 163 LYS cc_start: 0.8325 (mtpp) cc_final: 0.8095 (mptt) REVERT: C 168 GLU cc_start: 0.8133 (mp0) cc_final: 0.7314 (mp0) REVERT: C 209 ILE cc_start: 0.9553 (mt) cc_final: 0.9264 (mm) REVERT: C 210 TYR cc_start: 0.8142 (m-80) cc_final: 0.7876 (m-80) REVERT: C 256 GLN cc_start: 0.8780 (pt0) cc_final: 0.8407 (pt0) REVERT: C 266 HIS cc_start: 0.8905 (p-80) cc_final: 0.8597 (p90) REVERT: C 290 GLU cc_start: 0.8414 (tt0) cc_final: 0.8148 (tt0) REVERT: C 367 ASP cc_start: 0.8391 (p0) cc_final: 0.8105 (p0) REVERT: C 377 MET cc_start: 0.8042 (ttp) cc_final: 0.6615 (ttp) REVERT: C 388 TRP cc_start: 0.9045 (m100) cc_final: 0.8800 (m100) REVERT: L 2 ARG cc_start: 0.8499 (mtm180) cc_final: 0.8074 (ptt-90) REVERT: L 25 CYS cc_start: 0.8675 (m) cc_final: 0.8423 (m) REVERT: L 85 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8019 (mm-40) REVERT: L 91 GLN cc_start: 0.8476 (mt0) cc_final: 0.8187 (mt0) REVERT: L 102 ASN cc_start: 0.8611 (t0) cc_final: 0.8105 (t0) REVERT: L 121 ARG cc_start: 0.8305 (mmm160) cc_final: 0.8050 (mmm160) REVERT: L 152 LEU cc_start: 0.9391 (tp) cc_final: 0.9163 (tp) REVERT: L 163 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8109 (mptt) REVERT: L 202 PHE cc_start: 0.8698 (m-10) cc_final: 0.8426 (m-10) REVERT: L 210 TYR cc_start: 0.8438 (m-80) cc_final: 0.8053 (m-80) REVERT: L 211 ASP cc_start: 0.8661 (t0) cc_final: 0.8116 (t70) REVERT: L 221 ARG cc_start: 0.8227 (mtt90) cc_final: 0.7997 (mmt90) REVERT: L 256 GLN cc_start: 0.8667 (pt0) cc_final: 0.7988 (tm-30) REVERT: L 266 HIS cc_start: 0.8971 (p-80) cc_final: 0.8479 (p90) REVERT: L 290 GLU cc_start: 0.8467 (tt0) cc_final: 0.8241 (tt0) REVERT: L 308 ARG cc_start: 0.9004 (mtm180) cc_final: 0.8745 (mtm-85) REVERT: L 326 LYS cc_start: 0.8917 (tttm) cc_final: 0.8379 (mmtm) REVERT: L 347 CYS cc_start: 0.8938 (t) cc_final: 0.8631 (t) REVERT: L 376 CYS cc_start: 0.9206 (t) cc_final: 0.8960 (t) REVERT: L 377 MET cc_start: 0.7940 (ttp) cc_final: 0.7349 (ttm) REVERT: L 378 LEU cc_start: 0.9069 (mt) cc_final: 0.8796 (mt) REVERT: L 380 ASN cc_start: 0.8936 (t0) cc_final: 0.8475 (t0) REVERT: A 85 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8011 (mm-40) REVERT: A 125 LEU cc_start: 0.9283 (mm) cc_final: 0.8953 (tt) REVERT: A 127 ASP cc_start: 0.9137 (m-30) cc_final: 0.8865 (m-30) REVERT: A 163 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8022 (mptt) REVERT: A 168 GLU cc_start: 0.8612 (mp0) cc_final: 0.8176 (mp0) REVERT: A 202 PHE cc_start: 0.8798 (m-80) cc_final: 0.8596 (m-10) REVERT: A 217 LEU cc_start: 0.9069 (mt) cc_final: 0.8817 (mt) REVERT: A 227 LEU cc_start: 0.9556 (mp) cc_final: 0.9339 (mp) REVERT: A 230 LEU cc_start: 0.9092 (mp) cc_final: 0.8820 (tt) REVERT: A 256 GLN cc_start: 0.8840 (pt0) cc_final: 0.8305 (pt0) REVERT: A 313 MET cc_start: 0.8761 (pmm) cc_final: 0.7964 (pmm) REVERT: A 380 ASN cc_start: 0.8787 (t0) cc_final: 0.8293 (t0) REVERT: K 85 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7863 (tp-100) REVERT: K 121 ARG cc_start: 0.7956 (mmm160) cc_final: 0.7649 (tpt170) REVERT: K 152 LEU cc_start: 0.9368 (tp) cc_final: 0.9059 (tp) REVERT: K 163 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8264 (mptt) REVERT: K 172 TYR cc_start: 0.8535 (t80) cc_final: 0.8047 (t80) REVERT: K 202 PHE cc_start: 0.9070 (m-80) cc_final: 0.8648 (m-10) REVERT: K 203 MET cc_start: 0.9208 (mmp) cc_final: 0.8816 (mmp) REVERT: K 211 ASP cc_start: 0.8748 (t0) cc_final: 0.8458 (t70) REVERT: K 230 LEU cc_start: 0.9131 (mp) cc_final: 0.8867 (tt) REVERT: K 256 GLN cc_start: 0.8644 (pt0) cc_final: 0.7825 (tm-30) REVERT: K 313 MET cc_start: 0.8907 (pmm) cc_final: 0.8148 (pmm) REVERT: K 326 LYS cc_start: 0.8903 (tttm) cc_final: 0.8487 (mmtt) REVERT: K 380 ASN cc_start: 0.8917 (t0) cc_final: 0.8233 (t0) REVERT: G 14 ASN cc_start: 0.9245 (m-40) cc_final: 0.8833 (m-40) REVERT: G 25 SER cc_start: 0.9327 (m) cc_final: 0.8888 (p) REVERT: G 51 TYR cc_start: 0.8699 (m-80) cc_final: 0.8352 (m-80) REVERT: G 91 VAL cc_start: 0.9494 (t) cc_final: 0.9233 (p) REVERT: G 115 SER cc_start: 0.9645 (m) cc_final: 0.9410 (p) REVERT: G 152 ILE cc_start: 0.9276 (mt) cc_final: 0.9072 (mm) REVERT: G 265 PHE cc_start: 0.9204 (m-80) cc_final: 0.8829 (m-10) REVERT: G 297 LYS cc_start: 0.8566 (ptpt) cc_final: 0.7665 (mmtt) REVERT: G 300 MET cc_start: 0.8562 (mtt) cc_final: 0.8019 (mtm) REVERT: G 347 ASN cc_start: 0.9132 (m-40) cc_final: 0.8926 (m-40) REVERT: G 367 PHE cc_start: 0.9071 (t80) cc_final: 0.8835 (t80) REVERT: G 375 GLN cc_start: 0.8293 (pp30) cc_final: 0.7905 (pp30) REVERT: G 406 MET cc_start: 0.8437 (tpp) cc_final: 0.8148 (mpp) REVERT: G 427 ASP cc_start: 0.7980 (m-30) cc_final: 0.7534 (t70) REVERT: D 14 ASN cc_start: 0.9301 (m-40) cc_final: 0.8968 (m-40) REVERT: D 81 PHE cc_start: 0.7542 (m-80) cc_final: 0.7287 (m-10) REVERT: D 95 SER cc_start: 0.9113 (m) cc_final: 0.8837 (t) REVERT: D 100 ASN cc_start: 0.9105 (t0) cc_final: 0.8856 (t0) REVERT: D 130 LEU cc_start: 0.9202 (tp) cc_final: 0.8670 (tt) REVERT: D 164 MET cc_start: 0.8248 (tpt) cc_final: 0.8029 (tpt) REVERT: D 167 PHE cc_start: 0.8623 (m-80) cc_final: 0.8376 (m-10) REVERT: D 205 GLU cc_start: 0.8520 (tp30) cc_final: 0.8111 (tp30) REVERT: D 233 MET cc_start: 0.8146 (ttt) cc_final: 0.7773 (ttt) REVERT: D 265 PHE cc_start: 0.9242 (m-80) cc_final: 0.8801 (m-10) REVERT: D 276 ARG cc_start: 0.8524 (mmm-85) cc_final: 0.8197 (mmp80) REVERT: D 293 MET cc_start: 0.8041 (mtm) cc_final: 0.7821 (mtt) REVERT: D 306 ARG cc_start: 0.8711 (mtt90) cc_final: 0.8293 (ttm110) REVERT: D 312 THR cc_start: 0.9069 (p) cc_final: 0.8677 (t) REVERT: D 313 VAL cc_start: 0.9391 (t) cc_final: 0.9127 (m) REVERT: D 322 SER cc_start: 0.9203 (m) cc_final: 0.8986 (t) REVERT: D 323 MET cc_start: 0.8268 (mmm) cc_final: 0.7596 (mmm) REVERT: D 327 ASP cc_start: 0.8884 (m-30) cc_final: 0.8673 (p0) REVERT: D 355 ASP cc_start: 0.8160 (m-30) cc_final: 0.7760 (m-30) REVERT: D 397 TRP cc_start: 0.8621 (m100) cc_final: 0.8256 (m100) REVERT: D 427 ASP cc_start: 0.7855 (m-30) cc_final: 0.7439 (t70) REVERT: I 14 ASN cc_start: 0.9298 (m-40) cc_final: 0.8869 (m-40) REVERT: I 52 ASN cc_start: 0.9315 (m-40) cc_final: 0.9066 (m-40) REVERT: I 95 SER cc_start: 0.9191 (m) cc_final: 0.8732 (t) REVERT: I 130 LEU cc_start: 0.9246 (tp) cc_final: 0.8826 (tt) REVERT: I 187 LEU cc_start: 0.9360 (mt) cc_final: 0.9160 (mp) REVERT: I 207 LEU cc_start: 0.9471 (mp) cc_final: 0.9255 (mt) REVERT: I 276 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.8177 (mmp80) REVERT: I 306 ARG cc_start: 0.8835 (mtt90) cc_final: 0.8305 (ttm110) REVERT: I 312 THR cc_start: 0.9115 (p) cc_final: 0.8721 (t) REVERT: I 313 VAL cc_start: 0.9427 (t) cc_final: 0.9197 (m) REVERT: I 323 MET cc_start: 0.8163 (mmm) cc_final: 0.7511 (mmm) REVERT: I 355 ASP cc_start: 0.8083 (m-30) cc_final: 0.7617 (m-30) REVERT: I 379 LYS cc_start: 0.9306 (mtpt) cc_final: 0.9051 (ttmm) REVERT: I 397 TRP cc_start: 0.8179 (m100) cc_final: 0.7938 (m-10) REVERT: I 427 ASP cc_start: 0.7777 (m-30) cc_final: 0.7569 (t70) REVERT: B 14 ASN cc_start: 0.9230 (m-40) cc_final: 0.8958 (m-40) REVERT: B 111 GLU cc_start: 0.8575 (pp20) cc_final: 0.8357 (pp20) REVERT: B 115 SER cc_start: 0.9565 (m) cc_final: 0.9217 (p) REVERT: B 130 LEU cc_start: 0.8962 (tp) cc_final: 0.8368 (tt) REVERT: B 203 ASP cc_start: 0.7927 (m-30) cc_final: 0.7643 (m-30) REVERT: B 233 MET cc_start: 0.8438 (ttm) cc_final: 0.8226 (ttm) REVERT: B 297 LYS cc_start: 0.8706 (ptpt) cc_final: 0.7732 (mmtt) REVERT: B 323 MET cc_start: 0.8695 (mmp) cc_final: 0.8392 (mmm) REVERT: B 343 GLU cc_start: 0.8384 (tp30) cc_final: 0.8094 (tp30) REVERT: B 351 THR cc_start: 0.9163 (m) cc_final: 0.8928 (t) REVERT: B 388 MET cc_start: 0.9198 (mtm) cc_final: 0.8989 (mtp) REVERT: B 406 MET cc_start: 0.8469 (tpp) cc_final: 0.7984 (mpp) REVERT: B 427 ASP cc_start: 0.8113 (m-30) cc_final: 0.7662 (t70) REVERT: H 14 ASN cc_start: 0.9256 (m-40) cc_final: 0.8961 (m-40) REVERT: H 86 ARG cc_start: 0.8131 (mtp180) cc_final: 0.7908 (mtp85) REVERT: H 91 VAL cc_start: 0.9682 (t) cc_final: 0.9444 (p) REVERT: H 115 SER cc_start: 0.9576 (m) cc_final: 0.9169 (p) REVERT: H 130 LEU cc_start: 0.9125 (tp) cc_final: 0.8606 (tt) REVERT: H 152 ILE cc_start: 0.9414 (mt) cc_final: 0.9066 (mm) REVERT: H 155 ILE cc_start: 0.9366 (mt) cc_final: 0.8975 (mt) REVERT: H 167 PHE cc_start: 0.8706 (m-80) cc_final: 0.8052 (m-10) REVERT: H 178 THR cc_start: 0.8133 (m) cc_final: 0.7848 (p) REVERT: H 233 MET cc_start: 0.8605 (ttt) cc_final: 0.8206 (ttt) REVERT: H 313 VAL cc_start: 0.9333 (t) cc_final: 0.9113 (m) REVERT: H 330 MET cc_start: 0.8871 (mmp) cc_final: 0.8605 (mmm) REVERT: H 340 TYR cc_start: 0.8678 (m-10) cc_final: 0.8456 (m-80) REVERT: H 397 TRP cc_start: 0.8669 (m100) cc_final: 0.8263 (m-10) REVERT: H 403 MET cc_start: 0.8688 (tpp) cc_final: 0.8307 (mmt) REVERT: H 406 MET cc_start: 0.8520 (tpp) cc_final: 0.8101 (tpp) REVERT: H 423 GLN cc_start: 0.8759 (tp40) cc_final: 0.8557 (tm-30) REVERT: H 427 ASP cc_start: 0.7986 (m-30) cc_final: 0.7593 (t70) outliers start: 1 outliers final: 0 residues processed: 1310 average time/residue: 0.2475 time to fit residues: 534.1238 Evaluate side-chains 1003 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1003 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 16 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 378 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 chunk 494 optimal weight: 8.9990 chunk 269 optimal weight: 10.0000 chunk 310 optimal weight: 20.0000 chunk 495 optimal weight: 7.9990 chunk 301 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN ** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN H 37 HIS ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 375 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.092149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.081353 restraints weight = 95562.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.084012 restraints weight = 52903.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.085860 restraints weight = 33270.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.087168 restraints weight = 22664.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.088076 restraints weight = 16390.350| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 41820 Z= 0.229 Angle : 0.656 13.704 56826 Z= 0.338 Chirality : 0.047 0.218 6216 Planarity : 0.005 0.043 7398 Dihedral : 11.143 168.640 5778 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.02 % Allowed : 2.57 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.11), residues: 5130 helix: -0.44 (0.10), residues: 2298 sheet: -0.41 (0.20), residues: 708 loop : -1.64 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 2 TYR 0.020 0.002 TYR A 210 PHE 0.017 0.002 PHE B 266 TRP 0.019 0.002 TRP K 21 HIS 0.009 0.001 HIS J 197 Details of bonding type rmsd covalent geometry : bond 0.00502 (41820) covalent geometry : angle 0.65581 (56826) hydrogen bonds : bond 0.04888 ( 1566) hydrogen bonds : angle 4.90314 ( 4644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1170 time to evaluate : 2.392 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: E 2 ARG cc_start: 0.8539 (mtm180) cc_final: 0.8130 (mtm-85) REVERT: E 21 TRP cc_start: 0.9574 (m100) cc_final: 0.9016 (m100) REVERT: E 24 TYR cc_start: 0.8658 (m-10) cc_final: 0.8349 (m-80) REVERT: E 36 MET cc_start: 0.8766 (ptm) cc_final: 0.8539 (ptm) REVERT: E 85 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8090 (tp40) REVERT: E 127 ASP cc_start: 0.8851 (m-30) cc_final: 0.8594 (m-30) REVERT: E 152 LEU cc_start: 0.9359 (tp) cc_final: 0.9157 (tp) REVERT: E 163 LYS cc_start: 0.8386 (mtpp) cc_final: 0.7870 (mmtt) REVERT: E 183 GLU cc_start: 0.8913 (tt0) cc_final: 0.8551 (tt0) REVERT: E 202 PHE cc_start: 0.9127 (m-80) cc_final: 0.8281 (m-10) REVERT: E 266 HIS cc_start: 0.8919 (p90) cc_final: 0.8717 (p90) REVERT: E 367 ASP cc_start: 0.8755 (p0) cc_final: 0.8321 (p0) REVERT: E 368 LEU cc_start: 0.9446 (mp) cc_final: 0.9238 (mp) REVERT: E 380 ASN cc_start: 0.8919 (t0) cc_final: 0.8383 (t0) REVERT: F 8 GLN cc_start: 0.8859 (mt0) cc_final: 0.8587 (mt0) REVERT: F 14 ASN cc_start: 0.9438 (m-40) cc_final: 0.8919 (m-40) REVERT: F 37 HIS cc_start: 0.7582 (m-70) cc_final: 0.7377 (m90) REVERT: F 45 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8115 (mt-10) REVERT: F 51 TYR cc_start: 0.8569 (m-80) cc_final: 0.8361 (m-80) REVERT: F 205 GLU cc_start: 0.8094 (tp30) cc_final: 0.7819 (tp30) REVERT: F 257 MET cc_start: 0.9048 (mmm) cc_final: 0.8686 (mmp) REVERT: F 300 MET cc_start: 0.8411 (mtt) cc_final: 0.8205 (mtm) REVERT: F 320 ARG cc_start: 0.7570 (mmt180) cc_final: 0.6929 (mmt180) REVERT: F 375 GLN cc_start: 0.8785 (pp30) cc_final: 0.8195 (pp30) REVERT: F 379 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8930 (mmmm) REVERT: F 427 ASP cc_start: 0.8255 (m-30) cc_final: 0.7789 (t70) REVERT: J 2 ARG cc_start: 0.8617 (mtm180) cc_final: 0.8066 (ptt-90) REVERT: J 21 TRP cc_start: 0.9569 (m100) cc_final: 0.9068 (m100) REVERT: J 85 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8074 (tp40) REVERT: J 102 ASN cc_start: 0.8518 (t0) cc_final: 0.7900 (t0) REVERT: J 127 ASP cc_start: 0.8875 (m-30) cc_final: 0.8590 (m-30) REVERT: J 163 LYS cc_start: 0.8308 (mtpp) cc_final: 0.7949 (mmtt) REVERT: J 168 GLU cc_start: 0.8909 (mp0) cc_final: 0.8298 (mp0) REVERT: J 172 TYR cc_start: 0.8427 (t80) cc_final: 0.8180 (t80) REVERT: J 183 GLU cc_start: 0.8275 (pt0) cc_final: 0.8063 (pt0) REVERT: J 202 PHE cc_start: 0.9120 (m-80) cc_final: 0.8716 (m-10) REVERT: J 203 MET cc_start: 0.9206 (mmp) cc_final: 0.8870 (mmm) REVERT: J 230 LEU cc_start: 0.9006 (mp) cc_final: 0.8796 (tp) REVERT: J 256 GLN cc_start: 0.8978 (pt0) cc_final: 0.8495 (tm-30) REVERT: J 271 THR cc_start: 0.9113 (m) cc_final: 0.8155 (p) REVERT: J 343 PHE cc_start: 0.8693 (m-80) cc_final: 0.8487 (m-10) REVERT: J 345 ASP cc_start: 0.8496 (t70) cc_final: 0.8259 (t0) REVERT: J 367 ASP cc_start: 0.8562 (p0) cc_final: 0.8172 (p0) REVERT: J 377 MET cc_start: 0.7815 (ttm) cc_final: 0.7557 (ttp) REVERT: C 2 ARG cc_start: 0.8505 (mtm110) cc_final: 0.8109 (ptt-90) REVERT: C 25 CYS cc_start: 0.8691 (m) cc_final: 0.8022 (p) REVERT: C 85 GLN cc_start: 0.8453 (mm-40) cc_final: 0.7983 (mm-40) REVERT: C 102 ASN cc_start: 0.8570 (t0) cc_final: 0.8166 (t0) REVERT: C 150 THR cc_start: 0.9276 (m) cc_final: 0.9033 (p) REVERT: C 163 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7996 (mptt) REVERT: C 185 TYR cc_start: 0.8689 (m-10) cc_final: 0.8451 (m-10) REVERT: C 256 GLN cc_start: 0.8696 (pt0) cc_final: 0.8435 (pt0) REVERT: C 266 HIS cc_start: 0.8898 (p-80) cc_final: 0.8679 (p90) REVERT: C 313 MET cc_start: 0.8559 (pmm) cc_final: 0.7464 (pmm) REVERT: C 367 ASP cc_start: 0.8668 (p0) cc_final: 