Starting phenix.real_space_refine on Tue Sep 15 15:13:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ew0_3965/09_2026/6ew0_3965.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ew0_3965/09_2026/6ew0_3965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ew0_3965/09_2026/6ew0_3965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ew0_3965/09_2026/6ew0_3965.map" model { file = "/net/cci-nas-00/data/ceres_data/6ew0_3965/09_2026/6ew0_3965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ew0_3965/09_2026/6ew0_3965.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ew0_3965/09_2026/6ew0_3965.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ew0_3965/09_2026/6ew0_3965.cif" } resolution = 3.8 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= 0.012 sd= 0.043 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 30 5.49 5 Mg 6 5.21 5 S 276 5.16 5 C 25956 2.51 5 N 6984 2.21 5 O 7986 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41238 Number of models: 1 Model: "" Number of chains: 25 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 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: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.63, per 1000 atoms: 0.23 Number of scatterers: 41238 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 276 16.00 P 30 15.00 Mg 6 11.99 O 7986 8.00 N 6984 7.00 C 25956 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: 3.24 Conformation dependent library (CDL) restraints added in 1.7 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: 222 helices and 42 sheets defined 49.8% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'E' and resid 10 through 27 removed outlier: 3.834A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 51 removed outlier: 4.348A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 81 removed outlier: 3.836A pdb=" N ASP E 76 " --> pdb=" O PRO E 72 " (cutoff:3.500A) removed outlier: 3.555A 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: 4.030A pdb=" N ILE E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.597A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER E 151 " --> pdb=" O SER E 147 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER E 158 " --> pdb=" O MET E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 3.914A pdb=" N ILE E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 223 through 239 removed outlier: 3.725A pdb=" N LEU E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 244 removed outlier: 3.665A pdb=" N ARG E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 259 removed outlier: 3.589A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 293 removed outlier: 4.197A pdb=" N ASN E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.623A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.680A pdb=" N ASN E 329 " --> pdb=" O PRO E 325 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 401 removed outlier: 3.535A pdb=" N LEU E 397 " --> pdb=" O HIS E 393 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 3.531A pdb=" N GLY E 410 " --> pdb=" O HIS E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 437 removed outlier: 3.871A pdb=" N GLU E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP E 431 " --> pdb=" O ALA E 427 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 27 removed outlier: 3.553A pdb=" N LYS F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 49 removed outlier: 3.813A 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: 4.695A 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 106 through 111 removed outlier: 3.764A pdb=" N ALA F 110 " --> pdb=" O TYR F 106 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU F 111 " --> pdb=" O THR F 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 111' Processing helix chain 'F' and resid 112 through 127 removed outlier: 3.959A pdb=" N VAL F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER F 126 " --> pdb=" O LYS F 122 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS F 127 " --> pdb=" O GLU F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 159 removed outlier: 3.643A pdb=" N GLY F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU F 158 " --> pdb=" O LYS F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 193 removed outlier: 3.521A pdb=" N THR F 186 " --> pdb=" O PRO F 182 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 removed outlier: 3.580A pdb=" N ASP F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE F 212 " --> pdb=" O TYR F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 235 removed outlier: 3.809A pdb=" N HIS F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 240 removed outlier: 4.269A pdb=" N CYS F 239 " --> pdb=" O VAL F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 Processing helix chain 'F' and resid 276 through 280 removed outlier: 4.018A pdb=" N GLN F 279 " --> pdb=" O ARG F 276 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN F 280 " --> pdb=" O GLY F 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 276 through 280' Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.874A pdb=" N GLN F 292 " --> pdb=" O GLU F 288 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE F 294 " --> pdb=" O THR F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 299 removed outlier: 3.673A pdb=" N MET F 299 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 336 removed outlier: 3.612A pdb=" N ASN F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 390 Processing helix chain 'F' and resid 395 through 400 Processing helix chain 'F' and resid 404 through 428 removed outlier: 4.000A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP F 427 " --> pdb=" O GLN F 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 27 removed outlier: 3.834A pdb=" N ALA J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU J 26 " --> pdb=" O GLU J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 51 removed outlier: 4.348A pdb=" N THR J 51 " --> pdb=" O SER J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 81 removed outlier: 3.836A pdb=" N ASP J 76 " --> pdb=" O PRO J 72 " (cutoff:3.500A) removed outlier: 3.555A 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: 4.029A pdb=" N ILE J 114 " --> pdb=" O ILE J 110 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASP J 116 " --> pdb=" O LYS J 112 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS J 129 " --> pdb=" O LEU J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 161 removed outlier: 4.598A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER J 151 " --> pdb=" O SER J 147 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU J 155 " --> pdb=" O SER J 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER J 158 " --> pdb=" O MET J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 195 removed outlier: 3.915A pdb=" N ILE J 188 " --> pdb=" O PRO J 184 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 216 Processing helix chain 'J' and resid 223 through 239 removed outlier: 3.725A pdb=" N LEU J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 244 removed outlier: 3.666A pdb=" N ARG J 243 " --> pdb=" O THR J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 259 removed outlier: 3.588A pdb=" N PHE J 255 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 293 removed outlier: 4.197A pdb=" N ASN J 293 " --> pdb=" O ALA J 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 301 removed outlier: 3.623A pdb=" N GLN J 301 " --> pdb=" O PRO J 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 336 removed outlier: 3.680A pdb=" N ASN J 329 " --> pdb=" O PRO J 325 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE J 335 " --> pdb=" O ALA J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 401 removed outlier: 3.535A pdb=" N LEU J 397 " --> pdb=" O HIS J 393 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET J 398 " --> pdb=" O LYS J 394 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS J 401 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 410 removed outlier: 3.532A pdb=" N GLY J 410 " --> pdb=" O HIS J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 437 removed outlier: 3.870A pdb=" N GLU J 420 " --> pdb=" O GLY J 416 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP J 431 " --> pdb=" O ALA J 427 