0.8450 (p0) REVERT: C 378 LEU cc_start: 0.9204 (mp) cc_final: 0.8927 (mm) REVERT: C 380 ASN cc_start: 0.8916 (t0) cc_final: 0.8262 (t0) REVERT: C 433 GLU cc_start: 0.8836 (pm20) cc_final: 0.8321 (mm-30) REVERT: L 2 ARG cc_start: 0.8657 (mtm180) cc_final: 0.8370 (ptt-90) REVERT: L 24 TYR cc_start: 0.8467 (m-10) cc_final: 0.7922 (m-80) REVERT: L 25 CYS cc_start: 0.8605 (m) cc_final: 0.7989 (p) REVERT: L 85 GLN cc_start: 0.8587 (mm-40) cc_final: 0.7992 (mm-40) REVERT: L 91 GLN cc_start: 0.8260 (mt0) cc_final: 0.7975 (mt0) REVERT: L 102 ASN cc_start: 0.8696 (t0) cc_final: 0.8335 (t0) REVERT: L 152 LEU cc_start: 0.9515 (tp) cc_final: 0.9161 (tt) REVERT: L 163 LYS cc_start: 0.8280 (mtpp) cc_final: 0.8024 (mptt) REVERT: L 202 PHE cc_start: 0.8625 (m-10) cc_final: 0.8392 (m-10) REVERT: L 210 TYR cc_start: 0.8517 (m-80) cc_final: 0.8309 (m-80) REVERT: L 211 ASP cc_start: 0.8757 (t0) cc_final: 0.8287 (t70) REVERT: L 221 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7829 (mtt90) REVERT: L 235 VAL cc_start: 0.8683 (t) cc_final: 0.8370 (t) REVERT: L 256 GLN cc_start: 0.8668 (pt0) cc_final: 0.8062 (tm-30) REVERT: L 266 HIS cc_start: 0.8764 (p-80) cc_final: 0.8480 (p90) REVERT: L 313 MET cc_start: 0.8236 (pmm) cc_final: 0.7464 (pmm) REVERT: L 326 LYS cc_start: 0.8909 (tttm) cc_final: 0.8319 (mmtm) REVERT: L 347 CYS cc_start: 0.8999 (t) cc_final: 0.8719 (t) REVERT: L 376 CYS cc_start: 0.9379 (t) cc_final: 0.9110 (t) REVERT: L 378 LEU cc_start: 0.9159 (mt) cc_final: 0.8925 (mt) REVERT: L 380 ASN cc_start: 0.8907 (t0) cc_final: 0.8413 (t0) REVERT: L 392 ASP cc_start: 0.8050 (p0) cc_final: 0.6943 (p0) REVERT: A 2 ARG cc_start: 0.8587 (mtm110) cc_final: 0.7780 (ptt-90) REVERT: A 21 TRP cc_start: 0.9468 (m100) cc_final: 0.9132 (m100) REVERT: A 85 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8290 (mm-40) REVERT: A 163 LYS cc_start: 0.8611 (mtpp) cc_final: 0.8068 (mptt) REVERT: A 202 PHE cc_start: 0.8869 (m-80) cc_final: 0.8644 (m-10) REVERT: A 217 LEU cc_start: 0.9076 (mt) cc_final: 0.8817 (mt) REVERT: A 230 LEU cc_start: 0.9028 (mp) cc_final: 0.8702 (tt) REVERT: A 234 ILE cc_start: 0.8999 (tp) cc_final: 0.8706 (tp) REVERT: A 256 GLN cc_start: 0.8733 (pt0) cc_final: 0.8276 (pt0) REVERT: A 266 HIS cc_start: 0.9060 (p90) cc_final: 0.8612 (p-80) REVERT: A 313 MET cc_start: 0.8829 (pmm) cc_final: 0.8015 (pmm) REVERT: A 380 ASN cc_start: 0.8888 (t0) cc_final: 0.8490 (t0) REVERT: K 2 ARG cc_start: 0.8568 (mtm110) cc_final: 0.7735 (ptt-90) REVERT: K 21 TRP cc_start: 0.9480 (m100) cc_final: 0.9135 (m100) REVERT: K 85 GLN cc_start: 0.8484 (mm-40) cc_final: 0.7768 (tp-100) REVERT: K 152 LEU cc_start: 0.9510 (tp) cc_final: 0.9238 (tt) REVERT: K 163 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8195 (mptt) REVERT: K 202 PHE cc_start: 0.9155 (m-80) cc_final: 0.8771 (m-10) REVERT: K 217 LEU cc_start: 0.8995 (mt) cc_final: 0.8715 (mp) REVERT: K 230 LEU cc_start: 0.9171 (mp) cc_final: 0.8862 (tt) REVERT: K 256 GLN cc_start: 0.8719 (pt0) cc_final: 0.7699 (tm-30) REVERT: K 266 HIS cc_start: 0.9025 (p90) cc_final: 0.8525 (p-80) REVERT: K 313 MET cc_start: 0.8860 (pmm) cc_final: 0.8043 (pmm) REVERT: K 326 LYS cc_start: 0.9027 (tttm) cc_final: 0.8690 (tppt) REVERT: K 377 MET cc_start: 0.8312 (ttp) cc_final: 0.8019 (ttm) REVERT: K 380 ASN cc_start: 0.9045 (t0) cc_final: 0.8462 (t0) REVERT: G 8 GLN cc_start: 0.8918 (mt0) cc_final: 0.8680 (mt0) REVERT: G 14 ASN cc_start: 0.9411 (m-40) cc_final: 0.8886 (m-40) REVERT: G 51 TYR cc_start: 0.8567 (m-80) cc_final: 0.8309 (m-80) REVERT: G 181 GLU cc_start: 0.8759 (pp20) cc_final: 0.8293 (pp20) REVERT: G 265 PHE cc_start: 0.9250 (m-80) cc_final: 0.8647 (m-10) REVERT: G 297 LYS cc_start: 0.8648 (ptpt) cc_final: 0.7849 (mmtt) REVERT: G 299 MET cc_start: 0.8754 (mmp) cc_final: 0.8445 (mmp) REVERT: G 300 MET cc_start: 0.8409 (mtt) cc_final: 0.7945 (mtm) REVERT: G 320 ARG cc_start: 0.7451 (mpt180) cc_final: 0.6774 (mpt180) REVERT: G 347 ASN cc_start: 0.9026 (m-40) cc_final: 0.8714 (m-40) REVERT: G 375 GLN cc_start: 0.8399 (pp30) cc_final: 0.7784 (pp30) REVERT: G 379 LYS cc_start: 0.9320 (mmmm) cc_final: 0.8965 (mmmm) REVERT: G 406 MET cc_start: 0.8331 (tpp) cc_final: 0.8111 (mpp) REVERT: G 427 ASP cc_start: 0.8114 (m-30) cc_final: 0.7583 (t70) REVERT: D 14 ASN cc_start: 0.9294 (m-40) cc_final: 0.9053 (m-40) REVERT: D 95 SER cc_start: 0.9351 (m) cc_final: 0.8762 (t) REVERT: D 130 LEU cc_start: 0.9194 (tp) cc_final: 0.8727 (tt) REVERT: D 167 PHE cc_start: 0.8597 (m-80) cc_final: 0.8369 (m-10) REVERT: D 192 LEU cc_start: 0.9530 (mm) cc_final: 0.9254 (mm) REVERT: D 203 ASP cc_start: 0.8270 (t0) cc_final: 0.7132 (m-30) REVERT: D 257 MET cc_start: 0.8787 (mmp) cc_final: 0.8362 (mmm) REVERT: D 265 PHE cc_start: 0.9213 (m-80) cc_final: 0.8925 (m-10) REVERT: D 276 ARG cc_start: 0.8585 (mmm-85) cc_final: 0.8134 (mmp80) REVERT: D 300 MET cc_start: 0.8160 (mtm) cc_final: 0.7858 (mtm) REVERT: D 306 ARG cc_start: 0.8759 (mtt90) cc_final: 0.8268 (ttm110) REVERT: D 320 ARG cc_start: 0.7631 (mpt180) cc_final: 0.7327 (mpt180) REVERT: D 323 MET cc_start: 0.8269 (mmm) cc_final: 0.7843 (mmm) REVERT: D 347 ASN cc_start: 0.9043 (m-40) cc_final: 0.8690 (t0) REVERT: D 355 ASP cc_start: 0.8311 (m-30) cc_final: 0.7733 (m-30) REVERT: D 397 TRP cc_start: 0.8296 (m100) cc_final: 0.7849 (m100) REVERT: D 427 ASP cc_start: 0.8036 (m-30) cc_final: 0.7532 (t70) REVERT: I 14 ASN cc_start: 0.9327 (m-40) cc_final: 0.9073 (m-40) REVERT: I 95 SER cc_start: 0.9230 (m) cc_final: 0.8702 (t) REVERT: I 130 LEU cc_start: 0.9224 (tp) cc_final: 0.8826 (tt) REVERT: I 205 GLU cc_start: 0.8329 (tp30) cc_final: 0.8064 (tp30) REVERT: I 233 MET cc_start: 0.8327 (ttt) cc_final: 0.8081 (ttt) REVERT: I 265 PHE cc_start: 0.9406 (m-10) cc_final: 0.9163 (m-10) REVERT: I 276 ARG cc_start: 0.8584 (mmm-85) cc_final: 0.8190 (mmp80) REVERT: I 306 ARG cc_start: 0.8856 (mtt90) cc_final: 0.8291 (ttm110) REVERT: I 320 ARG cc_start: 0.7503 (mpt180) cc_final: 0.7229 (mpt180) REVERT: I 323 MET cc_start: 0.8219 (mmm) cc_final: 0.7741 (mmm) REVERT: I 340 TYR cc_start: 0.8725 (m-80) cc_final: 0.8517 (m-10) REVERT: I 347 ASN cc_start: 0.9018 (m-40) cc_final: 0.8738 (m-40) REVERT: I 355 ASP cc_start: 0.8069 (m-30) cc_final: 0.7604 (m-30) REVERT: I 379 LYS cc_start: 0.9352 (mtpt) cc_final: 0.9135 (ttmm) REVERT: I 427 ASP cc_start: 0.7933 (m-30) cc_final: 0.7498 (t70) REVERT: B 14 ASN cc_start: 0.9384 (m-40) cc_final: 0.9018 (m-40) REVERT: B 95 SER cc_start: 0.9136 (m) cc_final: 0.8772 (t) REVERT: B 130 LEU cc_start: 0.8915 (tp) cc_final: 0.8379 (tt) REVERT: B 215 LEU cc_start: 0.9019 (mt) cc_final: 0.8541 (mt) REVERT: B 257 MET cc_start: 0.8777 (mmm) cc_final: 0.8262 (mmm) REVERT: B 297 LYS cc_start: 0.8761 (ptpt) cc_final: 0.7824 (mmtt) REVERT: B 312 THR cc_start: 0.9159 (p) cc_final: 0.8705 (p) REVERT: B 323 MET cc_start: 0.8623 (mmp) cc_final: 0.8039 (mmm) REVERT: B 343 GLU cc_start: 0.8518 (tp30) cc_final: 0.8112 (tp30) REVERT: B 368 ILE cc_start: 0.8832 (mm) cc_final: 0.8598 (mm) REVERT: B 388 MET cc_start: 0.9239 (mtm) cc_final: 0.9034 (mtp) REVERT: B 406 MET cc_start: 0.8637 (tpp) cc_final: 0.8243 (tpp) REVERT: B 427 ASP cc_start: 0.8249 (m-30) cc_final: 0.7745 (t70) REVERT: H 14 ASN cc_start: 0.9363 (m-40) cc_final: 0.9013 (m-40) REVERT: H 95 SER cc_start: 0.8957 (m) cc_final: 0.8707 (t) REVERT: H 130 LEU cc_start: 0.9013 (tp) cc_final: 0.8505 (tt) REVERT: H 197 ASP cc_start: 0.8825 (m-30) cc_final: 0.8572 (m-30) REVERT: H 203 ASP cc_start: 0.8106 (t0) cc_final: 0.7100 (m-30) REVERT: H 246 LEU cc_start: 0.9308 (tt) cc_final: 0.9086 (tt) REVERT: H 253 LEU cc_start: 0.9258 (mt) cc_final: 0.9053 (mm) REVERT: H 297 LYS cc_start: 0.8590 (ptpt) cc_final: 0.7566 (mmtt) REVERT: H 299 MET cc_start: 0.8511 (mmm) cc_final: 0.7969 (mmp) REVERT: H 347 ASN cc_start: 0.8606 (m-40) cc_final: 0.8301 (m-40) REVERT: H 349 VAL cc_start: 0.9547 (t) cc_final: 0.9150 (t) REVERT: H 397 TRP cc_start: 0.8535 (m100) cc_final: 0.8225 (m-10) REVERT: H 406 MET cc_start: 0.8539 (tpp) cc_final: 0.8198 (tpp) REVERT: H 415 MET cc_start: 0.8872 (ttm) cc_final: 0.8573 (ttp) REVERT: H 427 ASP cc_start: 0.8148 (m-30) cc_final: 0.7686 (t70) outliers start: 1 outliers final: 0 residues processed: 1171 average time/residue: 0.2594 time to fit residues: 504.8825 Evaluate side-chains 935 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 935 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 476 optimal weight: 4.9990 chunk 364 optimal weight: 8.9990 chunk 337 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 20.0000 chunk 345 optimal weight: 0.9990 chunk 325 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 239 optimal weight: 0.6980 chunk 293 optimal weight: 8.9990 chunk 391 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN L 128 GLN ** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 HIS ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS G 307 HIS G 334 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 HIS B 37 HIS B 375 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 375 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.095496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.084815 restraints weight = 92024.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.087570 restraints weight = 50455.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.089481 restraints weight = 31284.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.090818 restraints weight = 20977.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.091760 restraints weight = 14907.867| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 41820 Z= 0.111 Angle : 0.550 10.970 56826 Z= 0.277 Chirality : 0.043 0.165 6216 Planarity : 0.004 0.040 7398 Dihedral : 10.701 169.163 5778 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.02 % Allowed : 1.91 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.11), residues: 5130 helix: 0.15 (0.11), residues: 2244 sheet: 0.21 (0.21), residues: 696 loop : -1.38 (0.12), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 359 TYR 0.029 0.001 TYR E 224 PHE 0.014 0.001 PHE H 266 TRP 0.016 0.002 TRP F 21 HIS 0.005 0.001 HIS H 28 Details of bonding type rmsd covalent geometry : bond 0.00238 (41820) covalent geometry : angle 0.55028 (56826) hydrogen bonds : bond 0.03922 ( 1566) hydrogen bonds : angle 4.46302 ( 4644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1229 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1228 time to evaluate : 1.744 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: symmetry clash REVERT: E 2 ARG cc_start: 0.8370 (mtm180) cc_final: 0.7696 (ptt-90) REVERT: E 21 TRP cc_start: 0.9546 (m100) cc_final: 0.9022 (m100) REVERT: E 36 MET cc_start: 0.8793 (ptm) cc_final: 0.8543 (ptm) REVERT: E 85 GLN cc_start: 0.8461 (mm-40) cc_final: 0.7850 (tp-100) REVERT: E 127 ASP cc_start: 0.8782 (m-30) cc_final: 0.8415 (m-30) REVERT: E 163 LYS cc_start: 0.8305 (mtpp) cc_final: 0.7819 (mmtt) REVERT: E 198 SER cc_start: 0.8395 (p) cc_final: 0.8055 (p) REVERT: E 203 MET cc_start: 0.9186 (mmp) cc_final: 0.8808 (mmp) REVERT: E 234 ILE cc_start: 0.9069 (tp) cc_final: 0.8693 (tp) REVERT: E 235 VAL cc_start: 0.8629 (t) cc_final: 0.8348 (t) REVERT: E 266 HIS cc_start: 0.8746 (p90) cc_final: 0.8526 (p90) REVERT: E 290 GLU cc_start: 0.7949 (pt0) cc_final: 0.7696 (pp20) REVERT: E 313 MET cc_start: 0.8763 (pmm) cc_final: 0.8114 (pmm) REVERT: E 367 ASP cc_start: 0.8611 (p0) cc_final: 0.8059 (p0) REVERT: E 376 CYS cc_start: 0.8544 (t) cc_final: 0.8306 (t) REVERT: E 377 MET cc_start: 0.8293 (ttp) cc_final: 0.7618 (ttp) REVERT: E 380 ASN cc_start: 0.8741 (t0) cc_final: 0.8127 (t0) REVERT: F 14 ASN cc_start: 0.9361 (m-40) cc_final: 0.8929 (m-40) REVERT: F 37 HIS cc_start: 0.7478 (m-70) cc_final: 0.7216 (m90) REVERT: F 51 TYR cc_start: 0.8439 (m-80) cc_final: 0.8231 (m-80) REVERT: F 205 GLU cc_start: 0.8048 (tp30) cc_final: 0.7819 (tp30) REVERT: F 257 MET cc_start: 0.8935 (mmm) cc_final: 0.7906 (mmp) REVERT: F 300 MET cc_start: 0.8581 (mtt) cc_final: 0.8354 (mtm) REVERT: F 312 THR cc_start: 0.9300 (p) cc_final: 0.8103 (p) REVERT: F 347 ASN cc_start: 0.8935 (m-40) cc_final: 0.8707 (m-40) REVERT: F 375 GLN cc_start: 0.8749 (pp30) cc_final: 0.8140 (pp30) REVERT: F 379 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8578 (mmmm) REVERT: F 427 ASP cc_start: 0.8202 (m-30) cc_final: 0.7758 (t70) REVERT: J 3 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7877 (mm-30) REVERT: J 21 TRP cc_start: 0.9572 (m100) cc_final: 0.9045 (m100) REVERT: J 36 MET cc_start: 0.8778 (ptm) cc_final: 0.8483 (ptm) REVERT: J 51 THR cc_start: 0.8987 (p) cc_final: 0.8699 (p) REVERT: J 85 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7876 (tp-100) REVERT: J 102 ASN cc_start: 0.8436 (t0) cc_final: 0.8001 (t0) REVERT: J 127 ASP cc_start: 0.8890 (m-30) cc_final: 0.8607 (m-30) REVERT: J 163 LYS cc_start: 0.8334 (mtpp) cc_final: 0.7871 (mmtt) REVERT: J 168 GLU cc_start: 0.8897 (mp0) cc_final: 0.8296 (mp0) REVERT: J 202 PHE cc_start: 0.9032 (m-80) cc_final: 0.8490 (m-10) REVERT: J 203 MET cc_start: 0.8993 (mmp) cc_final: 0.8781 (mmm) REVERT: J 256 GLN cc_start: 0.8904 (pt0) cc_final: 0.8370 (tm-30) REVERT: J 271 THR cc_start: 0.9019 (m) cc_final: 0.8714 (p) REVERT: J 345 ASP cc_start: 0.8479 (t70) cc_final: 0.8225 (t0) REVERT: J 367 ASP cc_start: 0.8532 (p0) cc_final: 0.8111 (p0) REVERT: C 2 ARG cc_start: 0.8335 (mtm110) cc_final: 0.8060 (ptt-90) REVERT: C 21 TRP cc_start: 0.9535 (m100) cc_final: 0.9306 (m100) REVERT: C 24 TYR cc_start: 0.8206 (m-10) cc_final: 0.7525 (m-80) REVERT: C 25 CYS cc_start: 0.8676 (m) cc_final: 0.8001 (p) REVERT: C 85 GLN cc_start: 0.8577 (mm-40) cc_final: 0.7872 (mm-40) REVERT: C 127 ASP cc_start: 0.9021 (m-30) cc_final: 0.8737 (m-30) REVERT: C 150 THR cc_start: 0.9201 (m) cc_final: 0.8983 (p) REVERT: C 152 LEU cc_start: 0.9588 (tp) cc_final: 0.9224 (tt) REVERT: C 163 LYS cc_start: 0.8112 (mtpp) cc_final: 0.7776 (mptt) REVERT: C 266 HIS cc_start: 0.8809 (p-80) cc_final: 0.8550 (p90) REVERT: C 313 MET cc_start: 0.8490 (pmm) cc_final: 0.7514 (pmm) REVERT: C 347 CYS cc_start: 0.8997 (t) cc_final: 0.8586 (t) REVERT: C 380 ASN cc_start: 0.8866 (t0) cc_final: 0.8404 (t0) REVERT: C 392 ASP cc_start: 0.8044 (p0) cc_final: 0.7036 (p0) REVERT: L 2 ARG cc_start: 0.8584 (mtm180) cc_final: 0.8110 (ptt-90) REVERT: L 25 CYS cc_start: 0.8573 (m) cc_final: 0.8355 (m) REVERT: L 102 ASN cc_start: 0.8518 (t0) cc_final: 0.7983 (t0) REVERT: L 152 LEU cc_start: 0.9557 (tp) cc_final: 0.9160 (tt) REVERT: L 163 LYS cc_start: 0.8212 (mtpp) cc_final: 0.7929 (mptt) REVERT: L 221 ARG cc_start: 0.8194 (mtt90) cc_final: 0.7815 (mtt90) REVERT: L 256 GLN cc_start: 0.8608 (pt0) cc_final: 0.7979 (tm-30) REVERT: L 266 HIS cc_start: 0.8656 (p90) cc_final: 0.8358 (p90) REVERT: L 302 MET cc_start: 0.8692 (mtm) cc_final: 0.7959 (mtm) REVERT: L 313 MET cc_start: 0.8750 (pmm) cc_final: 0.8020 (pmm) REVERT: L 326 LYS cc_start: 0.8858 (tttm) cc_final: 0.8258 (mmtm) REVERT: L 347 CYS cc_start: 0.8769 (t) cc_final: 0.8557 (t) REVERT: L 376 CYS cc_start: 0.9368 (t) cc_final: 0.9030 (t) REVERT: L 377 MET cc_start: 0.8290 (ttm) cc_final: 0.8071 (ttm) REVERT: L 378 LEU cc_start: 0.9108 (mt) cc_final: 0.8825 (mt) REVERT: L 380 ASN cc_start: 0.8967 (t0) cc_final: 0.8675 (t0) REVERT: L 388 TRP cc_start: 0.9061 (m100) cc_final: 0.8774 (m100) REVERT: L 392 ASP cc_start: 0.7864 (p0) cc_final: 0.6932 (p0) REVERT: L 432 TYR cc_start: 0.9107 (m-80) cc_final: 0.8896 (m-80) REVERT: A 36 MET cc_start: 0.8627 (ptm) cc_final: 0.8163 (ptm) REVERT: A 85 GLN cc_start: 0.8472 (mm-40) cc_final: 0.7805 (tp-100) REVERT: A 102 ASN cc_start: 0.8734 (t0) cc_final: 0.8414 (t0) REVERT: A 163 LYS cc_start: 0.8530 (mtpp) cc_final: 0.8037 (mptt) REVERT: A 168 GLU cc_start: 0.8688 (mp0) cc_final: 0.8237 (mp0) REVERT: A 198 SER cc_start: 0.8337 (p) cc_final: 0.8128 (p) REVERT: A 202 PHE cc_start: 0.8855 (m-80) cc_final: 0.8581 (m-10) REVERT: A 234 ILE cc_start: 0.8888 (tp) cc_final: 0.8492 (tp) REVERT: A 256 GLN cc_start: 0.8667 (pt0) cc_final: 0.8228 (pt0) REVERT: A 266 HIS cc_start: 0.8946 (p90) cc_final: 0.8487 (p-80) REVERT: A 313 MET cc_start: 0.8705 (pmm) cc_final: 0.7828 (pmm) REVERT: A 335 ILE cc_start: 0.9394 (mm) cc_final: 0.9121 (tp) REVERT: A 380 ASN cc_start: 0.8943 (t0) cc_final: 0.8539 (t0) REVERT: A 415 GLU cc_start: 0.7583 (tm-30) cc_final: 0.6963 (tm-30) REVERT: K 2 ARG cc_start: 0.8488 (mtm110) cc_final: 0.7815 (ptt-90) REVERT: K 21 TRP cc_start: 0.9453 (m100) cc_final: 0.9066 (m100) REVERT: K 85 GLN cc_start: 0.8404 (mm-40) cc_final: 0.7827 (tp-100) REVERT: K 102 ASN cc_start: 0.8678 (t0) cc_final: 0.8103 (t0) REVERT: K 152 LEU cc_start: 0.9492 (tp) cc_final: 0.9229 (tt) REVERT: K 163 LYS cc_start: 0.8544 (mtpp) cc_final: 0.8161 (mptt) REVERT: K 168 GLU cc_start: 0.8640 (mp0) cc_final: 0.8148 (mp0) REVERT: K 172 TYR cc_start: 0.8560 (t80) cc_final: 0.8186 (t80) REVERT: K 194 THR cc_start: 0.8180 (t) cc_final: 0.7902 (t) REVERT: K 198 SER cc_start: 0.8276 (p) cc_final: 0.8000 (p) REVERT: K 202 PHE cc_start: 0.9068 (m-80) cc_final: 0.8734 (m-10) REVERT: K 203 MET cc_start: 0.9286 (mmp) cc_final: 0.8532 (mmp) REVERT: K 230 LEU cc_start: 0.9013 (mp) cc_final: 0.8731 (tt) REVERT: K 256 GLN cc_start: 0.8603 (pt0) cc_final: 0.7711 (tm-30) REVERT: K 266 HIS cc_start: 0.8915 (p90) cc_final: 0.8416 (p-80) REVERT: K 313 MET cc_start: 0.8817 (pmm) cc_final: 0.8001 (pmm) REVERT: K 326 LYS cc_start: 0.8929 (tttm) cc_final: 0.8611 (tppt) REVERT: K 367 ASP cc_start: 0.8372 (p0) cc_final: 0.8139 (p0) REVERT: K 380 ASN cc_start: 0.9031 (t0) cc_final: 0.8541 (t0) REVERT: G 14 ASN cc_start: 0.9429 (m-40) cc_final: 0.8984 (m-40) REVERT: G 25 SER cc_start: 0.9404 (m) cc_final: 0.9116 (p) REVERT: G 181 GLU cc_start: 0.8732 (pp20) cc_final: 0.8439 (pp20) REVERT: G 257 MET cc_start: 0.8968 (mmm) cc_final: 0.8203 (mmp) REVERT: G 265 PHE cc_start: 0.9195 (m-80) cc_final: 0.8834 (m-10) REVERT: G 297 LYS cc_start: 0.8460 (ptpt) cc_final: 0.7685 (mmtt) REVERT: G 300 MET cc_start: 0.8359 (mtt) cc_final: 0.7808 (mtm) REVERT: G 347 ASN cc_start: 0.8847 (m-40) cc_final: 0.8452 (m-40) REVERT: G 355 ASP cc_start: 0.8668 (t0) cc_final: 0.8178 (t70) REVERT: G 375 GLN cc_start: 0.8305 (pp30) cc_final: 0.7843 (pp30) REVERT: G 427 ASP cc_start: 0.8154 (m-30) cc_final: 0.7758 (t70) REVERT: D 14 ASN cc_start: 0.9264 (m-40) cc_final: 0.8955 (m-40) REVERT: D 95 SER cc_start: 0.9415 (m) cc_final: 0.8837 (t) REVERT: D 111 GLU cc_start: 0.8601 (pp20) cc_final: 0.8373 (pp20) REVERT: D 192 LEU cc_start: 0.9453 (mm) cc_final: 0.9246 (mm) REVERT: D 203 ASP cc_start: 0.8295 (t0) cc_final: 0.6897 (m-30) REVERT: D 205 GLU cc_start: 0.8343 (tt0) cc_final: 0.8050 (mt-10) REVERT: D 265 PHE cc_start: 0.9114 (m-80) cc_final: 0.8711 (m-10) REVERT: D 276 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.8106 (mmp80) REVERT: D 306 ARG cc_start: 0.8732 (mtt90) cc_final: 0.8279 (ttm110) REVERT: D 312 THR cc_start: 0.9082 (p) cc_final: 0.8795 (p) REVERT: D 320 ARG cc_start: 0.7523 (mpt180) cc_final: 0.7285 (mpt180) REVERT: D 323 MET cc_start: 0.8131 (mmm) cc_final: 0.7817 (mmm) REVERT: D 346 PRO cc_start: 0.9328 (Cg_endo) cc_final: 0.9059 (Cg_exo) REVERT: D 347 ASN cc_start: 0.9048 (m-40) cc_final: 0.8708 (m-40) REVERT: D 355 ASP cc_start: 0.8212 (m-30) cc_final: 0.7582 (m-30) REVERT: D 370 ASN cc_start: 0.9239 (t0) cc_final: 0.8910 (t0) REVERT: D 397 TRP cc_start: 0.8208 (m100) cc_final: 0.7767 (m100) REVERT: D 407 GLU cc_start: 0.9095 (tp30) cc_final: 0.8613 (tp30) REVERT: D 427 ASP cc_start: 0.7957 (m-30) cc_final: 0.7496 (t70) REVERT: I 14 ASN cc_start: 0.9337 (m-40) cc_final: 0.9045 (m-40) REVERT: I 95 SER cc_start: 0.9241 (m) cc_final: 0.8849 (t) REVERT: I 187 LEU cc_start: 0.9467 (mp) cc_final: 0.9183 (mp) REVERT: I 265 PHE cc_start: 0.9317 (m-10) cc_final: 0.8726 (m-10) REVERT: I 276 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.8121 (mmp80) REVERT: I 300 MET cc_start: 0.8393 (mtt) cc_final: 0.8165 (mtm) REVERT: I 306 ARG cc_start: 0.8822 (mtt90) cc_final: 0.8311 (ttm110) REVERT: I 323 MET cc_start: 0.8085 (mmm) cc_final: 0.7791 (mmm) REVERT: I 347 ASN cc_start: 0.9014 (m-40) cc_final: 0.8748 (m-40) REVERT: I 355 ASP cc_start: 0.8098 (m-30) cc_final: 0.7573 (m-30) REVERT: I 370 ASN cc_start: 0.9273 (t0) cc_final: 0.8797 (t0) REVERT: I 379 LYS cc_start: 0.9316 (mtpt) cc_final: 0.9088 (ttmm) REVERT: I 427 ASP cc_start: 0.7886 (m-30) cc_final: 0.7521 (t70) REVERT: B 8 GLN cc_start: 0.7960 (mt0) cc_final: 0.7733 (mt0) REVERT: B 14 ASN cc_start: 0.9424 (m-40) cc_final: 0.9034 (m-40) REVERT: B 95 SER cc_start: 0.9128 (m) cc_final: 0.8759 (t) REVERT: B 100 ASN cc_start: 0.9039 (t0) cc_final: 0.8804 (t0) REVERT: B 265 PHE cc_start: 0.9280 (m-10) cc_final: 0.8794 (m-10) REVERT: B 297 LYS cc_start: 0.8633 (ptpt) cc_final: 0.7694 (mmtt) REVERT: B 299 MET cc_start: 0.8507 (mmm) cc_final: 0.7986 (mmt) REVERT: B 343 GLU cc_start: 0.8520 (tp30) cc_final: 0.8074 (tp30) REVERT: B 406 MET cc_start: 0.8442 (tpp) cc_final: 0.8009 (mpp) REVERT: B 422 TYR cc_start: 0.8862 (m-80) cc_final: 0.8620 (m-80) REVERT: B 427 ASP cc_start: 0.8186 (m-30) cc_final: 0.7852 (t70) REVERT: H 14 ASN cc_start: 0.9482 (m-40) cc_final: 0.8961 (m-40) REVERT: H 95 SER cc_start: 0.9014 (m) cc_final: 0.8761 (t) REVERT: H 181 GLU cc_start: 0.8671 (pt0) cc_final: 0.8071 (mt-10) REVERT: H 193 VAL cc_start: 0.8929 (m) cc_final: 0.8714 (m) REVERT: H 257 MET cc_start: 0.8764 (mmm) cc_final: 0.8234 (mmm) REVERT: H 312 THR cc_start: 0.9202 (p) cc_final: 0.8730 (p) REVERT: H 347 ASN cc_start: 0.8646 (m-40) cc_final: 0.8266 (m-40) REVERT: H 368 ILE cc_start: 0.8900 (mm) cc_final: 0.8654 (mm) REVERT: H 397 TRP cc_start: 0.8439 (m100) cc_final: 0.8162 (m-10) REVERT: H 406 MET cc_start: 0.8432 (tpp) cc_final: 0.8131 (mpp) REVERT: H 427 ASP cc_start: 0.8084 (m-30) cc_final: 0.7781 (t70) outliers start: 1 outliers final: 0 residues processed: 1229 average time/residue: 0.2457 time to fit residues: 508.2297 Evaluate side-chains 964 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 964 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 8 optimal weight: 4.9990 chunk 388 optimal weight: 10.0000 chunk 356 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 423 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 175 optimal weight: 30.0000 chunk 87 optimal weight: 10.0000 chunk 332 optimal weight: 0.7980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN E 293 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN ** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS A 293 ASN ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 307 HIS I 347 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN B 375 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 375 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.084108 restraints weight = 92994.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086829 restraints weight = 51365.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.088713 restraints weight = 32050.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.090014 restraints weight = 21619.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.090965 restraints weight = 15520.557| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41820 Z= 0.139 Angle : 0.565 11.393 56826 Z= 0.284 Chirality : 0.044 0.207 6216 Planarity : 0.004 0.043 7398 Dihedral : 10.500 177.632 5778 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.02 % Allowed : 1.89 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.12), residues: 5130 helix: 0.46 (0.11), residues: 2286 sheet: 0.43 (0.21), residues: 696 loop : -1.36 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 320 TYR 0.030 0.001 TYR L 24 PHE 0.015 0.001 PHE I 266 TRP 0.018 0.002 TRP A 21 HIS 0.005 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00312 (41820) covalent geometry : angle 0.56479 (56826) hydrogen bonds : bond 0.03800 ( 1566) hydrogen bonds : angle 4.40326 ( 4644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1149 time to evaluate : 1.592 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: E 2 ARG cc_start: 0.8046 (mtm180) cc_final: 0.7624 (ptt-90) REVERT: E 21 TRP cc_start: 0.9512 (m100) cc_final: 0.8975 (m100) REVERT: E 36 MET cc_start: 0.8779 (ptm) cc_final: 0.8487 (ptm) REVERT: E 85 GLN cc_start: 0.8485 (mm-40) cc_final: 0.7836 (tp-100) REVERT: E 127 ASP cc_start: 0.8868 (m-30) cc_final: 0.8478 (m-30) REVERT: E 163 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7675 (mmtt) REVERT: E 198 SER cc_start: 0.8138 (p) cc_final: 0.7825 (p) REVERT: E 203 MET cc_start: 0.9144 (mmp) cc_final: 0.8825 (mmm) REVERT: E 290 GLU cc_start: 0.7926 (pt0) cc_final: 0.7559 (pp20) REVERT: E 297 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7636 (tm-30) REVERT: E 313 MET cc_start: 0.8771 (pmm) cc_final: 0.8085 (pmm) REVERT: E 367 ASP cc_start: 0.8586 (p0) cc_final: 0.8006 (p0) REVERT: F 14 ASN cc_start: 0.9375 (m-40) cc_final: 0.8981 (m-40) REVERT: F 21 TRP cc_start: 0.9443 (m100) cc_final: 0.8739 (m100) REVERT: F 257 MET cc_start: 0.8934 (mmm) cc_final: 0.7790 (mmp) REVERT: F 300 MET cc_start: 0.8529 (mtt) cc_final: 0.8260 (mtm) REVERT: F 312 THR cc_start: 0.9415 (p) cc_final: 0.8368 (p) REVERT: F 347 ASN cc_start: 0.8908 (m-40) cc_final: 0.8624 (m-40) REVERT: F 375 GLN cc_start: 0.8691 (pp30) cc_final: 0.8245 (pp30) REVERT: F 427 ASP cc_start: 0.8285 (m-30) cc_final: 0.7781 (t70) REVERT: J 21 TRP cc_start: 0.9534 (m100) cc_final: 0.9016 (m100) REVERT: J 24 TYR cc_start: 0.8872 (m-10) cc_final: 0.8395 (m-80) REVERT: J 36 MET cc_start: 0.8776 (ptm) cc_final: 0.8424 (ptm) REVERT: J 51 THR cc_start: 0.8999 (p) cc_final: 0.8773 (m) REVERT: J 85 GLN cc_start: 0.8451 (mm-40) cc_final: 0.7894 (tp-100) REVERT: J 121 ARG cc_start: 0.6904 (tpt90) cc_final: 0.6590 (tpt170) REVERT: J 127 ASP cc_start: 0.8997 (m-30) cc_final: 0.8533 (m-30) REVERT: J 163 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7752 (mmtt) REVERT: J 168 GLU cc_start: 0.8887 (mp0) cc_final: 0.8399 (mp0) REVERT: J 202 PHE cc_start: 0.9027 (m-80) cc_final: 0.8272 (m-10) REVERT: J 235 VAL cc_start: 0.8654 (t) cc_final: 0.8446 (t) REVERT: J 256 GLN cc_start: 0.8914 (pt0) cc_final: 0.8488 (tm-30) REVERT: J 271 THR cc_start: 0.9106 (m) cc_final: 0.8270 (p) REVERT: J 295 CYS cc_start: 0.8812 (m) cc_final: 0.8605 (m) REVERT: J 302 MET cc_start: 0.8828 (mtm) cc_final: 0.8032 (mtm) REVERT: J 345 ASP cc_start: 0.8485 (t70) cc_final: 0.8251 (t0) REVERT: J 367 ASP cc_start: 0.8568 (p0) cc_final: 0.8112 (p0) REVERT: J 377 MET cc_start: 0.7832 (ttm) cc_final: 0.7579 (ttp) REVERT: C 2 ARG cc_start: 0.8464 (mtm110) cc_final: 0.8094 (ptt-90) REVERT: C 21 TRP cc_start: 0.9527 (m100) cc_final: 0.9324 (m100) REVERT: C 25 CYS cc_start: 0.8708 (m) cc_final: 0.8039 (p) REVERT: C 127 ASP cc_start: 0.9031 (m-30) cc_final: 0.8736 (m-30) REVERT: C 150 THR cc_start: 0.9215 (m) cc_final: 0.8965 (p) REVERT: C 152 LEU cc_start: 0.9605 (tp) cc_final: 0.9221 (tt) REVERT: C 163 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7783 (mptt) REVERT: C 211 ASP cc_start: 0.8344 (t0) cc_final: 0.8083 (t70) REVERT: C 266 HIS cc_start: 0.8777 (p90) cc_final: 0.8504 (p90) REVERT: C 313 MET cc_start: 0.8654 (pmm) cc_final: 0.7359 (pmm) REVERT: C 347 CYS cc_start: 0.9043 (t) cc_final: 0.8655 (t) REVERT: C 380 ASN cc_start: 0.8777 (t0) cc_final: 0.8048 (t0) REVERT: C 392 ASP cc_start: 0.7953 (p0) cc_final: 0.7228 (p0) REVERT: L 25 CYS cc_start: 0.8755 (m) cc_final: 0.8022 (p) REVERT: L 163 LYS cc_start: 0.8216 (mtpp) cc_final: 0.7909 (mptt) REVERT: L 168 GLU cc_start: 0.8628 (mp0) cc_final: 0.8215 (mp0) REVERT: L 172 TYR cc_start: 0.8352 (t80) cc_final: 0.8142 (t80) REVERT: L 203 MET cc_start: 0.8655 (mmm) cc_final: 0.8173 (mmp) REVERT: L 256 GLN cc_start: 0.8619 (pt0) cc_final: 0.8047 (tm-30) REVERT: L 266 HIS cc_start: 0.8777 (p90) cc_final: 0.8553 (p90) REVERT: L 302 MET cc_start: 0.8714 (mtm) cc_final: 0.8051 (mtm) REVERT: L 313 MET cc_start: 0.8696 (pmm) cc_final: 0.7877 (pmm) REVERT: L 326 LYS cc_start: 0.8829 (tttm) cc_final: 0.8282 (mmtm) REVERT: L 347 CYS cc_start: 0.8827 (t) cc_final: 0.8598 (t) REVERT: L 376 CYS cc_start: 0.9442 (t) cc_final: 0.9101 (t) REVERT: L 378 LEU cc_start: 0.9192 (mt) cc_final: 0.8874 (mt) REVERT: L 380 ASN cc_start: 0.8870 (t0) cc_final: 0.8523 (t0) REVERT: L 392 ASP cc_start: 0.7830 (p0) cc_final: 0.7197 (p0) REVERT: A 21 TRP cc_start: 0.9469 (m100) cc_final: 0.8925 (m100) REVERT: A 36 MET cc_start: 0.8636 (ptm) cc_final: 0.8165 (ptm) REVERT: A 102 ASN cc_start: 0.8681 (t0) cc_final: 0.8287 (t0) REVERT: A 127 ASP cc_start: 0.9060 (m-30) cc_final: 0.8804 (m-30) REVERT: A 152 LEU cc_start: 0.9496 (tp) cc_final: 0.9235 (tt) REVERT: A 163 LYS cc_start: 0.8478 (mtpp) cc_final: 0.7988 (mptt) REVERT: A 198 SER cc_start: 0.8346 (p) cc_final: 0.7959 (p) REVERT: A 217 LEU cc_start: 0.9072 (mt) cc_final: 0.8483 (mt) REVERT: A 256 GLN cc_start: 0.8677 (pt0) cc_final: 0.8213 (pt0) REVERT: A 266 HIS cc_start: 0.9005 (p90) cc_final: 0.8577 (p-80) REVERT: A 302 MET cc_start: 0.9274 (mtt) cc_final: 0.9015 (mtm) REVERT: A 313 MET cc_start: 0.8829 (pmm) cc_final: 0.8130 (pmm) REVERT: A 335 ILE cc_start: 0.9392 (mm) cc_final: 0.9113 (tp) REVERT: A 367 ASP cc_start: 0.8737 (p0) cc_final: 0.8456 (p0) REVERT: A 380 ASN cc_start: 0.8991 (t0) cc_final: 0.8533 (t0) REVERT: A 415 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7034 (tm-30) REVERT: A 425 MET