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR J 432 " --> pdb=" O LEU J 428 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU J 433 " --> pdb=" O GLU J 429 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 27 removed outlier: 3.834A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 4.348A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.835A pdb=" N ASP C 76 " --> pdb=" O PRO C 72 " (cutoff:3.500A) removed outlier: 3.555A 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: 4.030A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.598A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.914A pdb=" N ILE C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.725A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 removed outlier: 3.665A pdb=" N ARG C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 removed outlier: 3.588A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 293 removed outlier: 4.197A pdb=" N ASN C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 removed outlier: 3.623A pdb=" N GLN C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.680A pdb=" N ASN C 329 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.535A pdb=" N LEU C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET C 398 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.532A pdb=" N GLY C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 437 removed outlier: 3.871A pdb=" N GLU C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP C 431 " --> pdb=" O ALA C 427 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 27 removed outlier: 3.834A pdb=" N ALA L 19 " --> pdb=" O GLN L 15 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU L 26 " --> pdb=" O GLU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 51 removed outlier: 4.349A pdb=" N THR L 51 " --> pdb=" O SER L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 81 removed outlier: 3.836A pdb=" N ASP L 76 " --> pdb=" O PRO L 72 " (cutoff:3.500A) removed outlier: 3.554A 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: 4.030A pdb=" N ILE L 114 " --> pdb=" O ILE L 110 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASP L 116 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU L 117 " --> pdb=" O GLU L 113 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS L 129 " --> pdb=" O LEU L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 161 removed outlier: 4.598A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER L 151 " --> pdb=" O SER L 147 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU L 155 " --> pdb=" O SER L 151 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER L 158 " --> pdb=" O MET L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 195 removed outlier: 3.913A pdb=" N ILE L 188 " --> pdb=" O PRO L 184 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR L 193 " --> pdb=" O LEU L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 216 Processing helix chain 'L' and resid 223 through 239 removed outlier: 3.725A pdb=" N LEU L 230 " --> pdb=" O ASN L 226 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE L 234 " --> pdb=" O LEU L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 244 removed outlier: 3.666A pdb=" N ARG L 243 " --> pdb=" O THR L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 259 removed outlier: 3.588A pdb=" N PHE L 255 " --> pdb=" O ASP L 251 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 293 removed outlier: 4.198A pdb=" N ASN L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 301 removed outlier: 3.623A pdb=" N GLN L 301 " --> pdb=" O PRO L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 336 removed outlier: 3.680A pdb=" N ASN L 329 " --> pdb=" O PRO L 325 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE L 335 " --> pdb=" O ALA L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 401 removed outlier: 3.536A pdb=" N LEU L 397 " --> pdb=" O HIS L 393 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET L 398 " --> pdb=" O LYS L 394 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 410 removed outlier: 3.532A pdb=" N GLY L 410 " --> pdb=" O HIS L 406 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 437 removed outlier: 3.871A pdb=" N GLU L 420 " --> pdb=" O GLY L 416 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP L 431 " --> pdb=" O ALA L 427 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR L 432 " --> pdb=" O LEU L 428 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU L 433 " --> pdb=" O GLU L 429 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.834A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 4.348A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.837A pdb=" N ASP A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 3.554A 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: 4.029A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.598A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.914A pdb=" N ILE A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.724A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.666A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.589A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 293 removed outlier: 4.197A pdb=" N ASN A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.623A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.680A pdb=" N ASN A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.535A pdb=" N LEU A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.532A pdb=" N GLY A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 437 removed outlier: 3.871A pdb=" N GLU A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 27 removed outlier: 3.834A pdb=" N ALA K 19 " --> pdb=" O GLN K 15 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU K 26 " --> pdb=" O GLU K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 51 removed outlier: 4.348A pdb=" N THR K 51 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.836A pdb=" N ASP K 76 " --> pdb=" O PRO K 72 " (cutoff:3.500A) removed outlier: 3.554A 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: 4.030A pdb=" N ILE K 114 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASP K 116 " --> pdb=" O LYS K 112 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU K 117 " --> pdb=" O GLU K 113 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS K 129 " --> pdb=" O LEU K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 161 removed outlier: 4.598A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER K 151 " --> pdb=" O SER K 147 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER K 158 " --> pdb=" O MET K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 195 removed outlier: 3.914A pdb=" N ILE K 188 " --> pdb=" O PRO K 184 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 216 Processing helix chain 'K' and resid 223 through 239 removed outlier: 3.725A pdb=" N LEU K 230 " --> pdb=" O ASN K 226 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE K 234 " --> pdb=" O LEU K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 244 removed outlier: 3.666A pdb=" N ARG K 243 " --> pdb=" O THR K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 259 removed outlier: 3.587A pdb=" N PHE K 255 " --> pdb=" O ASP K 251 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 293 removed outlier: 4.197A pdb=" N ASN K 293 " --> pdb=" O ALA K 289 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 301 removed outlier: 3.623A pdb=" N GLN K 301 " --> pdb=" O PRO K 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 336 removed outlier: 3.680A pdb=" N ASN K 329 " --> pdb=" O PRO K 325 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE K 335 " --> pdb=" O ALA K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 401 removed outlier: 3.536A pdb=" N LEU K 397 " --> pdb=" O HIS K 393 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET K 398 " --> pdb=" O LYS K 394 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 removed outlier: 3.532A pdb=" N GLY K 410 " --> pdb=" O HIS K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 437 removed outlier: 3.871A pdb=" N GLU K 420 " --> pdb=" O GLY K 416 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP K 431 " --> pdb=" O ALA K 427 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR K 432 " --> pdb=" O