cc_start: 0.9057 (tpt) cc_final: 0.8736 (tpp) REVERT: K 2 ARG cc_start: 0.8471 (mtm110) cc_final: 0.7629 (ptt-90) REVERT: K 51 THR cc_start: 0.9109 (p) cc_final: 0.8845 (t) REVERT: K 85 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7947 (tp-100) REVERT: K 102 ASN cc_start: 0.8698 (t0) cc_final: 0.8136 (t0) REVERT: K 163 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8123 (mptt) REVERT: K 168 GLU cc_start: 0.8545 (mp0) cc_final: 0.8047 (mp0) REVERT: K 194 THR cc_start: 0.8228 (t) cc_final: 0.8002 (t) REVERT: K 198 SER cc_start: 0.8380 (p) cc_final: 0.8126 (p) REVERT: K 202 PHE cc_start: 0.9084 (m-80) cc_final: 0.8756 (m-10) REVERT: K 203 MET cc_start: 0.9211 (mmp) cc_final: 0.8525 (mmp) REVERT: K 230 LEU cc_start: 0.9132 (mp) cc_final: 0.8870 (tt) REVERT: K 256 GLN cc_start: 0.8653 (pt0) cc_final: 0.7697 (tm-30) REVERT: K 266 HIS cc_start: 0.8977 (p90) cc_final: 0.8499 (p-80) REVERT: K 313 MET cc_start: 0.8957 (pmm) cc_final: 0.8233 (pmm) REVERT: K 326 LYS cc_start: 0.8896 (tttm) cc_final: 0.8421 (mmtp) REVERT: K 367 ASP cc_start: 0.8544 (p0) cc_final: 0.8265 (p0) REVERT: K 380 ASN cc_start: 0.9078 (t0) cc_final: 0.8574 (t0) REVERT: K 415 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7080 (tm-30) REVERT: G 14 ASN cc_start: 0.9488 (m-40) cc_final: 0.9069 (m-40) REVERT: G 37 HIS cc_start: 0.7728 (m90) cc_final: 0.7278 (m90) REVERT: G 150 LEU cc_start: 0.9543 (tp) cc_final: 0.9312 (tp) REVERT: G 181 GLU cc_start: 0.8762 (pp20) cc_final: 0.8517 (pp20) REVERT: G 265 PHE cc_start: 0.9200 (m-80) cc_final: 0.8786 (m-10) REVERT: G 297 LYS cc_start: 0.8547 (ptpt) cc_final: 0.7707 (mmtm) REVERT: G 300 MET cc_start: 0.8442 (mtt) cc_final: 0.8084 (mtm) REVERT: G 347 ASN cc_start: 0.8714 (m-40) cc_final: 0.8436 (m-40) REVERT: G 375 GLN cc_start: 0.8299 (pp30) cc_final: 0.7808 (pp30) REVERT: G 379 LYS cc_start: 0.9025 (mmmm) cc_final: 0.8780 (mmmm) REVERT: G 427 ASP cc_start: 0.8221 (m-30) cc_final: 0.7786 (t70) REVERT: D 14 ASN cc_start: 0.9231 (m-40) cc_final: 0.8918 (m-40) REVERT: D 65 LEU cc_start: 0.9049 (mp) cc_final: 0.8794 (mp) REVERT: D 95 SER cc_start: 0.9465 (m) cc_final: 0.8884 (t) REVERT: D 100 ASN cc_start: 0.9061 (t0) cc_final: 0.8822 (t0) REVERT: D 111 GLU cc_start: 0.8468 (pp20) cc_final: 0.8229 (pp20) REVERT: D 130 LEU cc_start: 0.9191 (tp) cc_final: 0.8722 (tt) REVERT: D 167 PHE cc_start: 0.8764 (m-80) cc_final: 0.8518 (m-10) REVERT: D 192 LEU cc_start: 0.9457 (mm) cc_final: 0.9233 (mm) REVERT: D 257 MET cc_start: 0.8860 (mmm) cc_final: 0.8517 (mmm) REVERT: D 265 PHE cc_start: 0.9121 (m-80) cc_final: 0.8745 (m-10) REVERT: D 276 ARG cc_start: 0.8621 (mmm-85) cc_final: 0.8158 (mmp80) REVERT: D 306 ARG cc_start: 0.8824 (mtt90) cc_final: 0.8381 (ttm110) REVERT: D 340 TYR cc_start: 0.8593 (m-80) cc_final: 0.8391 (m-10) REVERT: D 346 PRO cc_start: 0.9222 (Cg_endo) cc_final: 0.8992 (Cg_exo) REVERT: D 347 ASN cc_start: 0.9065 (m-40) cc_final: 0.8824 (m-40) REVERT: D 355 ASP cc_start: 0.8258 (m-30) cc_final: 0.7682 (m-30) REVERT: D 397 TRP cc_start: 0.8222 (m100) cc_final: 0.7935 (m100) REVERT: D 427 ASP cc_start: 0.8009 (m-30) cc_final: 0.7550 (t70) REVERT: I 14 ASN cc_start: 0.9413 (m-40) cc_final: 0.9136 (m-40) REVERT: I 95 SER cc_start: 0.9249 (m) cc_final: 0.8792 (t) REVERT: I 100 ASN cc_start: 0.8908 (t0) cc_final: 0.8660 (t0) REVERT: I 187 LEU cc_start: 0.9477 (mp) cc_final: 0.9179 (mp) REVERT: I 192 LEU cc_start: 0.9437 (mm) cc_final: 0.9209 (mm) REVERT: I 265 PHE cc_start: 0.9328 (m-10) cc_final: 0.9112 (m-10) REVERT: I 276 ARG cc_start: 0.8593 (mmm-85) cc_final: 0.8167 (mmp80) REVERT: I 300 MET cc_start: 0.8469 (mtt) cc_final: 0.8142 (mtm) REVERT: I 306 ARG cc_start: 0.8839 (mtt90) cc_final: 0.8337 (ttm110) REVERT: I 323 MET cc_start: 0.8070 (mmm) cc_final: 0.7817 (mmm) REVERT: I 328 GLU cc_start: 0.8505 (tt0) cc_final: 0.8295 (tp30) REVERT: I 347 ASN cc_start: 0.9009 (m110) cc_final: 0.8653 (t0) REVERT: I 355 ASP cc_start: 0.8182 (m-30) cc_final: 0.7599 (m-30) REVERT: I 370 ASN cc_start: 0.9279 (t0) cc_final: 0.8902 (t0) REVERT: I 379 LYS cc_start: 0.9282 (mtpt) cc_final: 0.9029 (ttmm) REVERT: I 427 ASP cc_start: 0.7942 (m-30) cc_final: 0.7514 (t70) REVERT: B 8 GLN cc_start: 0.8109 (mt0) cc_final: 0.7902 (mt0) REVERT: B 14 ASN cc_start: 0.9454 (m-40) cc_final: 0.9108 (m-40) REVERT: B 95 SER cc_start: 0.9137 (m) cc_final: 0.8794 (t) REVERT: B 100 ASN cc_start: 0.9029 (t0) cc_final: 0.8810 (t0) REVERT: B 133 PHE cc_start: 0.8357 (m-80) cc_final: 0.7802 (m-80) REVERT: B 246 LEU cc_start: 0.9435 (tt) cc_final: 0.9193 (tt) REVERT: B 265 PHE cc_start: 0.9262 (m-10) cc_final: 0.8801 (m-10) REVERT: B 297 LYS cc_start: 0.8682 (ptpt) cc_final: 0.7739 (mmtt) REVERT: B 299 MET cc_start: 0.8495 (mmm) cc_final: 0.8018 (mmt) REVERT: B 343 GLU cc_start: 0.8482 (tp30) cc_final: 0.8067 (tp30) REVERT: B 388 MET cc_start: 0.9197 (mtm) cc_final: 0.8981 (mtp) REVERT: B 406 MET cc_start: 0.8540 (tpp) cc_final: 0.8032 (mpp) REVERT: B 422 TYR cc_start: 0.8916 (m-80) cc_final: 0.8696 (m-80) REVERT: B 427 ASP cc_start: 0.8243 (m-30) cc_final: 0.7878 (t70) REVERT: H 14 ASN cc_start: 0.9464 (m-40) cc_final: 0.9009 (m-40) REVERT: H 95 SER cc_start: 0.9034 (m) cc_final: 0.8762 (t) REVERT: H 246 LEU cc_start: 0.9230 (tt) cc_final: 0.8971 (tt) REVERT: H 257 MET cc_start: 0.8715 (mmm) cc_final: 0.8172 (mmm) REVERT: H 299 MET cc_start: 0.8485 (mmp) cc_final: 0.8183 (mmp) REVERT: H 312 THR cc_start: 0.9197 (p) cc_final: 0.8774 (p) REVERT: H 340 TYR cc_start: 0.8714 (m-10) cc_final: 0.8438 (m-80) REVERT: H 347 ASN cc_start: 0.8572 (m-40) cc_final: 0.8272 (t0) REVERT: H 368 ILE cc_start: 0.8924 (mm) cc_final: 0.8659 (mm) REVERT: H 397 TRP cc_start: 0.8435 (m100) cc_final: 0.8175 (m-10) REVERT: H 406 MET cc_start: 0.8525 (tpp) cc_final: 0.8149 (mpp) REVERT: H 415 MET cc_start: 0.8897 (ttt) cc_final: 0.8257 (tpp) REVERT: H 427 ASP cc_start: 0.8172 (m-30) cc_final: 0.7800 (t70) outliers start: 1 outliers final: 0 residues processed: 1150 average time/residue: 0.2416 time to fit residues: 469.0263 Evaluate side-chains 936 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 936 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 384 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 267 optimal weight: 6.9990 chunk 322 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 214 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 396 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN L 293 ASN L 356 ASN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN K 293 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 370 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 375 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.094065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.083345 restraints weight = 94022.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.086105 restraints weight = 51608.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.088008 restraints weight = 32020.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.089327 restraints weight = 21551.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.090222 restraints weight = 15380.153| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41820 Z= 0.150 Angle : 0.571 12.015 56826 Z= 0.288 Chirality : 0.044 0.236 6216 Planarity : 0.004 0.058 7398 Dihedral : 10.374 176.734 5778 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.02 % Allowed : 1.09 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.12), residues: 5130 helix: 0.65 (0.11), residues: 2292 sheet: 0.51 (0.21), residues: 696 loop : -1.29 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 2 TYR 0.024 0.001 TYR K 210 PHE 0.017 0.001 PHE I 266 TRP 0.020 0.002 TRP K 21 HIS 0.006 0.001 HIS D 37 Details of bonding type rmsd covalent geometry : bond 0.00340 (41820) covalent geometry : angle 0.57076 (56826) hydrogen bonds : bond 0.03720 ( 1566) hydrogen bonds : angle 4.37123 ( 4644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1130 time to evaluate : 1.776 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: E 2 ARG cc_start: 0.8067 (mtm180) cc_final: 0.7527 (ptt-90) REVERT: E 21 TRP cc_start: 0.9508 (m100) cc_final: 0.8926 (m100) REVERT: E 36 MET cc_start: 0.8788 (ptm) cc_final: 0.8462 (ptm) REVERT: E 85 GLN cc_start: 0.8541 (mm-40) cc_final: 0.7859 (tp-100) REVERT: E 127 ASP cc_start: 0.8841 (m-30) cc_final: 0.8439 (m-30) REVERT: E 163 LYS cc_start: 0.8147 (mtpp) cc_final: 0.7703 (mmtt) REVERT: E 203 MET cc_start: 0.9029 (mmp) cc_final: 0.8742 (mmm) REVERT: E 290 GLU cc_start: 0.7835 (pt0) cc_final: 0.7378 (pp20) REVERT: E 297 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7707 (tm-30) REVERT: E 367 ASP cc_start: 0.8561 (p0) cc_final: 0.8093 (p0) REVERT: E 415 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7026 (tm-30) REVERT: E 425 MET cc_start: 0.9217 (mmm) cc_final: 0.8942 (tpp) REVERT: F 14 ASN cc_start: 0.9398 (m-40) cc_final: 0.9020 (m-40) REVERT: F 21 TRP cc_start: 0.9440 (m100) cc_final: 0.8849 (m100) REVERT: F 100 ASN cc_start: 0.8939 (t0) cc_final: 0.8695 (t0) REVERT: F 150 LEU cc_start: 0.9585 (tp) cc_final: 0.9303 (tp) REVERT: F 257 MET cc_start: 0.8912 (mmm) cc_final: 0.7814 (mmp) REVERT: F 297 LYS cc_start: 0.8600 (ptpt) cc_final: 0.7726 (mmtt) REVERT: F 300 MET cc_start: 0.8569 (mtt) cc_final: 0.8292 (mtm) REVERT: F 312 THR cc_start: 0.9412 (p) cc_final: 0.8497 (p) REVERT: F 321 MET cc_start: 0.8534 (ptp) cc_final: 0.8314 (ptp) REVERT: F 347 ASN cc_start: 0.8813 (m-40) cc_final: 0.8376 (m-40) REVERT: F 375 GLN cc_start: 0.8812 (pp30) cc_final: 0.8406 (pp30) REVERT: F 427 ASP cc_start: 0.8288 (m-30) cc_final: 0.7780 (t70) REVERT: J 21 TRP cc_start: 0.9532 (m100) cc_final: 0.9014 (m100) REVERT: J 36 MET cc_start: 0.8776 (ptm) cc_final: 0.8449 (ptm) REVERT: J 85 GLN cc_start: 0.8501 (mm-40) cc_final: 0.7884 (tp-100) REVERT: J 127 ASP cc_start: 0.8860 (m-30) cc_final: 0.8333 (m-30) REVERT: J 163 LYS cc_start: 0.8138 (mtpp) cc_final: 0.7768 (mmtt) REVERT: J 168 GLU cc_start: 0.8899 (mp0) cc_final: 0.8424 (mp0) REVERT: J 176 GLN cc_start: 0.8851 (mp10) cc_final: 0.8625 (mp10) REVERT: J 256 GLN cc_start: 0.8900 (pt0) cc_final: 0.7747 (tm-30) REVERT: J 271 THR cc_start: 0.9142 (m) cc_final: 0.8280 (p) REVERT: J 295 CYS cc_start: 0.8846 (m) cc_final: 0.8609 (m) REVERT: J 302 MET cc_start: 0.8861 (mtm) cc_final: 0.8093 (mtm) REVERT: J 345 ASP cc_start: 0.8507 (t70) cc_final: 0.8244 (t0) REVERT: J 367 ASP cc_start: 0.8669 (p0) cc_final: 0.8167 (p0) REVERT: J 377 MET cc_start: 0.7919 (ttm) cc_final: 0.7628 (ttp) REVERT: C 2 ARG cc_start: 0.8598 (mtm110) cc_final: 0.8039 (ptt-90) REVERT: C 21 TRP cc_start: 0.9520 (m100) cc_final: 0.9293 (m100) REVERT: C 24 TYR cc_start: 0.8390 (m-10) cc_final: 0.7912 (m-80) REVERT: C 25 CYS cc_start: 0.8759 (m) cc_final: 0.8030 (p) REVERT: C 51 THR cc_start: 0.9233 (p) cc_final: 0.8965 (t) REVERT: C 127 ASP cc_start: 0.9058 (m-30) cc_final: 0.8793 (m-30) REVERT: C 150 THR cc_start: 0.9217 (m) cc_final: 0.8961 (p) REVERT: C 152 LEU cc_start: 0.9596 (tp) cc_final: 0.9196 (tt) REVERT: C 163 LYS cc_start: 0.8028 (mtpp) cc_final: 0.7690 (mptt) REVERT: C 235 VAL cc_start: 0.9022 (t) cc_final: 0.8804 (t) REVERT: C 256 GLN cc_start: 0.8547 (pt0) cc_final: 0.8204 (pt0) REVERT: C 313 MET cc_start: 0.8826 (pmm) cc_final: 0.7637 (pmm) REVERT: C 347 CYS cc_start: 0.9149 (t) cc_final: 0.8783 (t) REVERT: C 380 ASN cc_start: 0.8792 (t0) cc_final: 0.7891 (t0) REVERT: L 25 CYS cc_start: 0.8792 (m) cc_final: 0.8495 (m) REVERT: L 127 ASP cc_start: 0.8878 (m-30) cc_final: 0.8638 (m-30) REVERT: L 163 LYS cc_start: 0.8180 (mtpp) cc_final: 0.7882 (mptt) REVERT: L 256 GLN cc_start: 0.8627 (pt0) cc_final: 0.8016 (tm-30) REVERT: L 266 HIS cc_start: 0.8782 (p90) cc_final: 0.8566 (p90) REVERT: L 302 MET cc_start: 0.8815 (mtm) cc_final: 0.8179 (mtm) REVERT: L 313 MET cc_start: 0.8755 (pmm) cc_final: 0.7675 (pmm) REVERT: L 326 LYS cc_start: 0.8803 (tttm) cc_final: 0.8302 (mmtt) REVERT: L 347 CYS cc_start: 0.8854 (t) cc_final: 0.8616 (t) REVERT: L 376 CYS cc_start: 0.9441 (t) cc_final: 0.9111 (t) REVERT: L 378 LEU cc_start: 0.9173 (mt) cc_final: 0.8920 (mt) REVERT: L 380 ASN cc_start: 0.8786 (t0) cc_final: 0.8203 (t0) REVERT: A 21 TRP cc_start: 0.9449 (m100) cc_final: 0.9043 (m100) REVERT: A 36 MET cc_start: 0.8619 (ptm) cc_final: 0.8104 (ptm) REVERT: A 102 ASN cc_start: 0.8685 (t0) cc_final: 0.8373 (t0) REVERT: A 152 LEU cc_start: 0.9489 (tp) cc_final: 0.9257 (tt) REVERT: A 163 LYS cc_start: 0.8502 (mtpp) cc_final: 0.7883 (mptt) REVERT: A 198 SER cc_start: 0.8333 (p) cc_final: 0.7956 (p) REVERT: A 234 ILE cc_start: 0.8917 (tp) cc_final: 0.8669 (tp) REVERT: A 235 VAL cc_start: 0.8918 (t) cc_final: 0.8670 (t) REVERT: A 256 GLN cc_start: 0.8714 (pt0) cc_final: 0.8199 (pt0) REVERT: A 266 HIS cc_start: 0.9067 (p90) cc_final: 0.8547 (p-80) REVERT: A 302 MET cc_start: 0.9198 (mtt) cc_final: 0.8995 (mtm) REVERT: A 313 MET cc_start: 0.8870 (pmm) cc_final: 0.7929 (pmm) REVERT: A 335 ILE cc_start: 0.9394 (mm) cc_final: 0.9128 (tp) REVERT: A 367 ASP cc_start: 0.8841 (p0) cc_final: 0.8535 (p0) REVERT: A 380 ASN cc_start: 0.8966 (t0) cc_final: 0.8572 (t0) REVERT: A 401 LYS cc_start: 0.9229 (mmtt) cc_final: 0.9020 (mmtm) REVERT: A 415 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7031 (tm-30) REVERT: K 21 TRP cc_start: 0.9503 (m100) cc_final: 0.9095 (m100) REVERT: K 85 GLN cc_start: 0.8639 (mm-40) cc_final: 0.7746 (tp-100) REVERT: K 102 ASN cc_start: 0.8635 (t0) cc_final: 0.8280 (t0) REVERT: K 163 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8093 (mptt) REVERT: K 168 GLU cc_start: 0.8417 (mp0) cc_final: 0.8023 (mp0) REVERT: K 194 THR cc_start: 0.8274 (t) cc_final: 0.8038 (t) REVERT: K 198 SER cc_start: 0.8368 (p) cc_final: 0.8115 (p) REVERT: K 202 PHE cc_start: 0.9102 (m-80) cc_final: 0.8815 (m-10) REVERT: K 230 LEU cc_start: 0.9121 (mp) cc_final: 0.8890 (tt) REVERT: K 235 VAL cc_start: 0.8617 (t) cc_final: 0.8373 (t) REVERT: K 256 GLN cc_start: 0.8660 (pt0) cc_final: 0.7920 (tm-30) REVERT: K 266 HIS cc_start: 0.9022 (p90) cc_final: 0.8551 (p-80) REVERT: K 313 MET cc_start: 0.8929 (pmm) cc_final: 0.7789 (pmm) REVERT: K 326 LYS cc_start: 0.8902 (tttm) cc_final: 0.8339 (mmtp) REVERT: K 380 ASN cc_start: 0.8988 (t0) cc_final: 0.8329 (t0) REVERT: K 415 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7071 (tm-30) REVERT: G 14 ASN cc_start: 0.9511 (m-40) cc_final: 0.9060 (m-40) REVERT: G 21 TRP cc_start: 0.9433 (m100) cc_final: 0.8678 (m100) REVERT: G 37 HIS cc_start: 0.7891 (m90) cc_final: 0.7322 (m90) REVERT: G 181 GLU cc_start: 0.8789 (pp20) cc_final: 0.8498 (pp20) REVERT: G 265 PHE cc_start: 0.9214 (m-80) cc_final: 0.8729 (m-10) REVERT: G 266 PHE cc_start: 0.8599 (m-10) cc_final: 0.8383 (m-10) REVERT: G 297 LYS cc_start: 0.8618 (ptpt) cc_final: 0.7716 (mmtm) REVERT: G 300 MET cc_start: 0.8265 (mtt) cc_final: 0.7859 (mtm) REVERT: G 347 ASN cc_start: 0.8728 (m-40) cc_final: 0.8303 (m-40) REVERT: G 368 ILE cc_start: 0.9037 (tp) cc_final: 0.8383 (mp) REVERT: G 375 GLN cc_start: 0.8306 (pp30) cc_final: 0.7654 (pp30) REVERT: G 379 LYS cc_start: 0.9110 (mmmm) cc_final: 0.8721 (mmmm) REVERT: G 427 ASP cc_start: 0.8284 (m-30) cc_final: 0.7805 (t70) REVERT: D 14 ASN cc_start: 0.9254 (m-40) cc_final: 0.8986 (m-40) REVERT: D 95 SER cc_start: 0.9468 (m) cc_final: 0.8963 (t) REVERT: D 100 ASN cc_start: 0.9065 (t0) cc_final: 0.8817 (t0) REVERT: D 111 GLU cc_start: 0.8587 (pp20) cc_final: 0.8296 (pp20) REVERT: D 130 LEU cc_start: 0.9221 (tp) cc_final: 0.8753 (tt) REVERT: D 192 LEU cc_start: 0.9499 (mm) cc_final: 0.9174 (mm) REVERT: D 257 MET cc_start: 0.8836 (mmm) cc_final: 0.8385 (mmm) REVERT: D 265 PHE cc_start: 0.9137 (m-80) cc_final: 0.8865 (m-10) REVERT: D 276 ARG cc_start: 0.8642 (mmm-85) cc_final: 0.8067 (mmp80) REVERT: D 300 MET cc_start: 0.7517 (mtm) cc_final: 0.7010 (mtm) REVERT: D 306 ARG cc_start: 0.8886 (mtt90) cc_final: 0.8427 (ttm110) REVERT: D 347 ASN cc_start: 0.9065 (m110) cc_final: 0.8720 (m-40) REVERT: D 355 ASP cc_start: 0.8234 (m-30) cc_final: 0.7615 (m-30) REVERT: D 397 TRP cc_start: 0.8220 (m100) cc_final: 0.7637 (m100) REVERT: D 427 ASP cc_start: 0.8013 (m-30) cc_final: 0.7521 (t70) REVERT: I 14 ASN cc_start: 0.9459 (m-40) cc_final: 0.9174 (m-40) REVERT: I 95 SER cc_start: 0.9218 (m) cc_final: 0.8790 (t) REVERT: I 100 ASN cc_start: 0.8831 (t0) cc_final: 0.8614 (t0) REVERT: I 187 LEU cc_start: 0.9483 (mp) cc_final: 0.9230 (mp) REVERT: I 265 PHE cc_start: 0.9296 (m-10) cc_final: 0.9092 (m-10) REVERT: I 276 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8160 (mmp80) REVERT: I 300 MET cc_start: 0.8453 (mtt) cc_final: 0.8051 (mtm) REVERT: I 306 ARG cc_start: 0.8897 (mtt90) cc_final: 0.8358 (ttm110) REVERT: I 312 THR cc_start: 0.9110 (p) cc_final: 0.8744 (p) REVERT: I 347 ASN cc_start: 0.9037 (m110) cc_final: 0.8652 (t0) REVERT: I 355 ASP cc_start: 0.8164 (m-30) cc_final: 0.7517 (m-30) REVERT: I 363 MET cc_start: 0.8723 (pmm) cc_final: 0.8449 (pmm) REVERT: I 370 ASN cc_start: 0.9187 (t0) cc_final: 0.8954 (t0) REVERT: I 379 LYS cc_start: 0.9282 (mtpt) cc_final: 0.9067 (ttmm) REVERT: I 427 ASP cc_start: 0.7961 (m-30) cc_final: 0.7532 (t70) REVERT: B 14 ASN cc_start: 0.9437 (m-40) cc_final: 0.9118 (m-40) REVERT: B 95 SER cc_start: 0.9143 (m) cc_final: 0.8802 (t) REVERT: B 100 ASN cc_start: 0.9016 (t0) cc_final: 0.8759 (t0) REVERT: B 125 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7860 (tt0) REVERT: B 130 LEU cc_start: 0.8998 (tp) cc_final: 0.8454 (tt) REVERT: B 147 MET cc_start: 0.9314 (tpp) cc_final: 0.9082 (tpp) REVERT: B 167 PHE cc_start: 0.8607 (m-80) cc_final: 0.7536 (m-10) REVERT: B 203 ASP cc_start: 0.7968 (t0) cc_final: 0.7094 (m-30) REVERT: B 246 LEU cc_start: 0.9348 (tt) cc_final: 0.9140 (tt) REVERT: B 299 MET cc_start: 0.8629 (mmm) cc_final: 0.8226 (mmp) REVERT: B 343 GLU cc_start: 0.8566 (tp30) cc_final: 0.8200 (tp30) REVERT: B 406 MET cc_start: 0.8559 (tpp) cc_final: 0.8055 (mpp) REVERT: B 422 TYR cc_start: 0.8921 (m-80) cc_final: 0.8708 (m-80) REVERT: B 427 ASP cc_start: 0.8294 (m-30) cc_final: 0.7898 (t70) REVERT: H 8 GLN cc_start: 0.8375 (mt0) cc_final: 0.8103 (mt0) REVERT: H 14 ASN cc_start: 0.9455 (m-40) cc_final: 0.9048 (m-40) REVERT: H 95 SER cc_start: 0.9032 (m) cc_final: 0.8758 (t) REVERT: H 299 MET cc_start: 0.8568 (mmp) cc_final: 0.8333 (mmp) REVERT: H 312 THR cc_start: 0.9120 (p) cc_final: 0.8761 (p) REVERT: H 340 TYR cc_start: 0.8701 (m-10) cc_final: 0.8401 (m-80) REVERT: H 347 ASN cc_start: 0.8480 (m-40) cc_final: 0.8250 (t0) REVERT: H 397 TRP cc_start: 0.8427 (m100) cc_final: 0.8194 (m-10) REVERT: H 406 MET cc_start: 0.8591 (tpp) cc_final: 0.8191 (tpp) REVERT: H 427 ASP cc_start: 0.8207 (m-30) cc_final: 0.7810 (t70) outliers start: 1 outliers final: 0 residues processed: 1131 average time/residue: 0.2418 time to fit residues: 460.8024 Evaluate side-chains 905 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 905 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 352 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 326 optimal weight: 20.0000 chunk 347 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 322 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** F 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 ASN ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN G 204 ASN ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN H 375 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.092583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081964 restraints weight = 94443.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.084666 restraints weight = 52084.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.086532 restraints weight = 32447.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.087842 restraints weight = 21893.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.088781 restraints weight = 15675.700| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 41820 Z= 0.179 Angle : 0.606 13.003 56826 Z= 0.305 Chirality : 0.046 0.242 6216 Planarity : 0.004 0.065 7398 Dihedral : 10.339 179.468 5778 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.02 % Allowed : 0.68 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.12), residues: 5130 helix: 0.65 (0.11), residues: 2328 sheet: 0.70 (0.21), residues: 678 loop : -1.24 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 64 TYR 0.026 0.002 TYR J 24 PHE 0.016 0.001 PHE H 378 TRP 0.021 0.002 TRP L 21 HIS 0.006 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00402 (41820) covalent geometry : angle 0.60559 (56826) hydrogen bonds : bond 0.03814 ( 1566) hydrogen bonds : angle 4.44828 ( 4644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1102 time to evaluate : 1.610 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: E 2 ARG cc_start: 0.7632 (mtm180) cc_final: 0.7371 (pmt170) REVERT: E 21 TRP cc_start: 0.9483 (m100) cc_final: 0.8876 (m100) REVERT: E 36 MET cc_start: 0.8702 (ptm) cc_final: 0.8455 (ptm) REVERT: E 85 GLN cc_start: 0.8573 (mm-40) cc_final: 0.7804 (tp-100) REVERT: E 163 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7683 (mmtt) REVERT: E 202 PHE cc_start: 0.8951 (m-10) cc_final: 0.8109 (m-10) REVERT: E 203 MET cc_start: 0.9036 (mmp) cc_final: 0.8834 (mmm) REVERT: E 210 TYR cc_start: 0.8561 (m-80) cc_final: 0.7774 (m-80) REVERT: E 290 GLU cc_start: 0.7413 (pt0) cc_final: 0.7082 (pp20) REVERT: E 367 ASP cc_start: 0.8695 (p0) cc_final: 0.8285 (p0) REVERT: E 425 MET cc_start: 0.9029 (mmm) cc_final: 0.8804 (tpp) REVERT: F 14 ASN cc_start: 0.9419 (m-40) cc_final: 0.9047 (m-40) REVERT: F 21 TRP cc_start: 0.9450 (m100) cc_final: 0.8809 (m100) REVERT: F 37 HIS cc_start: 0.7770 (m90) cc_final: 0.7404 (m90) REVERT: F 100 ASN cc_start: 0.9004 (t0) cc_final: 0.8778 (t0) REVERT: F 257 MET cc_start: 0.8948 (mmm) cc_final: 0.8057 (mmt) REVERT: F 297 LYS cc_start: 0.8663 (ptpt) cc_final: 0.7733 (mmtt) REVERT: F 312 THR cc_start: 0.9413 (p) cc_final: 0.8767 (p) REVERT: F 347 ASN cc_start: 0.8787 (m-40) cc_final: 0.8355 (m-40) REVERT: F 363 MET cc_start: 0.8868 (pmm) cc_final: 0.8623 (pmm) REVERT: F 368 ILE cc_start: 0.8820 (tp) cc_final: 0.8223 (mp) REVERT: F 375 GLN cc_start: 0.8789 (pp30) cc_final: 0.8327 (pp30) REVERT: F 427 ASP cc_start: 0.8228 (m-30) cc_final: 0.7720 (t70) REVERT: J 11 GLN cc_start: 0.8558 (tt0) cc_final: 0.8280 (tt0) REVERT: J 21 TRP cc_start: 0.9567 (m100) cc_final: 0.9065 (m100) REVERT: J 31 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8255 (mp10) REVERT: J 35 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8382 (mm110) REVERT: J 36 MET cc_start: 0.8752 (ptm) cc_final: 0.8242 (ptm) REVERT: J 85 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7896 (tp-100) REVERT: J 163 LYS cc_start: 0.8129 (mtpp) cc_final: 0.7821 (mptt) REVERT: J 168 GLU cc_start: 0.8913 (mp0) cc_final: 0.8308 (mp0) REVERT: J 224 TYR cc_start: 0.7918 (m-80) cc_final: 0.7366 (m-80) REVERT: J 256 GLN cc_start: 0.8929 (pt0) cc_final: 0.8395 (tm-30) REVERT: J 271 THR cc_start: 0.9103 (m) cc_final: 0.8883 (p) REVERT: J 302 MET cc_start: 0.8859 (mtm) cc_final: 0.8172 (mtm) REVERT: J 345 ASP cc_start: 0.8450 (t70) cc_final: 0.8215 (t0) REVERT: J 367 ASP cc_start: 0.8668 (p0) cc_final: 0.8270 (p0) REVERT: J 377 MET cc_start: 0.7952 (ttm) cc_final: 0.7074 (ttp) REVERT: J 423 GLU cc_start: 0.8122 (mp0) cc_final: 0.7780 (mp0) REVERT: C 2 ARG cc_start: 0.8477 (mtm110) cc_final: 0.8182 (ptt-90) REVERT: C 24 TYR cc_start: 0.8844 (m-10) cc_final: 0.8482 (m-80) REVERT: C 150 THR cc_start: 0.9220 (m) cc_final: 0.8980 (p) REVERT: C 152 LEU cc_start: 0.9603 (tp) cc_final: 0.9211 (tt) REVERT: C 163 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7764 (mptt) REVERT: C 235 VAL cc_start: 0.8968 (t) cc_final: 0.8724 (t) REVERT: C 256 GLN cc_start: 0.8457 (pt0) cc_final: 0.7920 (pt0) REVERT: C 313 MET cc_start: 0.8926 (pmm) cc_final: 0.7747 (pmm) REVERT: C 347 CYS cc_start: 0.9158 (t) cc_final: 0.8795 (t) REVERT: C 380 ASN cc_start: 0.8787 (t0) cc_final: 0.7925 (t0) REVERT: L 24 TYR cc_start: 0.8738 (m-10) cc_final: 0.8480 (m-80) REVERT: L 25 CYS cc_start: 0.8700 (m) cc_final: 0.8433 (m) REVERT: L 132 LEU cc_start: 0.8522 (tt) cc_final: 0.7619 (mp) REVERT: L 155 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8681 (mt-10) REVERT: L 163 LYS cc_start: 0.8120 (mtpp) cc_final: 0.7839 (mptt) REVERT: L 203 MET cc_start: 0.8754 (mmm) cc_final: 0.8187 (mmp) REVERT: L 256 GLN cc_start: 0.8630 (pt0) cc_final: 0.8043 (tm-30) REVERT: L 302 MET cc_start: 0.8730 (mtm) cc_final: 0.8423 (mtm) REVERT: L 313 MET cc_start: 0.8761 (pmm) cc_final: 0.7694 (pmm) REVERT: L 326 LYS cc_start: 0.8710 (tttm) cc_final: 0.8232 (mmtm) REVERT: L 347 CYS cc_start: 0.8905 (t) cc_final: 0.8669 (t) REVERT: L 376 CYS cc_start: 0.9408 (t) cc_final: 0.9141 (t) REVERT: L 378 LEU cc_start: 0.9114 (mt) cc_final: 0.8806 (mt) REVERT: L 380 ASN cc_start: 0.8785 (t0) cc_final: 0.8179 (t0) REVERT: A 36 MET cc_start: 0.8591 (ptm) cc_final: 0.8107 (ptm) REVERT: A 152 LEU cc_start: 0.9484 (tp) cc_final: 0.9259 (tt) REVERT: A 163 LYS cc_start: 0.8493 (mtpp) cc_final: 0.7864 (mptt) REVERT: A 203 MET cc_start: 0.8569 (mmm) cc_final: 0.8064 (mmm) REVERT: A 217 LEU cc_start: 0.9229 (mt) cc_final: 0.8651 (mt) REVERT: A 235 VAL cc_start: 0.8846 (t) cc_final: 0.8621 (t) REVERT: A 256 GLN cc_start: 0.8682 (pt0) cc_final: 0.8294 (pt0) REVERT: A 266 HIS cc_start: 0.9074 (p90) cc_final: 0.8398 (p-80) REVERT: A 302 MET cc_start: 0.9191 (mtt) cc_final: 0.8989 (mtm) REVERT: A 313 MET cc_start: 0.8946 (pmm) cc_final: 0.8188 (pmm) REVERT: A 335 ILE cc_start: 0.9481 (mm) cc_final: 0.9195 (tp) REVERT: A 380 ASN cc_start: 0.8953 (t0) cc_final: 0.8573 (t0) REVERT: A 401 LYS cc_start: 0.9214 (mmtt) cc_final: 0.8995 (mmtm) REVERT: A 415 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7100 (tm-30) REVERT: K 2 ARG cc_start: 0.8416 (mtm110) cc_final: 0.7774 (ptt-90) REVERT: K 21 TRP cc_start: 0.9519 (m100) cc_final: 0.9042 (m100) REVERT: K 51 THR cc_start: 0.9267 (p) cc_final: 0.9021 (t) REVERT: K 145 THR cc_start: 0.9079 (p) cc_final: 0.8878 (p) REVERT: K 163 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8006 (mptt) REVERT: K 168 GLU cc_start: 0.8524 (mp0) cc_final: 0.8062 (mp0) REVERT: K 202 PHE cc_start: 0.9118 (m-80) cc_final: 0.8782 (m-10) REVERT: K 203 MET cc_start: 0.9225 (mmp) cc_final: 0.8716 (mmm) REVERT: K 224 TYR cc_start: 0.7887 (m-80) cc_final: 0.6941 (m-80) REVERT: K 230 LEU cc_start: 0.9057 (mp) cc_final: 0.8798 (tt) REVERT: K 235 VAL cc_start: 0.8624 (t) cc_final: 0.8422 (t) REVERT: K 256 GLN cc_start: 0.8660 (pt0) cc_final: 0.7924 (tm-30) REVERT: K 313 MET cc_start: 0.8943 (pmm) cc_final: 0.8144 (pmm) REVERT: K 326 LYS cc_start: 0.8760 (tttm) cc_final: 0.8240 (mmtp) REVERT: K 380 ASN cc_start: 0.9028 (t0) cc_final: 0.8593 (t0) REVERT: K 415 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7132 (tm-30) REVERT: G 14 ASN cc_start: 0.9524 (m-40) cc_final: 0.9124 (m-40) REVERT: G 21 TRP cc_start: 0.9438 (m100) cc_final: 0.8869 (m100) REVERT: G 37 HIS cc_start: 0.7931 (m90) cc_final: 0.7407 (m90) REVERT: G 150 LEU cc_start: 0.9597 (tp) cc_final: 0.9376 (tp) REVERT: G 181 GLU cc_start: 0.8819 (pp20) cc_final: 0.8520 (pp20) REVERT: G 265 PHE cc_start: 0.9256 (m-80) cc_final: 0.8743 (m-10) REVERT: G 297 LYS cc_start: 0.8855 (ptpt) cc_final: 0.7916 (mmtm) REVERT: G 300 MET cc_start: 0.8395 (mtt) cc_final: 0.8050 (mtm) REVERT: G 347 ASN cc_start: 0.8860 (m-40) cc_final: 0.8408 (m-40) REVERT: G 363 MET cc_start: 0.8916 (pmm) cc_final: 0.8693 (pmm) REVERT: G 368 ILE cc_start: 0.9145 (tp) cc_final: 0.8359 (mp) REVERT: G 375 GLN cc_start: 0.8375 (pp30) cc_final: 0.7870 (pp30) REVERT: G 427 ASP cc_start: 0.8302 (m-30) cc_final: 0.7819 (t70) REVERT: D 14 ASN cc_start: 0.9159 (m-40) cc_final: 0.8952 (m-40) REVERT: D 95 SER cc_start: 0.9411 (m) cc_final: 0.8783 (t) REVERT: D 100 ASN cc_start: 0.9039 (t0) cc_final: 0.8801 (t0) REVERT: D 111 GLU cc_start: 0.8499 (pp20) cc_final: 0.8292 (pp20) REVERT: D 130 LEU cc_start: 0.9262 (tp) cc_final: 0.8828 (tt) REVERT: D 203 ASP cc_start: 0.8316 (t0) cc_final: 0.7005 (m-30) REVERT: D 205 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8504 (mt-10) REVERT: D 265 PHE cc_start: 0.9110 (m-80) cc_final: 0.8663 (m-10) REVERT: D 276 ARG cc_start: 0.8499 (mmm-85) cc_final: 0.8227 (mmp80) REVERT: D 300 MET cc_start: 0.7729 (mtm) cc_final: 0.6947 (mtm) REVERT: D 306 ARG cc_start: 0.8862 (mtt90) cc_final: 0.8381 (ttm110) REVERT: D 347 ASN cc_start: 0.9063 (m110) cc_final: 0.8830 (m-40) REVERT: D 355 ASP cc_start: 0.8255 (m-30) cc_final: 0.7693 (m-30) REVERT: D 397 TRP cc_start: 0.8313 (m100) cc_final: 0.7726 (m100) REVERT: D 406 MET cc_start: 0.8638 (mpp) cc_final: 0.8406 (mpp) REVERT: D 427 ASP cc_start: 0.8057 (m-30) cc_final: 0.7551 (t70) REVERT: I 14 ASN cc_start: 0.9475 (m-40) cc_final: 0.9177 (m-40) REVERT: I 95 SER cc_start: 0.9279 (m) cc_final: 0.8751 (t) REVERT: I 100 ASN cc_start: 0.8933 (t0) cc_final: 0.8727 (t0) REVERT: I 164 MET cc_start: 0.8503 (mtp) cc_final: 0.7891 (mtp) REVERT: I 257 MET cc_start: 0.8855 (mmm) cc_final: 0.8591 (mmm) REVERT: I 273 LEU cc_start: 0.8921 (mt) cc_final: 0.8596 (mt) REVERT: I 276 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8210 (mmp80) REVERT: I 300 MET cc_start: 0.8482 (mtt) cc_final: 0.8084 (mtm) REVERT: I 347 ASN cc_start: 0.9050 (m110) cc_final: 0.8695 (m-40) REVERT: I 355 ASP cc_start: 0.8201 (m-30) cc_final: 0.7542 (m-30) REVERT: I 363 