LEU K 428 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU K 433 " --> pdb=" O GLU K 429 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 27 removed outlier: 3.552A pdb=" N LYS G 19 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 49 removed outlier: 3.813A 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: 4.696A 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 106 through 111 removed outlier: 3.764A pdb=" N ALA G 110 " --> pdb=" O TYR G 106 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU G 111 " --> pdb=" O THR G 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 106 through 111' Processing helix chain 'G' and resid 112 through 127 removed outlier: 3.958A pdb=" N VAL G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS G 122 " --> pdb=" O ASP G 118 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER G 126 " --> pdb=" O LYS G 122 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS G 127 " --> pdb=" O GLU G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 159 removed outlier: 3.644A pdb=" N GLY G 148 " --> pdb=" O GLY G 144 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU G 157 " --> pdb=" O SER G 153 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 158 " --> pdb=" O LYS G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 193 removed outlier: 3.522A pdb=" N THR G 186 " --> pdb=" O PRO G 182 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN G 191 " --> pdb=" O LEU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 214 removed outlier: 3.580A pdb=" N ASP G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE G 212 " --> pdb=" O TYR G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 235 removed outlier: 3.809A pdb=" N HIS G 227 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL G 229 " --> pdb=" O LEU G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 240 removed outlier: 4.270A pdb=" N CYS G 239 " --> pdb=" O VAL G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 257 Processing helix chain 'G' and resid 276 through 280 removed outlier: 4.018A pdb=" N GLN G 279 " --> pdb=" O ARG G 276 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN G 280 " --> pdb=" O GLY G 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 276 through 280' Processing helix chain 'G' and resid 285 through 294 removed outlier: 3.874A pdb=" N GLN G 292 " --> pdb=" O GLU G 288 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE G 294 " --> pdb=" O THR G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 299 removed outlier: 3.672A pdb=" N MET G 299 " --> pdb=" O ALA G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 336 removed outlier: 3.613A pdb=" N ASN G 332 " --> pdb=" O GLU G 328 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN G 334 " --> pdb=" O MET G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 390 Processing helix chain 'G' and resid 395 through 400 Processing helix chain 'G' and resid 404 through 428 removed outlier: 4.000A pdb=" N PHE G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP G 427 " --> pdb=" O GLN G 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 27 removed outlier: 3.552A pdb=" N LYS D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 49 removed outlier: 3.812A 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: 4.696A 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 106 through 111 removed outlier: 3.765A pdb=" N ALA D 110 " --> pdb=" O TYR D 106 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 111' Processing helix chain 'D' and resid 112 through 127 removed outlier: 3.960A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 removed outlier: 3.643A pdb=" N GLY D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU D 158 " --> pdb=" O LYS D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 193 removed outlier: 3.522A pdb=" N THR D 186 " --> pdb=" O PRO D 182 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 removed outlier: 3.579A pdb=" N ASP D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 212 " --> pdb=" O TYR D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 235 removed outlier: 3.808A pdb=" N HIS D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 240 removed outlier: 4.270A pdb=" N CYS D 239 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 257 Processing helix chain 'D' and resid 276 through 280 removed outlier: 4.018A pdb=" N GLN D 279 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN D 280 " --> pdb=" O GLY D 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 276 through 280' Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.874A pdb=" N GLN D 292 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 299 removed outlier: 3.673A pdb=" N MET D 299 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 336 removed outlier: 3.613A pdb=" N ASN D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 390 Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 404 through 428 removed outlier: 4.000A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 27 removed outlier: 3.552A pdb=" N LYS I 19 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 49 removed outlier: 3.812A 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: 4.695A 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 106 through 111 removed outlier: 3.764A pdb=" N ALA I 110 " --> pdb=" O TYR I 106 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU I 111 " --> pdb=" O THR I 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 106 through 111' Processing helix chain 'I' and resid 112 through 127 removed outlier: 3.959A pdb=" N VAL I 119 " --> pdb=" O SER I 115 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS I 122 " --> pdb=" O ASP I 118 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS I 127 " --> pdb=" O GLU I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 159 removed outlier: 3.644A pdb=" N GLY I 148 " --> pdb=" O GLY I 144 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU I 157 " --> pdb=" O SER I 153 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU I 158 " --> pdb=" O LYS I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 193 removed outlier: 3.522A pdb=" N THR I 186 " --> pdb=" O PRO I 182 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 214 removed outlier: 3.579A pdb=" N ASP I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE I 212 " --> pdb=" O TYR I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 235 removed outlier: 3.808A pdb=" N HIS I 227 " --> pdb=" O GLY I 223 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU I 228 " --> pdb=" O ASP I 224 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL I 229 " --> pdb=" O LEU I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 240 removed outlier: 4.270A pdb=" N CYS I 239 " --> pdb=" O VAL I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 257 Processing helix chain 'I' and resid 276 through 280 removed outlier: 4.017A pdb=" N GLN I 279 " --> pdb=" O ARG I 276 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN I 280 " --> pdb=" O GLY I 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 276 through 280' Processing helix chain 'I' and resid 285 through 294 removed outlier: 3.875A pdb=" N GLN I 292 " --> pdb=" O GLU I 288 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE I 294 " --> pdb=" O THR I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 299 removed outlier: 3.673A pdb=" N MET I 299 " --> pdb=" O ALA I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 322 through 336 removed outlier: 3.613A pdb=" N ASN I 332 " --> pdb=" O GLU I 328 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN I 334 " --> pdb=" O MET I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 390 Processing helix chain 'I' and resid 395 through 400 Processing helix chain 'I' and resid 404 through 428 removed outlier: 4.001A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP I 427 " --> pdb=" O GLN I 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 27 removed outlier: 3.552A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.813A 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: 4.695A 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 106 through 111 removed outlier: 3.764A pdb=" N ALA B 110 " --> pdb=" O TYR B 106 