MET cc_start: 0.8854 (pmm) cc_final: 0.8501 (pmm) REVERT: I 379 LYS cc_start: 0.9359 (mtpt) cc_final: 0.9123 (ttmm) REVERT: I 412 GLU cc_start: 0.8671 (tp30) cc_final: 0.8147 (tp30) REVERT: I 427 ASP cc_start: 0.7949 (m-30) cc_final: 0.7533 (t70) REVERT: B 14 ASN cc_start: 0.9414 (m-40) cc_final: 0.9105 (m-40) REVERT: B 100 ASN cc_start: 0.9052 (t0) cc_final: 0.8786 (t0) REVERT: B 125 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7872 (tt0) REVERT: B 130 LEU cc_start: 0.9169 (tp) cc_final: 0.8663 (tt) REVERT: B 167 PHE cc_start: 0.8745 (m-80) cc_final: 0.7738 (m-10) REVERT: B 284 LEU cc_start: 0.8287 (pt) cc_final: 0.7770 (pt) REVERT: B 297 LYS cc_start: 0.8753 (ptpt) cc_final: 0.7825 (mmtt) REVERT: B 299 MET cc_start: 0.8491 (mmm) cc_final: 0.7986 (mmt) REVERT: B 330 MET cc_start: 0.9176 (mmm) cc_final: 0.8589 (mmm) REVERT: B 343 GLU cc_start: 0.8714 (tp30) cc_final: 0.8313 (tp30) REVERT: B 344 TRP cc_start: 0.8834 (p-90) cc_final: 0.8437 (p-90) REVERT: B 388 MET cc_start: 0.9282 (mtm) cc_final: 0.9049 (mtp) REVERT: B 406 MET cc_start: 0.8671 (tpp) cc_final: 0.8258 (tpp) REVERT: B 427 ASP cc_start: 0.8329 (m-30) cc_final: 0.7958 (t70) REVERT: H 8 GLN cc_start: 0.8419 (mt0) cc_final: 0.8158 (mt0) REVERT: H 14 ASN cc_start: 0.9406 (m-40) cc_final: 0.8953 (m-40) REVERT: H 95 SER cc_start: 0.9067 (m) cc_final: 0.8763 (t) REVERT: H 130 LEU cc_start: 0.9151 (tp) cc_final: 0.8733 (tt) REVERT: H 181 GLU cc_start: 0.8756 (pt0) cc_final: 0.8020 (mt-10) REVERT: H 203 ASP cc_start: 0.8075 (t0) cc_final: 0.7869 (t0) REVERT: H 246 LEU cc_start: 0.9406 (tt) cc_final: 0.9151 (tt) REVERT: H 299 MET cc_start: 0.8478 (mmp) cc_final: 0.8247 (mmp) REVERT: H 323 MET cc_start: 0.8406 (mmm) cc_final: 0.8165 (ttt) REVERT: H 340 TYR cc_start: 0.8676 (m-10) cc_final: 0.8395 (m-80) REVERT: H 368 ILE cc_start: 0.8884 (mm) cc_final: 0.8665 (mm) REVERT: H 397 TRP cc_start: 0.8440 (m100) cc_final: 0.8202 (m-10) REVERT: H 406 MET cc_start: 0.8415 (tpp) cc_final: 0.8134 (tpp) REVERT: H 422 TYR cc_start: 0.8933 (m-80) cc_final: 0.8604 (m-80) REVERT: H 427 ASP cc_start: 0.8232 (m-30) cc_final: 0.7836 (t70) outliers start: 1 outliers final: 0 residues processed: 1103 average time/residue: 0.2426 time to fit residues: 453.3386 Evaluate side-chains 880 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 880 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 63 optimal weight: 7.9990 chunk 368 optimal weight: 10.0000 chunk 407 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 302 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 338 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 228 optimal weight: 6.9990 chunk 106 optimal weight: 0.0270 chunk 467 optimal weight: 5.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 356 ASN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN K 356 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 375 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.093892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.083205 restraints weight = 93247.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.085945 restraints weight = 51340.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087828 restraints weight = 31919.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.089118 restraints weight = 21552.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090077 restraints weight = 15475.347| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41820 Z= 0.139 Angle : 0.575 12.215 56826 Z= 0.288 Chirality : 0.044 0.256 6216 Planarity : 0.004 0.063 7398 Dihedral : 10.101 174.927 5778 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.02 % Allowed : 0.68 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.12), residues: 5130 helix: 0.76 (0.11), residues: 2328 sheet: 0.77 (0.21), residues: 678 loop : -1.18 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 282 TYR 0.020 0.001 TYR K 224 PHE 0.016 0.001 PHE H 378 TRP 0.022 0.002 TRP C 21 HIS 0.005 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00318 (41820) covalent geometry : angle 0.57470 (56826) hydrogen bonds : bond 0.03550 ( 1566) hydrogen bonds : angle 4.32809 ( 4644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1114 time to evaluate : 1.669 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: E 2 ARG cc_start: 0.7685 (mtm180) cc_final: 0.7465 (pmt170) REVERT: E 21 TRP cc_start: 0.9520 (m100) cc_final: 0.8936 (m100) REVERT: E 36 MET cc_start: 0.8690 (ptm) cc_final: 0.8458 (ptm) REVERT: E 85 GLN cc_start: 0.8479 (mm-40) cc_final: 0.7788 (tp-100) REVERT: E 127 ASP cc_start: 0.8523 (m-30) cc_final: 0.8283 (m-30) REVERT: E 163 LYS cc_start: 0.8108 (mtpp) cc_final: 0.7581 (mmtt) REVERT: E 202 PHE cc_start: 0.8883 (m-10) cc_final: 0.8026 (m-10) REVERT: E 203 MET cc_start: 0.9069 (mmp) cc_final: 0.8794 (mmm) REVERT: E 210 TYR cc_start: 0.8604 (m-80) cc_final: 0.7835 (m-80) REVERT: E 290 GLU cc_start: 0.7495 (pt0) cc_final: 0.7158 (pp20) REVERT: E 367 ASP cc_start: 0.8641 (p0) cc_final: 0.8228 (p0) REVERT: F 14 ASN cc_start: 0.9414 (m-40) cc_final: 0.9063 (m-40) REVERT: F 21 TRP cc_start: 0.9422 (m100) cc_final: 0.8851 (m100) REVERT: F 37 HIS cc_start: 0.7697 (m90) cc_final: 0.7292 (m90) REVERT: F 95 SER cc_start: 0.9245 (m) cc_final: 0.8766 (t) REVERT: F 100 ASN cc_start: 0.8936 (t0) cc_final: 0.8717 (t0) REVERT: F 150 LEU cc_start: 0.9551 (tp) cc_final: 0.9288 (tp) REVERT: F 205 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8227 (pt0) REVERT: F 257 MET cc_start: 0.8901 (mmm) cc_final: 0.8189 (mmt) REVERT: F 297 LYS cc_start: 0.8562 (ptpt) cc_final: 0.7704 (mmtt) REVERT: F 312 THR cc_start: 0.9418 (p) cc_final: 0.8769 (p) REVERT: F 347 ASN cc_start: 0.8801 (m-40) cc_final: 0.8319 (m-40) REVERT: F 368 ILE cc_start: 0.8986 (tp) cc_final: 0.8268 (mp) REVERT: F 375 GLN cc_start: 0.8735 (pp30) cc_final: 0.8244 (pp30) REVERT: F 376 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7819 (tm-30) REVERT: F 427 ASP cc_start: 0.8228 (m-30) cc_final: 0.7713 (t70) REVERT: J 2 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7151 (mtm-85) REVERT: J 11 GLN cc_start: 0.8447 (tt0) cc_final: 0.8131 (tt0) REVERT: J 22 GLU cc_start: 0.9331 (tt0) cc_final: 0.8602 (pt0) REVERT: J 24 TYR cc_start: 0.8871 (m-10) cc_final: 0.8544 (m-10) REVERT: J 36 MET cc_start: 0.8755 (ptm) cc_final: 0.8498 (ptm) REVERT: J 85 GLN cc_start: 0.8446 (mm-40) cc_final: 0.7802 (tp-100) REVERT: J 163 LYS cc_start: 0.8172 (mtpp) cc_final: 0.7816 (mptt) REVERT: J 168 GLU cc_start: 0.8884 (mp0) cc_final: 0.8410 (mp0) REVERT: J 183 GLU cc_start: 0.8917 (pp20) cc_final: 0.8599 (pp20) REVERT: J 221 ARG cc_start: 0.8434 (mmt90) cc_final: 0.7990 (mmt180) REVERT: J 256 GLN cc_start: 0.8897 (pt0) cc_final: 0.8411 (tm-30) REVERT: J 271 THR cc_start: 0.9088 (m) cc_final: 0.7360 (p) REVERT: J 302 MET cc_start: 0.8766 (mtm) cc_final: 0.8225 (mtp) REVERT: J 345 ASP cc_start: 0.8459 (t70) cc_final: 0.8255 (t0) REVERT: J 367 ASP cc_start: 0.8665 (p0) cc_final: 0.8195 (p0) REVERT: J 377 MET cc_start: 0.8210 (ttm) cc_final: 0.7553 (ttp) REVERT: C 24 TYR cc_start: 0.8681 (m-10) cc_final: 0.8330 (m-80) REVERT: C 150 THR cc_start: 0.9197 (m) cc_final: 0.8963 (p) REVERT: C 152 LEU cc_start: 0.9588 (tp) cc_final: 0.9192 (tt) REVERT: C 163 LYS cc_start: 0.8140 (mtpp) cc_final: 0.7748 (mptt) REVERT: C 235 VAL cc_start: 0.8901 (t) cc_final: 0.8649 (t) REVERT: C 256 GLN cc_start: 0.8483 (pt0) cc_final: 0.7986 (pt0) REVERT: C 313 MET cc_start: 0.8898 (pmm) cc_final: 0.7793 (pmm) REVERT: C 347 CYS cc_start: 0.9134 (t) cc_final: 0.8804 (t) REVERT: C 380 ASN cc_start: 0.8826 (t0) cc_final: 0.7973 (t0) REVERT: C 398 MET cc_start: 0.8837 (mmt) cc_final: 0.8448 (tpp) REVERT: L 25 CYS cc_start: 0.8736 (m) cc_final: 0.8442 (m) REVERT: L 127 ASP cc_start: 0.8866 (m-30) cc_final: 0.8619 (m-30) REVERT: L 132 LEU cc_start: 0.8510 (tt) cc_final: 0.7658 (mp) REVERT: L 163 LYS cc_start: 0.8114 (mtpp) cc_final: 0.7800 (mptt) REVERT: L 203 MET cc_start: 0.8959 (mmm) cc_final: 0.8389 (mmp) REVERT: L 256 GLN cc_start: 0.8602 (pt0) cc_final: 0.8041 (tm-30) REVERT: L 313 MET cc_start: 0.8825 (pmm) cc_final: 0.7730 (pmm) REVERT: L 326 LYS cc_start: 0.8810 (tttm) cc_final: 0.8292 (mmtt) REVERT: L 376 CYS cc_start: 0.9408 (t) cc_final: 0.9135 (t) REVERT: L 378 LEU cc_start: 0.9047 (mt) cc_final: 0.8791 (mt) REVERT: L 380 ASN cc_start: 0.8822 (t0) cc_final: 0.8097 (t0) REVERT: A 21 TRP cc_start: 0.9425 (m100) cc_final: 0.9101 (m100) REVERT: A 36 MET cc_start: 0.8632 (ptm) cc_final: 0.8089 (ptm) REVERT: A 152 LEU cc_start: 0.9536 (tp) cc_final: 0.9296 (tt) REVERT: A 163 LYS cc_start: 0.8479 (mtpp) cc_final: 0.7835 (mptt) REVERT: A 198 SER cc_start: 0.8357 (p) cc_final: 0.7919 (p) REVERT: A 203 MET cc_start: 0.8583 (mmm) cc_final: 0.8195 (mmm) REVERT: A 256 GLN cc_start: 0.8613 (pt0) cc_final: 0.8173 (pt0) REVERT: A 266 HIS cc_start: 0.8967 (p90) cc_final: 0.8728 (p90) REVERT: A 313 MET cc_start: 0.8931 (pmm) cc_final: 0.8027 (pmm) REVERT: A 335 ILE cc_start: 0.9416 (mm) cc_final: 0.9155 (tp) REVERT: A 380 ASN cc_start: 0.8960 (t0) cc_final: 0.8444 (t0) REVERT: A 401 LYS cc_start: 0.9251 (mmtt) cc_final: 0.9023 (mmtm) REVERT: A 415 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7079 (tm-30) REVERT: K 2 ARG cc_start: 0.8381 (mtm110) cc_final: 0.7820 (ptt-90) REVERT: K 21 TRP cc_start: 0.9491 (m100) cc_final: 0.9059 (m100) REVERT: K 163 LYS cc_start: 0.8516 (mtpp) cc_final: 0.7992 (mptt) REVERT: K 168 GLU cc_start: 0.8509 (mp0) cc_final: 0.7995 (mp0) REVERT: K 172 TYR cc_start: 0.8569 (t80) cc_final: 0.7947 (t80) REVERT: K 194 THR cc_start: 0.8044 (t) cc_final: 0.7815 (t) REVERT: K 202 PHE cc_start: 0.9047 (m-80) cc_final: 0.8664 (m-80) REVERT: K 203 MET cc_start: 0.9221 (mmp) cc_final: 0.8458 (mmp) REVERT: K 230 LEU cc_start: 0.9050 (mp) cc_final: 0.8842 (tt) REVERT: K 235 VAL cc_start: 0.8623 (t) cc_final: 0.8367 (t) REVERT: K 256 GLN cc_start: 0.8419 (pt0) cc_final: 0.7922 (tm-30) REVERT: K 302 MET cc_start: 0.8643 (mtt) cc_final: 0.8204 (mtt) REVERT: K 313 MET cc_start: 0.9009 (pmm) cc_final: 0.8220 (pmm) REVERT: K 326 LYS cc_start: 0.8836 (tttm) cc_final: 0.8307 (mmtp) REVERT: K 380 ASN cc_start: 0.9021 (t0) cc_final: 0.8567 (t0) REVERT: K 415 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7107 (tm-30) REVERT: K 425 MET cc_start: 0.9038 (tpp) cc_final: 0.8793 (tpp) REVERT: G 14 ASN cc_start: 0.9543 (m-40) cc_final: 0.9114 (m-40) REVERT: G 21 TRP cc_start: 0.9430 (m100) cc_final: 0.8856 (m100) REVERT: G 37 HIS cc_start: 0.7908 (m90) cc_final: 0.7349 (m90) REVERT: G 181 GLU cc_start: 0.8827 (pp20) cc_final: 0.8524 (pp20) REVERT: G 265 PHE cc_start: 0.9204 (m-80) cc_final: 0.8709 (m-10) REVERT: G 297 LYS cc_start: 0.8807 (ptpt) cc_final: 0.7904 (mmtm) REVERT: G 300 MET cc_start: 0.8345 (mtt) cc_final: 0.7899 (mtm) REVERT: G 347 ASN cc_start: 0.8825 (m-40) cc_final: 0.8368 (m-40) REVERT: G 375 GLN cc_start: 0.8420 (pp30) cc_final: 0.7844 (pp30) REVERT: G 415 MET cc_start: 0.8441 (mmm) cc_final: 0.7891 (tpp) REVERT: G 427 ASP cc_start: 0.8189 (m-30) cc_final: 0.7748 (t70) REVERT: D 95 SER cc_start: 0.9451 (m) cc_final: 0.8826 (t) REVERT: D 100 ASN cc_start: 0.9010 (t0) cc_final: 0.8775 (t0) REVERT: D 111 GLU cc_start: 0.8514 (pp20) cc_final: 0.8290 (pp20) REVERT: D 130 LEU cc_start: 0.9220 (tp) cc_final: 0.8798 (tt) REVERT: D 257 MET cc_start: 0.8782 (mmm) cc_final: 0.8105 (mmm) REVERT: D 265 PHE cc_start: 0.9137 (m-80) cc_final: 0.8725 (m-10) REVERT: D 276 ARG cc_start: 0.8498 (mmm-85) cc_final: 0.8229 (mmp80) REVERT: D 300 MET cc_start: 0.7601 (mtm) cc_final: 0.7136 (mtm) REVERT: D 306 ARG cc_start: 0.8875 (mtt90) cc_final: 0.8377 (ttm110) REVERT: D 347 ASN cc_start: 0.9091 (m110) cc_final: 0.8842 (m-40) REVERT: D 355 ASP cc_start: 0.8211 (m-30) cc_final: 0.7600 (m-30) REVERT: D 367 PHE cc_start: 0.8498 (t80) cc_final: 0.8267 (t80) REVERT: D 368 ILE cc_start: 0.8679 (mm) cc_final: 0.8430 (mm) REVERT: D 397 TRP cc_start: 0.8323 (m100) cc_final: 0.7733 (m100) REVERT: D 406 MET cc_start: 0.8570 (mpp) cc_final: 0.8337 (mpp) REVERT: D 412 GLU cc_start: 0.8522 (tp30) cc_final: 0.8113 (tp30) REVERT: D 427 ASP cc_start: 0.8054 (m-30) cc_final: 0.7531 (t70) REVERT: I 14 ASN cc_start: 0.9427 (m-40) cc_final: 0.9135 (m-40) REVERT: I 95 SER cc_start: 0.9231 (m) cc_final: 0.8792 (t) REVERT: I 143 THR cc_start: 0.9100 (m) cc_final: 0.8802 (p) REVERT: I 164 MET cc_start: 0.8435 (mtp) cc_final: 0.7876 (mtp) REVERT: I 257 MET cc_start: 0.8760 (mmm) cc_final: 0.8263 (mmm) REVERT: I 276 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8119 (mmp80) REVERT: I 300 MET cc_start: 0.8458 (mtt) cc_final: 0.8089 (mtm) REVERT: I 306 ARG cc_start: 0.8710 (mpt180) cc_final: 0.8293 (mpt180) REVERT: I 347 ASN cc_start: 0.9209 (m110) cc_final: 0.8649 (m-40) REVERT: I 355 ASP cc_start: 0.8091 (m-30) cc_final: 0.7550 (m-30) REVERT: I 363 MET cc_start: 0.8873 (pmm) cc_final: 0.8498 (pmm) REVERT: I 379 LYS cc_start: 0.9326 (mtpt) cc_final: 0.9051 (ttmm) REVERT: I 427 ASP cc_start: 0.7969 (m-30) cc_final: 0.7520 (t70) REVERT: B 14 ASN cc_start: 0.9422 (m-40) cc_final: 0.9130 (m-40) REVERT: B 100 ASN cc_start: 0.9022 (t0) cc_final: 0.8778 (t0) REVERT: B 114 ASP cc_start: 0.8490 (m-30) cc_final: 0.7680 (t0) REVERT: B 125 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7813 (tt0) REVERT: B 130 LEU cc_start: 0.9184 (tp) cc_final: 0.8752 (tt) REVERT: B 134 GLN cc_start: 0.8744 (tt0) cc_final: 0.8492 (tt0) REVERT: B 147 MET cc_start: 0.9292 (tpp) cc_final: 0.9006 (tpp) REVERT: B 167 PHE cc_start: 0.8694 (m-80) cc_final: 0.7563 (m-10) REVERT: B 203 ASP cc_start: 0.8033 (t0) cc_final: 0.6759 (m-30) REVERT: B 205 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8811 (mt-10) REVERT: B 246 LEU cc_start: 0.9346 (tt) cc_final: 0.9006 (tt) REVERT: B 299 MET cc_start: 0.8601 (mmm) cc_final: 0.8166 (mmp) REVERT: B 330 MET cc_start: 0.9118 (mmm) cc_final: 0.8516 (mmm) REVERT: B 343 GLU cc_start: 0.8716 (tp30) cc_final: 0.8298 (tp30) REVERT: B 344 TRP cc_start: 0.8836 (p-90) cc_final: 0.8450 (p-90) REVERT: B 406 MET cc_start: 0.8623 (tpp) cc_final: 0.8158 (tpp) REVERT: B 427 ASP cc_start: 0.8311 (m-30) cc_final: 0.7946 (t70) REVERT: H 8 GLN cc_start: 0.8322 (mt0) cc_final: 0.8089 (mt0) REVERT: H 14 ASN cc_start: 0.9424 (m-40) cc_final: 0.9047 (m-40) REVERT: H 74 ASP cc_start: 0.8584 (t70) cc_final: 0.8377 (t70) REVERT: H 95 SER cc_start: 0.9037 (m) cc_final: 0.8719 (t) REVERT: H 181 GLU cc_start: 0.8734 (pt0) cc_final: 0.8012 (mt-10) REVERT: H 246 LEU cc_start: 0.9454 (tt) cc_final: 0.9168 (tt) REVERT: H 284 LEU cc_start: 0.8367 (pt) cc_final: 0.7726 (pt) REVERT: H 299 MET cc_start: 0.8460 (mmp) cc_final: 0.8011 (mmt) REVERT: H 340 TYR cc_start: 0.8726 (m-10) cc_final: 0.8446 (m-80) REVERT: H 397 TRP cc_start: 0.8409 (m100) cc_final: 0.8190 (m-10) REVERT: H 406 MET cc_start: 0.8281 (tpp) cc_final: 0.8047 (tpp) REVERT: H 422 TYR cc_start: 0.8916 (m-80) cc_final: 0.8605 (m-80) REVERT: H 427 ASP cc_start: 0.8227 (m-30) cc_final: 0.7830 (t70) outliers start: 1 outliers final: 0 residues processed: 1115 average time/residue: 0.2377 time to fit residues: 450.9495 Evaluate side-chains 907 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 907 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 111 optimal weight: 9.9990 chunk 409 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 411 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 355 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 407 optimal weight: 0.9980 chunk 501 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 HIS ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 GLN ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS B 335 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN H 375 GLN H 416 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.085138 restraints weight = 92932.