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 106 through 111' Processing helix chain 'B' and resid 112 through 127 removed outlier: 3.959A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.643A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.522A pdb=" N THR B 186 " --> pdb=" O PRO B 182 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 3.580A pdb=" N ASP B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 212 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 235 removed outlier: 3.809A pdb=" N HIS B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 240 removed outlier: 4.270A pdb=" N CYS B 239 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 257 Processing helix chain 'B' and resid 276 through 280 removed outlier: 4.018A pdb=" N GLN B 279 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN B 280 " --> pdb=" O GLY B 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 276 through 280' Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.875A pdb=" N GLN B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.673A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 336 removed outlier: 3.613A pdb=" N ASN B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 390 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 428 removed outlier: 4.001A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 27 removed outlier: 3.552A pdb=" N LYS H 19 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 49 removed outlier: 3.813A 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: 4.696A 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 106 through 111 removed outlier: 3.765A pdb=" N ALA H 110 " --> pdb=" O TYR H 106 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU H 111 " --> pdb=" O THR H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 111' Processing helix chain 'H' and resid 112 through 127 removed outlier: 3.959A pdb=" N VAL H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS H 122 " --> pdb=" O ASP H 118 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER H 126 " --> pdb=" O LYS H 122 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 159 removed outlier: 3.643A pdb=" N GLY H 148 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU H 157 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU H 158 " --> pdb=" O LYS H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 193 removed outlier: 3.522A pdb=" N THR H 186 " --> pdb=" O PRO H 182 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 214 removed outlier: 3.579A pdb=" N ASP H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE H 210 " --> pdb=" O ALA H 206 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE H 212 " --> pdb=" O TYR H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 235 removed outlier: 3.808A pdb=" N HIS H 227 " --> pdb=" O GLY H 223 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU H 228 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL H 229 " --> pdb=" O LEU H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 240 removed outlier: 4.270A pdb=" N CYS H 239 " --> pdb=" O VAL H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 257 Processing helix chain 'H' and resid 276 through 280 removed outlier: 4.018A pdb=" N GLN H 279 " --> pdb=" O ARG H 276 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN H 280 " --> pdb=" O GLY H 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 276 through 280' Processing helix chain 'H' and resid 285 through 294 removed outlier: 3.874A pdb=" N GLN H 292 " --> pdb=" O GLU H 288 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE H 294 " --> pdb=" O THR H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 299 removed outlier: 3.673A pdb=" N MET H 299 " --> pdb=" O ALA H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 336 removed outlier: 3.613A pdb=" N ASN H 332 " --> pdb=" O GLU H 328 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN H 334 " --> pdb=" O MET H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 390 Processing helix chain 'H' and resid 395 through 400 Processing helix chain 'H' and resid 404 through 428 removed outlier: 4.001A pdb=" N PHE H 408 " --> pdb=" O ASP H 404 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP H 427 " --> pdb=" O GLN H 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 65 through 68 removed outlier: 7.142A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.554A 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: 3.526A 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 91 removed outlier: 7.982A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLU F 3 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE F 163 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU F 198 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR F 166 " --> pdb=" O GLU F 198 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain 'F' and resid 267 through 271 removed outlier: 3.529A pdb=" N ALA F 271 " --> pdb=" O ALA F 365 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER F 364 " --> pdb=" O PHE F 317 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE F 317 " --> pdb=" O SER F 364 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR F 366 " --> pdb=" O ALA F 315 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA F 315 " --> pdb=" O THR F 366 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE F 368 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL F 313 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN F 370 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 65 through 68 removed outlier: 7.142A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE J 135 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE J 169 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL J 137 " --> pdb=" O PHE J 169 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE J 171 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LYS J 166 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N PHE J 202 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER J 170 " --> pdb=" O VAL J 204 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 53 through 55 removed outlier: 3.525A pdb=" N VAL J 62 " --> pdb=" O SER J 54 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 269 through 273 Processing sheet with id=AB2, first strand: chain 'C' and resid 65 through 68 removed outlier: 7.142A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.526A pdb=" N VAL C 62 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 269 through 273 Processing sheet with id=AB5, first strand: chain 'L' and resid 65 through 68 removed outlier: 7.143A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE L 135 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE L 169 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL L 137 " --> pdb=" O PHE L 169 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE L 171 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 53 through 55 removed outlier: 3.525A pdb=" N VAL L 62 " --> pdb=" O SER L 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 269 through 273 Processing sheet with id=AB8, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.142A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.526A pdb=" N VAL A 62 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 269 through 273 Processing sheet with id=AC2, first strand: chain 'K' and resid 65 through 68 removed outlier: 7.142A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE K 135 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE K 169 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL K 137 " --> pdb=" O PHE K 169 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE K 171 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 53 through 55 removed outlier: 3.526A pdb=" N VAL K 62 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 269 through 273 Processing sheet with id=AC5, first strand: chain 'G' and resid 90 through 91 removed outlier: 7.982A pdb=" N VAL G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU G 65 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLU G 3 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE G 163 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU G 198 " --> pdb=" O MET G 164 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR G 166 " --> pdb=" O GLU G 198 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 51 through 53 Processing sheet with id=AC7, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AC8, first strand: chain 'G' and resid 267 through 271 removed outlier: 3.527A pdb=" N ALA G 271 " --> pdb=" O ALA G 365 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER G 364 " --> pdb=" O PHE G 317 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE G 317 " --> pdb=" O SER G 364 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR G 366 " --> pdb=" O ALA G 315 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA G 315 " --> pdb=" O THR G 366 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE G 368 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL G 313 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASN G 370 " --> pdb=" O LEU G 311 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 90 through 91 removed outlier: 7.981A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLU D 3 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE D 163 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D 198 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 166 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AD2, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AD3, first strand: chain 'D' and resid 267 through 271 removed outlier: 3.528A pdb=" N ALA D 271 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER D 364 " --> pdb=" O PHE D 317 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE D 317 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR D 366 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA D 315 " --> pdb=" O THR D 366 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE D 368 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL D 313 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN D 370 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 90 through 91 removed outlier: 7.982A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLU I 3 " --> pdb=" O LEU I 130 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE I 163 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU I 198 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR I 166 " --> pdb=" O GLU I 198 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AD6, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AD7, first strand: chain 'I' and resid 267 through 271 removed outlier: 3.528A pdb=" N ALA I 271 " --> pdb=" O ALA I 365 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER I 364 " --> pdb=" O PHE I 317 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE I 317 " --> pdb=" O SER I 364 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR I 366 " --> pdb=" O ALA I 315 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA I 315 " --> pdb=" O THR I 366 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE I 368 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL I 313 " --> pdb=" O ILE I 368 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN I 370 " --> pdb=" O LEU I 311 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 90 through 91 removed outlier: 7.982A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 198 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 166 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AE1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AE2, first strand: chain 'B' and resid 267 through 271 removed outlier: 3.528A pdb=" N ALA B 271 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER B 364 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE B 317 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR B 366 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA B 315 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 368 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL B 313 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN B 370 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 90 through 91 removed outlier: 7.982A pdb=" N VAL H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU H 65 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLU H 3 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE H 163 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU H 198 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR H 166 " --> pdb=" O GLU H 198 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 51 through 53 Processing sheet with id=AE5, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AE6, first strand: chain 'H' and resid 267 through 271 removed outlier: 3.528A pdb=" N ALA H 271 " --> pdb=" O ALA H 365 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER H 364 " --> pdb=" O PHE H 317 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE H 317 " --> pdb=" O SER H 364 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR H 366 " --> pdb=" O ALA H 315 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA H 315 " --> pdb=" O THR H 366 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE H 368 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL H 313 " --> pdb=" O ILE H 368 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN H 370 " --> pdb=" O LEU H 311 " (cutoff:3.500A) 1620 hydrogen bonds defined for protein. 4698 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: 10.77 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6978 1.32 - 1.44: 11455 1.44 - 1.56: 23255 1.56 - 1.68: 84 1.68 - 1.81: 432 Bond restraints: 42204 Sorted by residual: bond pdb=" C5 GDP F 501 " pdb=" C4 GDP F 501 " ideal model delta sigma weight residual 1.490 1.372 0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" C5 GDP H 502 " pdb=" C4 GDP H 502 " ideal model delta sigma weight residual 1.490 1.374 0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C5 GDP I 502 " pdb=" C4 GDP I 502 " ideal model delta sigma weight residual 1.490 1.374 0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C5 GDP G 502 " pdb=" C4 GDP G 502 " ideal model delta sigma weight residual 1.490 1.374 0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C5 GDP B 502 " pdb=" C4 GDP B 502 " ideal model delta sigma weight residual 1.490 1.374 0.116 2.00e-02 2.50e+03 3.34e+01 ... (remaining 42199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 56977 3.98 - 7.96: 351 7.96 - 11.94: 62 11.94 - 15.92: 13 15.92 - 19.91: 11 Bond angle restraints: 57414 Sorted by residual: angle pdb=" C20 TA1 F 502 " pdb=" C21 TA1 F 502 " pdb=" C24 TA1 F 502 " ideal model delta sigma weight residual 107.07 126.98 -19.91 3.00e+00 1.11e-01 4.40e+01 angle pdb=" C20 TA1 G 501 " pdb=" C21 TA1 G 501 " pdb=" C24 TA1 G 501 " ideal model delta sigma weight residual 107.07 126.05 -18.98 3.00e+00 1.11e-01 4.00e+01 angle pdb=" C20 TA1 B 501 " pdb=" C21 TA1 B 501 " pdb=" C24 TA1 B 501 " ideal model delta sigma weight residual 107.07 126.03 -18.96 3.00e+00 1.11e-01 3.99e+01 angle pdb=" C20 TA1 D 501 " pdb=" C21 TA1 D 501 " pdb=" C24 TA1 D 501 " ideal model delta sigma weight residual 107.07 125.97 -18.90 3.00e+00 1.11e-01 3.97e+01 angle pdb=" C20 TA1 I 501 " pdb=" C21 TA1 I 501 " pdb=" C24 TA1 I 501 " ideal model delta sigma weight residual 107.07 125.93 -18.86 3.00e+00 1.11e-01 3.95e+01 ... (remaining 57409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 24648 34.18 - 68.35: 184 68.35 - 102.53: 30 102.53 - 136.70: 9 136.70 - 170.88: 17 Dihedral angle restraints: 24888 sinusoidal: 9960 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 -119.85 -170.88 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C8 GTP E 501 " pdb=" C1' GTP E 501 " pdb=" N9 GTP E 501 " pdb=" O4' GTP E 501 " ideal model delta sinusoidal sigma weight residual 104.59 -61.02 165.61 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C8 GTP C 501 " pdb=" C1' GTP C 501 " pdb=" N9 GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sinusoidal sigma weight residual 104.59 -59.63 164.23 1 2.00e+01 2.50e-03 4.71e+01 ... (remaining 24885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 5133 0.065 - 0.130: 1023 0.130 - 0.195: 90 0.195 - 0.260: 24 0.260 - 0.325: 12 Chirality restraints: 6282 Sorted by residual: chirality pdb=" C18 TA1 B 501 " pdb=" C10 TA1 B 501 " pdb=" C17 TA1 B 501 " pdb=" C20 TA1 B 501 " both_signs ideal model delta sigma weight residual False -3.16 -2.84 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" C18 TA1 I 501 " pdb=" C10 TA1 I 501 " pdb=" C17 TA1 I 501 " pdb=" C20 TA1 I 501 " both_signs ideal model delta sigma weight residual False -3.16 -2.84 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" C18 TA1 G 501 " pdb=" C10 TA1 G 501 " pdb=" C17 TA1 G 501 " pdb=" C20 TA1 G 501 " both_signs ideal model delta sigma weight residual False -3.16 -2.85 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 6279 not shown) Planarity restraints: 7452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 TA1 G 501 " 0.052 2.00e-02 2.50e+03 4.32e-02 2.33e+01 pdb=" C30 TA1 G 501 " -0.031 2.00e-02 2.50e+03 pdb=" C31 TA1 G 501 " 0.045 2.00e-02 2.50e+03 pdb=" N01 TA1 G 501 " -0.060 2.00e-02 2.50e+03 pdb=" O14 TA1 G 501 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C29 TA1 H 501 " 0.049 2.00e-02 2.50e+03 4.04e-02 2.04e+01 pdb=" C30 TA1 H 501 " -0.029 2.00e-02 2.50e+03 pdb=" C31 TA1 H 501 " 0.042 2.00e-02 2.50e+03 pdb=" N01 TA1 H 501 " -0.056 2.00e-02 2.50e+03 pdb=" O14 TA1 H 501 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C30 TA1 G 501 " -0.053 2.00e-02 2.50e+03 3.28e-02 1.89e+01 pdb=" C31 TA1 G 501 " 0.038 2.00e-02 2.50e+03 pdb=" C32 TA1 G 501 " 0.031 2.00e-02 2.50e+03 pdb=" C33 TA1 G 501 " -0.008 2.00e-02 2.50e+03 pdb=" C34 TA1 G 501 " -0.033 2.00e-02 2.50e+03 pdb=" C35 TA1 G 501 " -0.008 2.00e-02 2.50e+03 pdb=" C36 TA1 G 501 " 0.033 2.00e-02 2.50e+03 ... (remaining 7449 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 446 2.64 - 3.21: 35928 3.21 - 3.77: 61550 3.77 - 4.34: 88322 4.34 - 4.90: 144179 Nonbonded interactions: 330425 Sorted by model distance: nonbonded pdb=" O3G GTP L 501 " pdb="MG MG L 502 " model vdw 2.079 2.170 nonbonded pdb=" O1G GTP J 501 " pdb="MG MG J 502 " model vdw 2.081 2.170 nonbonded pdb=" O2G GTP A 501 " pdb="MG MG A 502 " model vdw 2.082 2.170 nonbonded pdb=" O1G GTP E 501 " pdb="MG MG E 502 " model vdw 2.091 2.170 nonbonded pdb=" O2B GTP K 501 " pdb="MG MG K 502 " model vdw 2.092 2.170 ... (remaining 330420 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'B' and resid 1 through 429) selection = (chain 'D' and resid 1 through 429) selection = (chain 'F' and resid 1 through 429) selection = (chain 'G' and resid 1 through 429) selection = (chain 'H' and resid 1 through 429) selection = (chain 'I' and resid 1 through 429) } 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: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 39.550 Find NCS groups from input model: 1.320 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 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 0.118 42204 Z= 0.282 Angle : 0.934 19.905 57414 Z= 0.447 Chirality : 0.054 0.325 6282 Planarity : 0.007 0.059 7452 Dihedral : 11.332 170.877 15312 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: -4.67 (0.09), residues: 5130 helix: -4.17 (0.04), residues: 2202 sheet: -0.54 (0.19), residues: 786 loop : -2.73 (0.10), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 390 TYR 0.023 0.002 TYR H 208 PHE 0.015 0.002 PHE C 202 TRP 0.027 0.003 TRP I 101 HIS 0.014 0.002 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.28 (42204) covalent geometry : angle 0.93380 / 0.45 (57414) hydrogen bonds : bond 0.31309 / 20.79 ( 1620) hydrogen bonds : angle 9.24372 / 6.48 ( 4698) *********************** 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 1472 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1472 time to evaluate : 1.496 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: symmetry clash REVERT: E 3 GLU cc_start: 0.8839 (mp0) cc_final: 0.8149 (mp0) REVERT: E 31 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8475 (mt0) REVERT: E 50 ASN cc_start: 0.9315 (t0) cc_final: 0.8775 (t0) REVERT: E 84 ARG cc_start: 0.8819 (ttp-110) cc_final: 0.8531 (mtm110) REVERT: E 115 ILE cc_start: 0.9160 (tp) cc_final: 0.8959 (tp) REVERT: E 120 ASP cc_start: 0.8920 (t70) cc_final: 0.8599 (t0) REVERT: E 123 ARG cc_start: 0.8753 (ttp-110) cc_final: 0.8525 (ttp-170) REVERT: E 124 LYS cc_start: 0.8695 (mttm) cc_final: 0.8307 (mmtm) REVERT: E 127 ASP cc_start: 0.8304 (m-30) cc_final: 0.8078 (m-30) REVERT: E 129 CYS cc_start: 0.8201 (m) cc_final: 0.7905 (m) REVERT: E 145 THR cc_start: 0.9291 (m) cc_final: 0.8943 (p) REVERT: E 154 MET cc_start: 0.9455 (mmm) cc_final: 0.9251 (mmm) REVERT: E 170 SER cc_start: 0.9100 (m) cc_final: 0.8770 (p) REVERT: E 205 ASP cc_start: 0.8565 (t0) cc_final: 0.8139 (t0) REVERT: E 210 TYR cc_start: 0.8934 (m-80) cc_final: 0.8640 (m-10) REVERT: E 221 ARG cc_start: 0.8905 (mtt90) cc_final: 0.8531 (mtt-85) REVERT: E 254 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7877 (mt-10) REVERT: E 313 MET cc_start: 0.8643 (mtm) cc_final: 0.7543 (mtm) REVERT: E 341 ILE cc_start: 0.9229 (mp) cc_final: 0.9013 (mp) REVERT: E 351 PHE cc_start: 0.9119 (m-80) cc_final: 0.8508 (m-80) REVERT: E 411 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8396 (mm-30) REVERT: E 419 SER cc_start: 0.8930 (t) cc_final: 0.8108 (m) REVERT: E 420 GLU cc_start: 0.8381 (tt0) cc_final: 0.7901 (tt0) REVERT: E 431 ASP cc_start: 0.8565 (m-30) cc_final: 0.8124 (m-30) REVERT: E 434 GLU cc_start: 0.8569 (tt0) cc_final: 0.8329 (mm-30) REVERT: F 129 CYS cc_start: 0.8706 (t) cc_final: 0.8211 (p) REVERT: F 136 THR cc_start: 0.9297 (m) cc_final: 0.8664 (p) REVERT: F 166 THR cc_start: 0.9238 (p) cc_final: 0.8972 (p) REVERT: F 174 LYS cc_start: 0.9384 (mtpt) cc_final: 0.9162 (mtpp) REVERT: F 181 GLU cc_start: 0.8410 (pt0) cc_final: 0.8191 (pt0) REVERT: F 233 MET cc_start: 0.8939 (mtp) cc_final: 0.8519 (mtp) REVERT: F 288 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7214 (tm-30) REVERT: F 355 ASP cc_start: 0.8219 (m-30) cc_final: 0.7764 (m-30) REVERT: F 377 LEU cc_start: 0.9438 (tp) cc_final: 0.9196 (tt) REVERT: F 379 LYS cc_start: 0.9284 (mtpt) cc_final: 0.8509 (ptpt) REVERT: F 380 ARG cc_start: 0.8583 (ttp-110) cc_final: 0.8339 (ttp80) REVERT: F 392 LYS cc_start: 0.9441 (mtmt) cc_final: 0.9136 (mtmm) REVERT: F 412 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7868 (tp30) REVERT: J 2 ARG cc_start: 0.7676 (mtm180) cc_final: 0.7078 (mmt90) REVERT: J 3 GLU cc_start: 0.8462 (mp0) cc_final: 0.8250 (mp0) REVERT: J 21 TRP cc_start: 0.9162 (m100) cc_final: 0.8742 (m100) REVERT: J 31 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7588 (mt0) REVERT: J 84 ARG cc_start: 0.8678 (ttp-110) cc_final: 0.8442 (mtp-110) REVERT: J 90 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7944 (mp0) REVERT: J 163 LYS cc_start: 0.8966 (mtpp) cc_final: 0.8764 (mmtt) REVERT: J 168 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6825 (mt-10) REVERT: J 183 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7574 (mt-10) REVERT: J 203 MET cc_start: 0.8799 (mmp) cc_final: 0.8437 (mmm) REVERT: J 221 ARG cc_start: 0.8971 (mtt90) cc_final: 0.8623 (mtt90) REVERT: J 258 ASN cc_start: 0.9285 (m110) cc_final: 0.8991 (m110) REVERT: J 313 MET cc_start: 0.8785 (mtm) cc_final: 0.8148 (mtm) REVERT: J 326 LYS cc_start: 0.9135 (tmtm) cc_final: 0.8919 (pttm) REVERT: J 357 TYR cc_start: 0.7918 (m-80) cc_final: 0.7566 (m-80) REVERT: J 398 MET cc_start: 0.9102 (mtp) cc_final: 0.8699 (mtm) REVERT: C 20 CYS cc_start: 0.8986 (m) cc_final: 0.8770 (m) REVERT: C 31 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8048 (mt0) REVERT: C 121 ARG cc_start: 0.8548 (mmm160) cc_final: 0.8117 (mmm160) REVERT: C 145 THR cc_start: 0.9443 (m) cc_final: 0.9094 (p) REVERT: C 154 MET cc_start: 0.9359 (mmm) cc_final: 0.9020 (mmm) REVERT: C 155 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8644 (mt-10) REVERT: C 170 SER cc_start: 0.8988 (m) cc_final: 0.8768 (t) REVERT: C 207 GLU cc_start: 0.8029 (tt0) cc_final: 0.7583 (tm-30) REVERT: C 213 CYS cc_start: 0.8948 (m) cc_final: 0.8661 (p) REVERT: C 218 ASP cc_start: 0.8875 (m-30) cc_final: 0.8675 (t0) REVERT: C 248 LEU cc_start: 0.9068 (tp) cc_final: 0.8856 (tt) REVERT: C 254 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8286 (mt-10) REVERT: C 351 PHE cc_start: 0.9005 (m-80) cc_final: 0.8644 (m-80) REVERT: C 376 CYS cc_start: 0.9089 (t) cc_final: 0.8812 (t) REVERT: C 392 ASP cc_start: 0.9062 (m-30) cc_final: 0.8637 (m-30) REVERT: C 431 ASP cc_start: 0.8937 (m-30) cc_final: 0.8714 (m-30) REVERT: C 434 GLU cc_start: 