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.087901 restraints weight = 51285.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.089826 restraints weight = 32025.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.091161 restraints weight = 21565.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.092109 restraints weight = 15414.214| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41820 Z= 0.111 Angle : 0.570 9.057 56826 Z= 0.283 Chirality : 0.044 0.294 6216 Planarity : 0.004 0.069 7398 Dihedral : 9.805 168.861 5778 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.02 % Allowed : 0.39 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.12), residues: 5130 helix: 0.81 (0.11), residues: 2328 sheet: 0.80 (0.20), residues: 696 loop : -1.12 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 221 TYR 0.018 0.001 TYR J 319 PHE 0.016 0.001 PHE I 266 TRP 0.019 0.002 TRP D 21 HIS 0.008 0.001 HIS E 197 Details of bonding type rmsd covalent geometry : bond 0.00255 (41820) covalent geometry : angle 0.57020 (56826) hydrogen bonds : bond 0.03385 ( 1566) hydrogen bonds : angle 4.21294 ( 4644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1138 time to evaluate : 1.653 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: E 2 ARG cc_start: 0.7666 (mtm180) cc_final: 0.7451 (pmt170) REVERT: E 21 TRP cc_start: 0.9501 (m100) cc_final: 0.8912 (m100) REVERT: E 36 MET cc_start: 0.8709 (ptm) cc_final: 0.8476 (ptm) REVERT: E 77 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8769 (mt-10) REVERT: E 85 GLN cc_start: 0.8451 (mm-40) cc_final: 0.7743 (tp-100) REVERT: E 127 ASP cc_start: 0.8472 (m-30) cc_final: 0.8243 (m-30) REVERT: E 163 LYS cc_start: 0.8089 (mtpp) cc_final: 0.7557 (mmtt) REVERT: E 202 PHE cc_start: 0.8801 (m-10) cc_final: 0.8014 (m-10) REVERT: E 203 MET cc_start: 0.9107 (mmp) cc_final: 0.8744 (mmm) REVERT: E 210 TYR cc_start: 0.8546 (m-80) cc_final: 0.7769 (m-80) REVERT: E 290 GLU cc_start: 0.7462 (pt0) cc_final: 0.7105 (pp20) REVERT: E 297 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8134 (tm-30) REVERT: E 367 ASP cc_start: 0.8629 (p0) cc_final: 0.8229 (p0) REVERT: E 425 MET cc_start: 0.9248 (mmm) cc_final: 0.8924 (tpp) REVERT: F 14 ASN cc_start: 0.9393 (m-40) cc_final: 0.9090 (m-40) REVERT: F 21 TRP cc_start: 0.9432 (m100) cc_final: 0.8864 (m100) REVERT: F 37 HIS cc_start: 0.7703 (m90) cc_final: 0.7453 (m90) REVERT: F 86 ARG cc_start: 0.7684 (mtp180) cc_final: 0.5547 (mmt-90) REVERT: F 95 SER cc_start: 0.9182 (m) cc_final: 0.8743 (t) REVERT: F 100 ASN cc_start: 0.8938 (t0) cc_final: 0.8622 (t0) REVERT: F 143 THR cc_start: 0.8472 (m) cc_final: 0.8123 (p) REVERT: F 205 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8139 (pt0) REVERT: F 257 MET cc_start: 0.8947 (mmm) cc_final: 0.8267 (mmt) REVERT: F 297 LYS cc_start: 0.8563 (ptpt) cc_final: 0.7665 (mmtt) REVERT: F 312 THR cc_start: 0.9451 (p) cc_final: 0.8866 (p) REVERT: F 347 ASN cc_start: 0.8705 (m-40) cc_final: 0.8265 (m-40) REVERT: F 368 ILE cc_start: 0.8982 (tp) cc_final: 0.8315 (mp) REVERT: F 375 GLN cc_start: 0.8804 (pp30) cc_final: 0.8391 (pp30) REVERT: F 427 ASP cc_start: 0.8243 (m-30) cc_final: 0.7719 (t70) REVERT: J 2 ARG cc_start: 0.7962 (mtm-85) cc_final: 0.6878 (mtm-85) REVERT: J 22 GLU cc_start: 0.9321 (tt0) cc_final: 0.8587 (pt0) REVERT: J 24 TYR cc_start: 0.8855 (m-10) cc_final: 0.8606 (m-10) REVERT: J 36 MET cc_start: 0.8694 (ptm) cc_final: 0.8466 (ptm) REVERT: J 85 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7816 (tp-100) REVERT: J 163 LYS cc_start: 0.8224 (mtpp) cc_final: 0.7843 (mptt) REVERT: J 168 GLU cc_start: 0.8868 (mp0) cc_final: 0.8406 (mp0) REVERT: J 183 GLU cc_start: 0.8859 (pp20) cc_final: 0.8545 (pp20) REVERT: J 210 TYR cc_start: 0.8440 (m-80) cc_final: 0.7740 (m-80) REVERT: J 221 ARG cc_start: 0.8556 (mmt90) cc_final: 0.8273 (mmt180) REVERT: J 256 GLN cc_start: 0.8898 (pt0) cc_final: 0.8384 (tm-30) REVERT: J 271 THR cc_start: 0.9028 (m) cc_final: 0.7681 (p) REVERT: J 297 GLU cc_start: 0.8681 (tm-30) cc_final: 0.7976 (tm-30) REVERT: J 302 MET cc_start: 0.8899 (mtm) cc_final: 0.8124 (mtm) REVERT: J 345 ASP cc_start: 0.8493 (t70) cc_final: 0.8205 (t0) REVERT: J 367 ASP cc_start: 0.8642 (p0) cc_final: 0.8108 (p0) REVERT: J 377 MET cc_start: 0.8176 (ttm) cc_final: 0.7759 (ttp) REVERT: C 127 ASP cc_start: 0.8924 (m-30) cc_final: 0.8499 (m-30) REVERT: C 150 THR cc_start: 0.9160 (m) cc_final: 0.8927 (p) REVERT: C 163 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7770 (mptt) REVERT: C 313 MET cc_start: 0.9006 (pmm) cc_final: 0.7953 (pmm) REVERT: C 377 MET cc_start: 0.8235 (ttm) cc_final: 0.6954 (mtp) REVERT: C 380 ASN cc_start: 0.8840 (t0) cc_final: 0.7840 (t0) REVERT: C 388 TRP cc_start: 0.8994 (m100) cc_final: 0.8753 (m100) REVERT: C 398 MET cc_start: 0.8844 (mmt) cc_final: 0.8427 (tpp) REVERT: L 24 TYR cc_start: 0.8764 (m-10) cc_final: 0.8502 (m-80) REVERT: L 25 CYS cc_start: 0.8741 (m) cc_final: 0.8427 (m) REVERT: L 127 ASP cc_start: 0.8811 (m-30) cc_final: 0.8513 (m-30) REVERT: L 132 LEU cc_start: 0.8551 (tt) cc_final: 0.7728 (mp) REVERT: L 155 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8630 (mt-10) REVERT: L 163 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7771 (mptt) REVERT: L 203 MET cc_start: 0.8884 (mmm) cc_final: 0.8567 (mmp) REVERT: L 256 GLN cc_start: 0.8563 (pt0) cc_final: 0.8007 (tm-30) REVERT: L 266 HIS cc_start: 0.8921 (p90) cc_final: 0.8568 (p-80) REVERT: L 302 MET cc_start: 0.8652 (mtm) cc_final: 0.8133 (mtm) REVERT: L 313 MET cc_start: 0.8907 (pmm) cc_final: 0.7852 (pmm) REVERT: L 326 LYS cc_start: 0.8773 (tttm) cc_final: 0.8275 (mmtt) REVERT: L 347 CYS cc_start: 0.8979 (t) cc_final: 0.8715 (t) REVERT: L 376 CYS cc_start: 0.9416 (t) cc_final: 0.9067 (t) REVERT: L 377 MET cc_start: 0.8297 (ttm) cc_final: 0.8067 (ttm) REVERT: L 378 LEU cc_start: 0.9152 (mt) cc_final: 0.8898 (mp) REVERT: L 380 ASN cc_start: 0.8784 (t0) cc_final: 0.7892 (t0) REVERT: A 21 TRP cc_start: 0.9444 (m100) cc_final: 0.9063 (m100) REVERT: A 36 MET cc_start: 0.8569 (ptm) cc_final: 0.8049 (ptm) REVERT: A 102 ASN cc_start: 0.8663 (t0) cc_final: 0.8249 (t0) REVERT: A 152 LEU cc_start: 0.9530 (tp) cc_final: 0.9289 (tt) REVERT: A 163 LYS cc_start: 0.8406 (mtpp) cc_final: 0.7778 (mptt) REVERT: A 198 SER cc_start: 0.8304 (p) cc_final: 0.7857 (p) REVERT: A 235 VAL cc_start: 0.8766 (t) cc_final: 0.8536 (t) REVERT: A 256 GLN cc_start: 0.8588 (pt0) cc_final: 0.8086 (pt0) REVERT: A 266 HIS cc_start: 0.8959 (p90) cc_final: 0.8655 (p90) REVERT: A 302 MET cc_start: 0.8755 (mtm) cc_final: 0.8503 (mtm) REVERT: A 313 MET cc_start: 0.9056 (pmm) cc_final: 0.8247 (pmm) REVERT: A 335 ILE cc_start: 0.9399 (mm) cc_final: 0.9132 (tp) REVERT: A 377 MET cc_start: 0.7980 (ttm) cc_final: 0.6081 (mtp) REVERT: A 380 ASN cc_start: 0.8976 (t0) cc_final: 0.8404 (t0) REVERT: A 401 LYS cc_start: 0.9190 (mmtt) cc_final: 0.8983 (mmtm) REVERT: A 415 GLU cc_start: 0.7565 (tm-30) cc_final: 0.6965 (tm-30) REVERT: K 2 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7654 (ptt-90) REVERT: K 21 TRP cc_start: 0.9495 (m100) cc_final: 0.9084 (m100) REVERT: K 145 THR cc_start: 0.8897 (p) cc_final: 0.8672 (p) REVERT: K 163 LYS cc_start: 0.8455 (mtpp) cc_final: 0.7973 (mptt) REVERT: K 168 GLU cc_start: 0.8458 (mp0) cc_final: 0.7968 (mp0) REVERT: K 202 PHE cc_start: 0.9002 (m-80) cc_final: 0.8634 (m-80) REVERT: K 203 MET cc_start: 0.9256 (mmp) cc_final: 0.8961 (mmp) REVERT: K 215 ARG cc_start: 0.8942 (ptp90) cc_final: 0.8711 (ptp90) REVERT: K 235 VAL cc_start: 0.8634 (t) cc_final: 0.8337 (t) REVERT: K 256 GLN cc_start: 0.8371 (pt0) cc_final: 0.7887 (tm-30) REVERT: K 302 MET cc_start: 0.8684 (mtt) cc_final: 0.8338 (mtt) REVERT: K 313 MET cc_start: 0.9111 (pmm) cc_final: 0.8147 (pmm) REVERT: K 326 LYS cc_start: 0.8856 (tttm) cc_final: 0.8314 (mmtp) REVERT: K 380 ASN cc_start: 0.8959 (t0) cc_final: 0.8325 (t0) REVERT: K 388 TRP cc_start: 0.9136 (m100) cc_final: 0.8917 (m100) REVERT: K 415 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7103 (tm-30) REVERT: G 14 ASN cc_start: 0.9531 (m-40) cc_final: 0.9129 (m-40) REVERT: G 21 TRP cc_start: 0.9378 (m100) cc_final: 0.8904 (m100) REVERT: G 37 HIS cc_start: 0.7886 (m90) cc_final: 0.7292 (m90) REVERT: G 86 ARG cc_start: 0.7663 (mtp180) cc_final: 0.5474 (mmt-90) REVERT: G 181 GLU cc_start: 0.8828 (pp20) cc_final: 0.8592 (pp20) REVERT: G 246 LEU cc_start: 0.9295 (tt) cc_final: 0.9080 (tt) REVERT: G 257 MET cc_start: 0.8556 (mmm) cc_final: 0.7373 (mmt) REVERT: G 265 PHE cc_start: 0.9159 (m-80) cc_final: 0.8764 (m-10) REVERT: G 297 LYS cc_start: 0.8789 (ptpt) cc_final: 0.7866 (mmtm) REVERT: G 300 MET cc_start: 0.8251 (mtt) cc_final: 0.7849 (mtm) REVERT: G 312 THR cc_start: 0.9444 (p) cc_final: 0.8442 (p) REVERT: G 347 ASN cc_start: 0.8753 (m-40) cc_final: 0.8217 (m-40) REVERT: G 368 ILE cc_start: 0.9088 (tp) cc_final: 0.8648 (mp) REVERT: G 375 GLN cc_start: 0.8407 (pp30) cc_final: 0.7873 (pp30) REVERT: G 379 LYS cc_start: 0.9195 (mmmm) cc_final: 0.8800 (mtmt) REVERT: G 427 ASP cc_start: 0.8166 (m-30) cc_final: 0.7747 (t70) REVERT: D 14 ASN cc_start: 0.9336 (m-40) cc_final: 0.9114 (m-40) REVERT: D 95 SER cc_start: 0.9422 (m) cc_final: 0.8891 (t) REVERT: D 100 ASN cc_start: 0.8989 (t0) cc_final: 0.8764 (t0) REVERT: D 111 GLU cc_start: 0.8504 (pp20) cc_final: 0.8292 (pp20) REVERT: D 164 MET cc_start: 0.9232 (ttm) cc_final: 0.8477 (mtp) REVERT: D 257 MET cc_start: 0.8728 (mmm) cc_final: 0.8110 (mmm) REVERT: D 265 PHE cc_start: 0.9107 (m-80) cc_final: 0.8732 (m-10) REVERT: D 276 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.8008 (mmp80) REVERT: D 300 MET cc_start: 0.7205 (mtm) cc_final: 0.6873 (mtm) REVERT: D 330 MET cc_start: 0.8716 (mmm) cc_final: 0.8341 (tpp) REVERT: D 347 ASN cc_start: 0.9161 (m110) cc_final: 0.8852 (m-40) REVERT: D 355 ASP cc_start: 0.8133 (m-30) cc_final: 0.7466 (m-30) REVERT: D 368 ILE cc_start: 0.8691 (mm) cc_final: 0.8376 (mm) REVERT: D 397 TRP cc_start: 0.8337 (m100) cc_final: 0.7994 (m100) REVERT: D 406 MET cc_start: 0.8534 (mpp) cc_final: 0.8293 (mpp) REVERT: D 412 GLU cc_start: 0.8635 (tp30) cc_final: 0.8372 (tp30) REVERT: D 427 ASP cc_start: 0.7989 (m-30) cc_final: 0.7473 (t70) REVERT: I 14 ASN cc_start: 0.9424 (m-40) cc_final: 0.9106 (m-40) REVERT: I 95 SER cc_start: 0.9191 (m) cc_final: 0.8954 (p) REVERT: I 100 ASN cc_start: 0.8881 (t0) cc_final: 0.8631 (t0) REVERT: I 112 LEU cc_start: 0.9302 (tp) cc_final: 0.9030 (tp) REVERT: I 143 THR cc_start: 0.9050 (m) cc_final: 0.8795 (p) REVERT: I 257 MET cc_start: 0.8753 (mmm) cc_final: 0.8322 (mmm) REVERT: I 265 PHE cc_start: 0.9229 (m-10) cc_final: 0.8991 (m-10) REVERT: I 276 ARG cc_start: 0.8650 (mmm-85) cc_final: 0.8192 (mmp80) REVERT: I 300 MET cc_start: 0.8409 (mtt) cc_final: 0.8029 (mtm) REVERT: I 306 ARG cc_start: 0.8689 (mpt180) cc_final: 0.8305 (mpt180) REVERT: I 347 ASN cc_start: 0.9206 (m110) cc_final: 0.8623 (t0) REVERT: I 355 ASP cc_start: 0.8073 (m-30) cc_final: 0.7351 (m-30) REVERT: I 363 MET cc_start: 0.8854 (pmm) cc_final: 0.8493 (pmm) REVERT: I 379 LYS cc_start: 0.9319 (mtpt) cc_final: 0.9104 (ttmm) REVERT: I 407 GLU cc_start: 0.9113 (tp30) cc_final: 0.8516 (tp30) REVERT: I 427 ASP cc_start: 0.7978 (m-30) cc_final: 0.7521 (t70) REVERT: B 14 ASN cc_start: 0.9420 (m-40) cc_final: 0.9104 (m-40) REVERT: B 37 HIS cc_start: 0.7442 (m90) cc_final: 0.6936 (m90) REVERT: B 95 SER cc_start: 0.9027 (m) cc_final: 0.8626 (t) REVERT: B 100 ASN cc_start: 0.9020 (t0) cc_final: 0.8798 (t0) REVERT: B 114 ASP cc_start: 0.8425 (m-30) cc_final: 0.7601 (t0) REVERT: B 125 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7802 (tt0) REVERT: B 130 LEU cc_start: 0.9190 (tp) cc_final: 0.8766 (tt) REVERT: B 164 MET cc_start: 0.9048 (ttm) cc_final: 0.8509 (ttm) REVERT: B 246 LEU cc_start: 0.9309 (tt) cc_final: 0.9103 (tt) REVERT: B 299 MET cc_start: 0.8377 (mmm) cc_final: 0.7950 (mmt) REVERT: B 343 GLU cc_start: 0.8726 (tp30) cc_final: 0.8276 (tp30) REVERT: B 344 TRP cc_start: 0.8828 (p-90) cc_final: 0.8495 (p-90) REVERT: B 406 MET cc_start: 0.8580 (tpp) cc_final: 0.8077 (mpp) REVERT: B 427 ASP cc_start: 0.8315 (m-30) cc_final: 0.7888 (t70) REVERT: H 14 ASN cc_start: 0.9434 (m-40) cc_final: 0.9098 (m-40) REVERT: H 74 ASP cc_start: 0.8538 (t70) cc_final: 0.8330 (t70) REVERT: H 95 SER cc_start: 0.8958 (m) cc_final: 0.8648 (t) REVERT: H 181 GLU cc_start: 0.8673 (pt0) cc_final: 0.7952 (mt-10) REVERT: H 299 MET cc_start: 0.8277 (mmp) cc_final: 0.8068 (mmp) REVERT: H 340 TYR cc_start: 0.8680 (m-10) cc_final: 0.8468 (m-80) REVERT: H 397 TRP cc_start: 0.8365 (m100) cc_final: 0.8149 (m-10) REVERT: H 406 MET cc_start: 0.8294 (tpp) cc_final: 0.8066 (mpp) REVERT: H 422 TYR cc_start: 0.8897 (m-80) cc_final: 0.8659 (m-80) REVERT: H 427 ASP cc_start: 0.8206 (m-30) cc_final: 0.7851 (t70) outliers start: 1 outliers final: 0 residues processed: 1139 average time/residue: 0.2445 time to fit residues: 470.2587 Evaluate side-chains 939 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 939 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 246 optimal weight: 0.0870 chunk 349 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 303 optimal weight: 5.9990 chunk 387 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 307 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 407 optimal weight: 5.9990 overall best weight: 5.