0.8713 (tt0) cc_final: 0.8447 (mm-30) REVERT: L 2 ARG cc_start: 0.7793 (mtm180) cc_final: 0.6946 (mmt90) REVERT: L 31 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8125 (mt0) REVERT: L 145 THR cc_start: 0.9383 (m) cc_final: 0.9022 (p) REVERT: L 170 SER cc_start: 0.9160 (m) cc_final: 0.8887 (t) REVERT: L 207 GLU cc_start: 0.8106 (tt0) cc_final: 0.7803 (tm-30) REVERT: L 254 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8174 (mm-30) REVERT: L 279 GLU cc_start: 0.8650 (pt0) cc_final: 0.8093 (pm20) REVERT: L 324 VAL cc_start: 0.9301 (t) cc_final: 0.9064 (p) REVERT: L 326 LYS cc_start: 0.9103 (tmtm) cc_final: 0.8858 (mttp) REVERT: L 351 PHE cc_start: 0.8804 (m-80) cc_final: 0.8535 (m-10) REVERT: L 392 ASP cc_start: 0.9018 (m-30) cc_final: 0.8799 (m-30) REVERT: L 431 ASP cc_start: 0.8961 (m-30) cc_final: 0.8697 (m-30) REVERT: L 434 GLU cc_start: 0.8656 (tt0) cc_final: 0.8402 (mm-30) REVERT: A 2 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7605 (ptp90) REVERT: A 3 GLU cc_start: 0.8773 (mp0) cc_final: 0.8301 (mp0) REVERT: A 35 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8102 (mp10) REVERT: A 36 MET cc_start: 0.8772 (ptm) cc_final: 0.8557 (ptm) REVERT: A 50 ASN cc_start: 0.9138 (t0) cc_final: 0.8626 (t0) REVERT: A 90 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7872 (tp30) REVERT: A 113 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8168 (mt-10) REVERT: A 123 ARG cc_start: 0.9000 (ttp-110) cc_final: 0.8774 (ttm110) REVERT: A 145 THR cc_start: 0.9401 (m) cc_final: 0.8897 (p) REVERT: A 170 SER cc_start: 0.9304 (m) cc_final: 0.8749 (p) REVERT: A 203 MET cc_start: 0.9127 (mmp) cc_final: 0.8836 (mmm) REVERT: A 205 ASP cc_start: 0.8549 (t0) cc_final: 0.8292 (t0) REVERT: A 207 GLU cc_start: 0.7993 (tt0) cc_final: 0.7778 (tm-30) REVERT: A 221 ARG cc_start: 0.8748 (mtt90) cc_final: 0.8345 (mtt-85) REVERT: A 279 GLU cc_start: 0.8826 (pt0) cc_final: 0.8477 (pm20) REVERT: A 351 PHE cc_start: 0.9045 (m-80) cc_final: 0.8748 (m-80) REVERT: A 415 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8440 (tm-30) REVERT: A 417 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8257 (tm-30) REVERT: A 431 ASP cc_start: 0.8696 (m-30) cc_final: 0.8337 (m-30) REVERT: K 2 ARG cc_start: 0.7879 (mtm180) cc_final: 0.6902 (mmt90) REVERT: K 3 GLU cc_start: 0.8625 (mp0) cc_final: 0.8076 (mp0) REVERT: K 23 LEU cc_start: 0.9634 (tp) cc_final: 0.9313 (tp) REVERT: K 36 MET cc_start: 0.8764 (ptm) cc_final: 0.8559 (ttp) REVERT: K 50 ASN cc_start: 0.9121 (t0) cc_final: 0.8600 (t0) REVERT: K 90 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7929 (tp30) REVERT: K 113 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8432 (mp0) REVERT: K 129 CYS cc_start: 0.8057 (m) cc_final: 0.7737 (m) REVERT: K 145 THR cc_start: 0.9466 (m) cc_final: 0.9219 (p) REVERT: K 155 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8631 (mt-10) REVERT: K 170 SER cc_start: 0.9236 (m) cc_final: 0.8919 (p) REVERT: K 183 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8180 (mt-10) REVERT: K 203 MET cc_start: 0.9156 (mmp) cc_final: 0.8708 (mmm) REVERT: K 205 ASP cc_start: 0.8659 (t0) cc_final: 0.8396 (t70) REVERT: K 221 ARG cc_start: 0.8847 (mtt90) cc_final: 0.8406 (mtt-85) REVERT: K 313 MET cc_start: 0.9054 (mtm) cc_final: 0.8415 (mtm) REVERT: K 326 LYS cc_start: 0.9293 (tmtm) cc_final: 0.8814 (mtmt) REVERT: K 397 LEU cc_start: 0.9147 (mt) cc_final: 0.8945 (mt) REVERT: K 415 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8399 (tm-30) REVERT: K 417 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8305 (tm-30) REVERT: K 431 ASP cc_start: 0.8736 (m-30) cc_final: 0.8280 (m-30) REVERT: K 434 GLU cc_start: 0.8585 (tt0) cc_final: 0.8174 (mm-30) REVERT: G 6 HIS cc_start: 0.9133 (t70) cc_final: 0.8931 (t-170) REVERT: G 83 GLN cc_start: 0.8803 (mm110) cc_final: 0.8533 (mm-40) REVERT: G 136 THR cc_start: 0.9347 (m) cc_final: 0.8728 (p) REVERT: G 180 VAL cc_start: 0.9392 (m) cc_final: 0.9049 (p) REVERT: G 218 THR cc_start: 0.8406 (p) cc_final: 0.8155 (p) REVERT: G 288 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7382 (tm-30) REVERT: G 289 LEU cc_start: 0.8810 (mp) cc_final: 0.8123 (mt) REVERT: G 313 VAL cc_start: 0.9590 (t) cc_final: 0.9237 (m) REVERT: G 344 TRP cc_start: 0.8528 (p-90) cc_final: 0.8203 (p-90) REVERT: G 363 MET cc_start: 0.8931 (ptp) cc_final: 0.8519 (ptp) REVERT: G 377 LEU cc_start: 0.9422 (tp) cc_final: 0.9021 (tt) REVERT: G 379 LYS cc_start: 0.9365 (mtpt) cc_final: 0.8544 (ptpt) REVERT: G 392 LYS cc_start: 0.9340 (mtmt) cc_final: 0.9049 (mtmm) REVERT: G 397 TRP cc_start: 0.8974 (m100) cc_final: 0.8712 (m-10) REVERT: D 129 CYS cc_start: 0.8572 (t) cc_final: 0.7847 (t) REVERT: D 136 THR cc_start: 0.9371 (m) cc_final: 0.8759 (p) REVERT: D 263 LEU cc_start: 0.9151 (mp) cc_final: 0.8899 (mt) REVERT: D 288 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6568 (tm-30) REVERT: D 329 GLN cc_start: 0.8789 (mm-40) cc_final: 0.7931 (mt0) REVERT: D 340 TYR cc_start: 0.8077 (m-80) cc_final: 0.7642 (m-80) REVERT: D 364 SER cc_start: 0.9335 (t) cc_final: 0.9059 (m) REVERT: D 374 ILE cc_start: 0.9200 (pp) cc_final: 0.8938 (mp) REVERT: D 377 LEU cc_start: 0.9367 (tp) cc_final: 0.9078 (tt) REVERT: I 129 CYS cc_start: 0.8676 (t) cc_final: 0.8048 (t) REVERT: I 136 THR cc_start: 0.9379 (m) cc_final: 0.8762 (p) REVERT: I 180 VAL cc_start: 0.9479 (m) cc_final: 0.9252 (p) REVERT: I 263 LEU cc_start: 0.9204 (mp) cc_final: 0.8947 (mt) REVERT: I 297 LYS cc_start: 0.8521 (ptpt) cc_final: 0.8305 (mtmm) REVERT: I 329 GLN cc_start: 0.8742 (mm-40) cc_final: 0.7818 (mt0) REVERT: I 340 TYR cc_start: 0.8027 (m-80) cc_final: 0.7544 (m-80) REVERT: I 364 SER cc_start: 0.9275 (t) cc_final: 0.9056 (m) REVERT: I 374 ILE cc_start: 0.9167 (pp) cc_final: 0.8901 (mp) REVERT: I 377 LEU cc_start: 0.9357 (tp) cc_final: 0.9100 (tt) REVERT: I 380 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.8125 (ttm170) REVERT: I 397 TRP cc_start: 0.9152 (m100) cc_final: 0.8636 (m-10) REVERT: I 407 GLU cc_start: 0.9010 (tp30) cc_final: 0.8656 (tp30) REVERT: B 3 GLU cc_start: 0.8334 (mp0) cc_final: 0.7138 (mp0) REVERT: B 108 GLU cc_start: 0.8648 (mp0) cc_final: 0.8410 (mp0) REVERT: B 129 CYS cc_start: 0.8278 (t) cc_final: 0.7945 (p) REVERT: B 136 THR cc_start: 0.9523 (m) cc_final: 0.8899 (p) REVERT: B 166 THR cc_start: 0.9346 (p) cc_final: 0.9145 (p) REVERT: B 180 VAL cc_start: 0.9455 (m) cc_final: 0.8973 (t) REVERT: B 190 HIS cc_start: 0.8949 (t-90) cc_final: 0.8664 (t-170) REVERT: B 198 GLU cc_start: 0.8702 (pt0) cc_final: 0.8409 (pm20) REVERT: B 288 GLU cc_start: 0.7623 (tm-30) cc_final: 0.6731 (tm-30) REVERT: B 313 VAL cc_start: 0.9415 (t) cc_final: 0.8833 (m) REVERT: B 329 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8217 (mt0) REVERT: B 340 TYR cc_start: 0.7832 (m-80) cc_final: 0.7594 (m-80) REVERT: B 363 MET cc_start: 0.9058 (ptp) cc_final: 0.8761 (ptp) REVERT: H 7 ILE cc_start: 0.9125 (mt) cc_final: 0.8887 (mt) REVERT: H 129 CYS cc_start: 0.8552 (t) cc_final: 0.8041 (p) REVERT: H 136 THR cc_start: 0.9529 (m) cc_final: 0.8876 (p) REVERT: H 166 THR cc_start: 0.9326 (p) cc_final: 0.9110 (p) REVERT: H 180 VAL cc_start: 0.9516 (m) cc_final: 0.9037 (p) REVERT: H 198 GLU cc_start: 0.8766 (pt0) cc_final: 0.8355 (pm20) REVERT: H 245 GLN cc_start: 0.8805 (mt0) cc_final: 0.8561 (mt0) REVERT: H 288 GLU cc_start: 0.7537 (tm-30) cc_final: 0.6582 (tm-30) REVERT: H 329 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8022 (mt0) REVERT: H 363 MET cc_start: 0.8908 (ptp) cc_final: 0.8432 (ptp) outliers start: 0 outliers final: 0 residues processed: 1472 average time/residue: 0.2527 time to fit residues: 603.5325 Evaluate side-chains 780 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 780 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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: 8.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 0.0970 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 494 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 overall best weight: 5.