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN E 197 HIS ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 ASN J 301 GLN ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 356 ASN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 ASN ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 370 ASN I 416 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN B 416 ASN H 37 HIS ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 375 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.095201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.084544 restraints weight = 92538.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.087292 restraints weight = 51313.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.089152 restraints weight = 31976.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.090487 restraints weight = 21618.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.091385 restraints weight = 15392.613| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41820 Z= 0.177 Angle : 0.612 10.295 56826 Z= 0.309 Chirality : 0.046 0.274 6216 Planarity : 0.004 0.060 7398 Dihedral : 9.836 164.733 5778 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.02 % Allowed : 0.30 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.12), residues: 5130 helix: 0.79 (0.11), residues: 2334 sheet: 0.63 (0.21), residues: 690 loop : -0.98 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 320 TYR 0.023 0.002 TYR A 224 PHE 0.020 0.001 PHE G 367 TRP 0.020 0.002 TRP L 21 HIS 0.006 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00402 (41820) covalent geometry : angle 0.61242 (56826) hydrogen bonds : bond 0.03655 ( 1566) hydrogen bonds : angle 4.42408 ( 4644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1076 time to evaluate : 1.716 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: E 21 TRP cc_start: 0.9558 (m100) cc_final: 0.8970 (m100) REVERT: E 36 MET cc_start: 0.8728 (ptm) cc_final: 0.8478 (ptm) REVERT: E 77 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8745 (mt-10) REVERT: E 85 GLN cc_start: 0.8380 (mm-40) cc_final: 0.7527 (tp-100) REVERT: E 163 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7580 (mmtt) REVERT: E 210 TYR cc_start: 0.8426 (m-80) cc_final: 0.7842 (m-80) REVERT: E 290 GLU cc_start: 0.7606 (pt0) cc_final: 0.7171 (pp20) REVERT: E 297 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7553 (tm-30) REVERT: E 367 ASP cc_start: 0.8866 (p0) cc_final: 0.8333 (p0) REVERT: F 14 ASN cc_start: 0.9488 (m-40) cc_final: 0.9145 (m-40) REVERT: F 21 TRP cc_start: 0.9448 (m100) cc_final: 0.8887 (m100) REVERT: F 37 HIS cc_start: 0.7636 (m90) cc_final: 0.7366 (m90) REVERT: F 86 ARG cc_start: 0.7684 (mtp180) cc_final: 0.5637 (mmt-90) REVERT: F 100 ASN cc_start: 0.8954 (t0) cc_final: 0.8703 (t0) REVERT: F 150 LEU cc_start: 0.9568 (tp) cc_final: 0.9330 (tp) REVERT: F 257 MET cc_start: 0.9000 (mmm) cc_final: 0.8277 (mmt) REVERT: F 297 LYS cc_start: 0.8625 (ptpt) cc_final: 0.7787 (mmtt) REVERT: F 312 THR cc_start: 0.9465 (p) cc_final: 0.8747 (p) REVERT: F 347 ASN cc_start: 0.8763 (m-40) cc_final: 0.8343 (m-40) REVERT: F 368 ILE cc_start: 0.9143 (tp) cc_final: 0.8775 (tp) REVERT: F 374 ILE cc_start: 0.8184 (pt) cc_final: 0.7925 (pt) REVERT: F 375 GLN cc_start: 0.8894 (pp30) cc_final: 0.8410 (pp30) REVERT: F 405 GLU cc_start: 0.8608 (mp0) cc_final: 0.8232 (mt-10) REVERT: F 427 ASP cc_start: 0.8252 (m-30) cc_final: 0.7707 (t70) REVERT: J 21 TRP cc_start: 0.9501 (m100) cc_final: 0.8950 (m100) REVERT: J 22 GLU cc_start: 0.9323 (tt0) cc_final: 0.8602 (pt0) REVERT: J 24 TYR cc_start: 0.8863 (m-10) cc_final: 0.8532 (m-10) REVERT: J 36 MET cc_start: 0.8728 (ptm) cc_final: 0.8461 (ptm) REVERT: J 85 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7301 (tp-100) REVERT: J 163 LYS cc_start: 0.8271 (mtpp) cc_final: 0.7870 (mptt) REVERT: J 168 GLU cc_start: 0.8876 (mp0) cc_final: 0.8296 (mp0) REVERT: J 183 GLU cc_start: 0.8917 (pp20) cc_final: 0.8584 (pp20) REVERT: J 256 GLN cc_start: 0.8922 (pt0) cc_final: 0.8352 (tm-30) REVERT: J 271 THR cc_start: 0.9121 (m) cc_final: 0.8704 (p) REVERT: J 297 GLU cc_start: 0.8564 (tm-30) cc_final: 0.7794 (tm-30) REVERT: J 345 ASP cc_start: 0.8463 (t70) cc_final: 0.8163 (t0) REVERT: J 367 ASP cc_start: 0.8667 (p0) cc_final: 0.8168 (p0) REVERT: J 377 MET cc_start: 0.8356 (ttm) cc_final: 0.8092 (ttp) REVERT: C 24 TYR cc_start: 0.8820 (m-10) cc_final: 0.8558 (m-80) REVERT: C 150 THR cc_start: 0.9201 (m) cc_final: 0.8971 (p) REVERT: C 163 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7782 (mptt) REVERT: C 235 VAL cc_start: 0.8696 (t) cc_final: 0.8423 (t) REVERT: C 313 MET cc_start: 0.9029 (pmm) cc_final: 0.8204 (pmm) REVERT: C 347 CYS cc_start: 0.9122 (t) cc_final: 0.8830 (t) REVERT: C 377 MET cc_start: 0.8243 (ttm) cc_final: 0.6763 (mtp) REVERT: C 380 ASN cc_start: 0.8733 (t0) cc_final: 0.8041 (t0) REVERT: C 398 MET cc_start: 0.8884 (mmt) cc_final: 0.8660 (tpp) REVERT: L 24 TYR cc_start: 0.8779 (m-10) cc_final: 0.8576 (m-80) REVERT: L 25 CYS cc_start: 0.8819 (m) cc_final: 0.8531 (m) REVERT: L 132 LEU cc_start: 0.8572 (tt) cc_final: 0.7986 (mp) REVERT: L 155 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8671 (mt-10) REVERT: L 163 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7845 (mptt) REVERT: L 203 MET cc_start: 0.8834 (mmm) cc_final: 0.8471 (mmp) REVERT: L 256 GLN cc_start: 0.8571 (pt0) cc_final: 0.8009 (tm-30) REVERT: L 266 HIS cc_start: 0.8888 (p90) cc_final: 0.8608 (p-80) REVERT: L 302 MET cc_start: 0.8696 (mtm) cc_final: 0.8448 (mtm) REVERT: L 313 MET cc_start: 0.8861 (pmm) cc_final: 0.7787 (pmm) REVERT: L 326 LYS cc_start: 0.8714 (tttm) cc_final: 0.8227 (mmtt) REVERT: L 347 CYS cc_start: 0.9068 (t) cc_final: 0.8787 (t) REVERT: L 377 MET cc_start: 0.8185 (ttm) cc_final: 0.7978 (ttm) REVERT: L 378 LEU cc_start: 0.9208 (mt) cc_final: 0.8965 (mt) REVERT: L 380 ASN cc_start: 0.8820 (t0) cc_final: 0.8042 (t0) REVERT: L 398 MET cc_start: 0.9212 (tpp) cc_final: 0.8823 (mmt) REVERT: A 21 TRP cc_start: 0.9462 (m100) cc_final: 0.9062 (m100) REVERT: A 36 MET cc_start: 0.8575 (ptm) cc_final: 0.8083 (ptm) REVERT: A 152 LEU cc_start: 0.9540 (tp) cc_final: 0.9293 (tt) REVERT: A 163 LYS cc_start: 0.8423 (mtpp) cc_final: 0.7813 (mptt) REVERT: A 256 GLN cc_start: 0.8600 (pt0) cc_final: 0.8140 (pt0) REVERT: A 266 HIS cc_start: 0.8943 (p90) cc_final: 0.8662 (p90) REVERT: A 313 MET cc_start: 0.9026 (pmm) cc_final: 0.8139 (pmm) REVERT: A 335 ILE cc_start: 0.9493 (mm) cc_final: 0.9172 (tp) REVERT: A 377 MET cc_start: 0.8023 (ttm) cc_final: 0.5927 (mtp) REVERT: A 380 ASN cc_start: 0.9002 (t0) cc_final: 0.8336 (t0) REVERT: A 401 LYS cc_start: 0.9245 (mmtt) cc_final: 0.9036 (mmtm) REVERT: A 415 GLU cc_start: 0.7577 (tm-30) cc_final: 0.6981 (tm-30) REVERT: K 2 ARG cc_start: 0.8221 (mtm110) cc_final: 0.7811 (ptt-90) REVERT: K 21 TRP cc_start: 0.9514 (m100) cc_final: 0.9067 (m100) REVERT: K 145 THR cc_start: 0.8912 (p) cc_final: 0.8670 (p) REVERT: K 163 LYS cc_start: 0.8480 (mtpp) cc_final: 0.7947 (mptt) REVERT: K 168 GLU cc_start: 0.8561 (mp0) cc_final: 0.8068 (mp0) REVERT: K 183 GLU cc_start: 0.8855 (tt0) cc_final: 0.8610 (tt0) REVERT: K 194 THR cc_start: 0.7955 (t) cc_final: 0.7746 (t) REVERT: K 202 PHE cc_start: 0.9134 (m-80) cc_final: 0.8676 (m-80) REVERT: K 203 MET cc_start: 0.9219 (mmp) cc_final: 0.8643 (mmp) REVERT: K 230 LEU cc_start: 0.9383 (tt) cc_final: 0.8795 (mm) REVERT: K 235 VAL cc_start: 0.8676 (t) cc_final: 0.8424 (t) REVERT: K 256 GLN cc_start: 0.8659 (pt0) cc_final: 0.7912 (tm-30) REVERT: K 302 MET cc_start: 0.9043 (mtt) cc_final: 0.8256 (mtp) REVERT: K 313 MET cc_start: 0.8983 (pmm) cc_final: 0.8039 (pmm) REVERT: K 326 LYS cc_start: 0.8838 (tttm) cc_final: 0.8302 (mmtp) REVERT: K 380 ASN cc_start: 0.8911 (t0) cc_final: 0.8262 (t0) REVERT: K 415 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7073 (tm-30) REVERT: G 14 ASN cc_start: 0.9513 (m-40) cc_final: 0.9139 (m-40) REVERT: G 21 TRP cc_start: 0.9410 (m100) cc_final: 0.8909 (m100) REVERT: G 37 HIS cc_start: 0.7913 (m90) cc_final: 0.7309 (m90) REVERT: G 74 ASP cc_start: 0.8384 (t70) cc_final: 0.8170 (t70) REVERT: G 181 GLU cc_start: 0.8883 (pp20) cc_final: 0.8502 (pp20) REVERT: G 257 MET cc_start: 0.8676 (mmm) cc_final: 0.7648 (mmt) REVERT: G 265 PHE cc_start: 0.9188 (m-80) cc_final: 0.8751 (m-10) REVERT: G 297 LYS cc_start: 0.8770 (ptpt) cc_final: 0.7933 (mmtt) REVERT: G 300 MET cc_start: 0.8335 (mtt) cc_final: 0.7967 (mtm) REVERT: G 312 THR cc_start: 0.9463 (p) cc_final: 0.8398 (p) REVERT: G 347 ASN cc_start: 0.8771 (m-40) cc_final: 0.8475 (m-40) REVERT: G 367 PHE cc_start: 0.9215 (t80) cc_final: 0.8820 (t80) REVERT: G 368 ILE cc_start: 0.9085 (tp) cc_final: 0.8331 (mp) REVERT: G 375 GLN cc_start: 0.8524 (pp30) cc_final: 0.7945 (pp30) REVERT: G 379 LYS cc_start: 0.9183 (mmmm) cc_final: 0.8784 (mtmt) REVERT: G 427 ASP cc_start: 0.8210 (m-30) cc_final: 0.7750 (t70) REVERT: D 14 ASN cc_start: 0.9299 (m-40) cc_final: 0.9098 (m-40) REVERT: D 95 SER cc_start: 0.9351 (m) cc_final: 0.8689 (t) REVERT: D 111 GLU cc_start: 0.8619 (pp20) cc_final: 0.8355 (pp20) REVERT: D 203 ASP cc_start: 0.7800 (t0) cc_final: 0.6509 (m-30) REVERT: D 205 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8469 (mt-10) REVERT: D 265 PHE cc_start: 0.9177 (m-80) cc_final: 0.8764 (m-10) REVERT: D 276 ARG cc_start: 0.8475 (mmm-85) cc_final: 0.8246 (mmp80) REVERT: D 300 MET cc_start: 0.7675 (mtm) cc_final: 0.6860 (mtm) REVERT: D 347 ASN cc_start: 0.9104 (m110) cc_final: 0.8653 (t0) REVERT: D 355 ASP cc_start: 0.8140 (m-30) cc_final: 0.7575 (m-30) REVERT: D 374 ILE cc_start: 0.8356 (pt) cc_final: 0.7812 (pt) REVERT: D 397 TRP cc_start: 0.8347 (m100) cc_final: 0.7884 (m100) REVERT: D 427 ASP cc_start: 0.8091 (m-30) cc_final: 0.7502 (t70) REVERT: I 6 HIS cc_start: 0.9250 (t70) cc_final: 0.8601 (t70) REVERT: I 14 ASN cc_start: 0.9320 (m-40) cc_final: 0.9067 (m-40) REVERT: I 95 SER cc_start: 0.9213 (m) cc_final: 0.8802 (t) REVERT: I 100 ASN cc_start: 0.8857 (t0) cc_final: 0.8642 (t0) REVERT: I 156 ARG cc_start: 0.9206 (tpp80) cc_final: 0.8823 (tpp80) REVERT: I 164 MET cc_start: 0.8480 (mtm) cc_final: 0.7377 (mtp) REVERT: I 273 LEU cc_start: 0.8866 (mt) cc_final: 0.8501 (mt) REVERT: I 276 ARG cc_start: 0.8710 (mmm-85) cc_final: 0.8344 (mmp80) REVERT: I 300 MET cc_start: 0.8476 (mtt) cc_final: 0.8029 (mtm) REVERT: I 306 ARG cc_start: 0.8696 (mpt180) cc_final: 0.8328 (mpt180) REVERT: I 347 ASN cc_start: 0.9172 (m110) cc_final: 0.8633 (m-40) REVERT: I 355 ASP cc_start: 0.8111 (m-30) cc_final: 0.7382 (m-30) REVERT: I 363 MET cc_start: 0.8977 (pmm) cc_final: 0.8484 (pmm) REVERT: I 379 LYS cc_start: 0.9355 (mtpt) cc_final: 0.9072 (ttmm) REVERT: I 407 GLU cc_start: 0.9128 (tp30) cc_final: 0.8493 (tp30) REVERT: I 427 ASP cc_start: 0.8024 (m-30) cc_final: 0.7518 (t70) REVERT: B 14 ASN cc_start: 0.9431 (m-40) cc_final: 0.9133 (m-40) REVERT: B 37 HIS cc_start: 0.7535 (m90) cc_final: 0.7057 (m90) REVERT: B 95 SER cc_start: 0.9057 (m) cc_final: 0.8680 (t) REVERT: B 100 ASN cc_start: 0.9070 (t0) cc_final: 0.8779 (t0) REVERT: B 114 ASP cc_start: 0.8509 (m-30) cc_final: 0.7800 (t0) REVERT: B 125 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7805 (tt0) REVERT: B 130 LEU cc_start: 0.9247 (tp) cc_final: 0.8823 (tt) REVERT: B 147 MET cc_start: 0.9327 (tpp) cc_final: 0.9041 (tpp) REVERT: B 164 MET cc_start: 0.9001 (ttm) cc_final: 0.8730 (ttm) REVERT: B 167 PHE cc_start: 0.8576 (m-80) cc_final: 0.7643 (m-10) REVERT: B 203 ASP cc_start: 0.8259 (t0) cc_final: 0.7820 (t0) REVERT: B 205 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8794 (mt-10) REVERT: B 246 LEU cc_start: 0.9472 (tt) cc_final: 0.9236 (tt) REVERT: B 299 MET cc_start: 0.8452 (mmm) cc_final: 0.7966 (mmt) REVERT: B 343 GLU cc_start: 0.8654 (tp30) cc_final: 0.8240 (tp30) REVERT: B 344 TRP cc_start: 0.8854 (p-90) cc_final: 0.8498 (p-90) REVERT: B 388 MET cc_start: 0.9153 (mtp) cc_final: 0.8943 (mtp) REVERT: B 406 MET cc_start: 0.8568 (tpp) cc_final: 0.8146 (mpp) REVERT: B 427 ASP cc_start: 0.8228 (m-30) cc_final: 0.7782 (t70) REVERT: H 14 ASN cc_start: 0.9412 (m-40) cc_final: 0.9074 (m-40) REVERT: H 74 ASP cc_start: 0.8608 (t70) cc_final: 0.8389 (t70) REVERT: H 95 SER cc_start: 0.8956 (m) cc_final: 0.8575 (t) REVERT: H 100 ASN cc_start: 0.8965 (t0) cc_final: 0.8765 (t0) REVERT: H 147 MET cc_start: 0.9455 (tpp) cc_final: 0.9210 (mmm) REVERT: H 181 GLU cc_start: 0.8765 (pt0) cc_final: 0.8011 (mt-10) REVERT: H 299 MET cc_start: 0.8415 (mmp) cc_final: 0.7966 (mmt) REVERT: H 340 TYR cc_start: 0.8677 (m-10) cc_final: 0.8444 (m-80) REVERT: H 363 MET cc_start: 0.8890 (pmm) cc_final: 0.8652 (pmm) REVERT: H 397 TRP cc_start: 0.8444 (m100) cc_final: 0.8217 (m-10) REVERT: H 406 MET cc_start: 0.8429 (tpp) cc_final: 0.8097 (tpp) REVERT: H 422 TYR cc_start: 0.8941 (m-80) cc_final: 0.8727 (m-80) REVERT: H 427 ASP cc_start: 0.8288 (m-30) cc_final: 0.7868 (t70) outliers start: 1 outliers final: 0 residues processed: 1077 average time/residue: 0.2377 time to fit residues: 435.2725 Evaluate side-chains 892 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 892 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 60 optimal weight: 0.9990 chunk 353 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 287 optimal weight: 7.9990 chunk 385 optimal weight: 9.9990 chunk 366 optimal weight: 7.9990 chunk 441 optimal weight: 7.9990 chunk 463 optimal weight: 5.9990 chunk 327 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN H 37 HIS ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN H 375 GLN H 416 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.095556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.084642 restraints weight = 94163.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.087370 restraints weight = 52878.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.089235 restraints weight = 33335.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.090556 restraints weight = 22746.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.091505 restraints weight = 16439.874| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 41820 Z= 0.166 Angle : 0.612 9.937 56826 Z= 0.306 Chirality : 0.046 0.304 6216 Planarity : 0.004 0.057 7398 Dihedral : 9.766 165.086 5778 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.02 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.12), residues: 5130 helix: 0.80 (0.11), residues: 2334 sheet: 0.57 (0.21), residues: 690 loop : -1.00 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 221 TYR 0.021 0.002 TYR L 224 PHE 0.019 0.001 PHE G 367 TRP 0.020 0.002 TRP L 21 HIS 0.008 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00379 (41820) covalent geometry : angle 0.61159 (56826) hydrogen bonds : bond 0.03582 ( 1566) hydrogen bonds : angle 4.40813 ( 4644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8457.86 seconds wall clock time: 146 minutes 38.24 seconds (8798.24 seconds total)