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 28 HIS E 107 HIS E 133 GLN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN E 283 HIS ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 HIS F 226 ASN F 291 GLN F 307 HIS F 329 GLN F 396 HIS J 28 HIS J 88 HIS J 107 HIS ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 192 HIS ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 HIS C 28 HIS C 85 GLN C 88 HIS C 107 HIS C 139 HIS C 192 HIS ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN C 258 ASN ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 HIS L 85 GLN L 88 HIS L 139 HIS L 192 HIS L 197 HIS L 206 ASN A 15 GLN A 28 HIS A 88 HIS A 139 HIS ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN A 258 ASN A 283 HIS K 15 GLN K 28 HIS K 88 HIS K 139 HIS ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS G 226 ASN G 307 HIS G 329 GLN G 396 HIS ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 226 ASN D 307 HIS D 396 HIS ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS I 226 ASN I 307 HIS I 396 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 307 HIS B 329 GLN B 332 ASN B 396 HIS H 6 HIS H 226 ASN H 307 HIS H 329 GLN H 332 ASN H 396 HIS Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.080300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.068981 restraints weight = 99536.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.071737 restraints weight = 47931.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.073604 restraints weight = 28247.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.074920 restraints weight = 18820.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.075868 restraints weight = 13597.138| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 42204 Z= 0.186 Angle : 0.678 8.817 57414 Z= 0.342 Chirality : 0.046 0.261 6282 Planarity : 0.005 0.045 7452 Dihedral : 11.473 179.507 5796 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.89 % Allowed : 10.09 % Favored : 88.02 % 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: -2.48 (0.10), residues: 5130 helix: -1.53 (0.09), residues: 2238 sheet: -0.42 (0.18), residues: 774 loop : -2.13 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 214 TYR 0.020 0.001 TYR D 208 PHE 0.015 0.001 PHE J 149 TRP 0.016 0.002 TRP D 21 HIS 0.007 0.001 HIS F 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (42204) covalent geometry : angle 0.67774 / 0.34 (57414) hydrogen bonds : bond 0.05453 / 3.62 ( 1620) hydrogen bonds : angle 5.06305 / 3.51 ( 4698) *********************** 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 933 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 850 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 ASN cc_start: 0.9265 (t0) cc_final: 0.8746 (t0) REVERT: E 84 ARG cc_start: 0.8800 (ttp-110) cc_final: 0.8546 (mtm110) REVERT: E 120 ASP cc_start: 0.9049 (t70) cc_final: 0.8842 (t0) REVERT: E 124 LYS cc_start: 0.9140 (mttm) cc_final: 0.8934 (mmtm) REVERT: E 227 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9165 (tp) REVERT: E 254 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7480 (mt-10) REVERT: E 313 MET cc_start: 0.8614 (mtm) cc_final: 0.8150 (mtm) REVERT: E 377 MET cc_start: 0.8977 (tmm) cc_final: 0.8745 (tmm) REVERT: E 419 SER cc_start: 0.8350 (t) cc_final: 0.7319 (m) REVERT: F 121 ARG cc_start: 0.8596 (ttm110) cc_final: 0.8388 (ptp-110) REVERT: F 181 GLU cc_start: 0.8239 (pt0) cc_final: 0.7934 (pt0) REVERT: F 203 ASP cc_start: 0.8302 (t70) cc_final: 0.8015 (t70) REVERT: F 291 GLN cc_start: 0.8706 (pt0) cc_final: 0.8236 (pt0) REVERT: F 293 MET cc_start: 0.8804 (mtm) cc_final: 0.8474 (mtt) REVERT: F 392 LYS cc_start: 0.9437 (mtmt) cc_final: 0.9150 (mtmm) REVERT: F 421 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8248 (mt-10) REVERT: J 2 ARG cc_start: 0.7601 (mtm180) cc_final: 0.6778 (mmt90) REVERT: J 23 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9117 (tt) REVERT: J 31 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7798 (mt0) REVERT: J 50 ASN cc_start: 0.9096 (t0) cc_final: 0.8480 (t0) REVERT: J 163 LYS cc_start: 0.8949 (mtpp) cc_final: 0.8741 (mmtt) REVERT: J 168 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6900 (mt-10) REVERT: J 207 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7936 (tm-30) REVERT: J 301 GLN cc_start: 0.8264 (mt0) cc_final: 0.7927 (mm110) REVERT: J 302 MET cc_start: 0.8916 (mpp) cc_final: 0.7583 (mpp) REVERT: J 313 MET cc_start: 0.8795 (mtm) cc_final: 0.6995 (mtm) REVERT: J 357 TYR cc_start: 0.7931 (m-80) cc_final: 0.7497 (m-80) REVERT: J 380 ASN cc_start: 0.8925 (t0) cc_final: 0.8182 (t0) REVERT: J 392 ASP cc_start: 0.8871 (m-30) cc_final: 0.8615 (m-30) REVERT: J 433 GLU cc_start: 0.9097 (mp0) cc_final: 0.8472 (mp0) REVERT: C 31 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8057 (mt0) REVERT: C 50 ASN cc_start: 0.9306 (t0) cc_final: 0.8814 (t0) REVERT: C 136 LEU cc_start: 0.9037 (mt) cc_final: 0.8818 (mt) REVERT: C 147 SER cc_start: 0.9139 (p) cc_final: 0.8802 (t) REVERT: C 154 MET cc_start: 0.9368 (mmm) cc_final: 0.8911 (mmm) REVERT: C 155 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8746 (mt-10) REVERT: C 170 SER cc_start: 0.9255 (m) cc_final: 0.8949 (t) REVERT: C 218 ASP cc_start: 0.8873 (m-30) cc_final: 0.8662 (t0) REVERT: C 254 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8005 (mt-10) REVERT: C 302 MET cc_start: 0.8552 (mpp) cc_final: 0.8337 (mpp) REVERT: C 351 PHE cc_start: 0.8994 (m-80) cc_final: 0.8770 (m-10) REVERT: C 392 ASP cc_start: 0.9107 (m-30) cc_final: 0.8869 (m-30) REVERT: C 431 ASP cc_start: 0.8943 (m-30) cc_final: 0.8727 (m-30) REVERT: L 2 ARG cc_start: 0.7891 (mtm180) cc_final: 0.7070 (mpt180) REVERT: L 31 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8086 (mt0) REVERT: L 35 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8063 (mp10) REVERT: L 50 ASN cc_start: 0.9275 (t0) cc_final: 0.8778 (t0) REVERT: L 77 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8804 (tp30) REVERT: L 145 THR cc_start: 0.9354 (m) cc_final: 0.9069 (p) REVERT: L 147 SER cc_start: 0.9215 (p) cc_final: 0.8801 (t) REVERT: L 170 SER cc_start: 0.9330 (m) cc_final: 0.9019 (t) REVERT: L 279 GLU cc_start: 0.8606 (pt0) cc_final: 0.7974 (pm20) REVERT: L 392 ASP cc_start: 0.9063 (m-30) cc_final: 0.8858 (m-30) REVERT: L 431 ASP cc_start: 0.8992 (m-30) cc_final: 0.8717 (m-30) REVERT: A 2 ARG cc_start: 0.7896 (mtm180) cc_final: 0.7603 (ptp90) REVERT: A 50 ASN cc_start: 0.9208 (t0) cc_final: 0.8668 (t0) REVERT: A 77 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8585 (tp30) REVERT: A 90 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7993 (tp30) REVERT: A 170 SER cc_start: 0.9433 (m) cc_final: 0.8915 (p) REVERT: A 203 MET cc_start: 0.9115 (mmp) cc_final: 0.8830 (mmm) REVERT: A 227 LEU cc_start: 0.9349 (mp) cc_final: 0.9044 (mp) REVERT: A 254 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7941 (mt-10) REVERT: A 279 GLU cc_start: 0.8687 (pt0) cc_final: 0.8423 (pm20) REVERT: A 313 MET cc_start: 0.8720 (mtm) cc_final: 0.7563 (mtm) REVERT: A 319 TYR cc_start: 0.9530 (m-80) cc_final: 0.9075 (m-80) REVERT: A 351 PHE cc_start: 0.9110 (m-80) cc_final: 0.8747 (m-80) REVERT: A 417 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7708 (tm-30) REVERT: A 431 ASP cc_start: 0.8826 (m-30) cc_final: 0.8425 (m-30) REVERT: K 2 ARG cc_start: 0.7973 (mtm180) cc_final: 0.6967 (mmt90) REVERT: K 23 LEU cc_start: 0.9651 (tp) cc_final: 0.9395 (tp) REVERT: K 36 MET cc_start: 0.8650 (ptm) cc_final: 0.8393 (ttp) REVERT: K 50 ASN cc_start: 0.9158 (t0) cc_final: 0.8631 (t0) REVERT: K 90 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7984 (tp30) REVERT: K 145 THR cc_start: 0.9440 (m) cc_final: 0.9225 (p) REVERT: K 155 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8683 (mt-10) REVERT: K 170 SER cc_start: 0.9505 (m) cc_final: 0.9131 (t) REVERT: K 183 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7840 (mt-10) REVERT: K 214 ARG cc_start: 0.9044 (ttp80) cc_final: 0.8677 (ttp80) REVERT: K 279 GLU cc_start: 0.8451 (pm20) cc_final: 0.8241 (pm20) REVERT: K 313 MET cc_start: 0.9124 (mtm) cc_final: 0.8042 (mtm) REVERT: K 417 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7693 (tm-30) REVERT: K 431 ASP cc_start: 0.8814 (m-30) cc_final: 0.8429 (m-30) REVERT: G 6 HIS cc_start: 0.9202 (t70) cc_final: 0.8973 (t-170) REVERT: G 14 ASN cc_start: 0.9303 (m-40) cc_final: 0.9074 (m-40) REVERT: G 288 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7181 (tm-30) REVERT: G 313 VAL cc_start: 0.9660 (t) cc_final: 0.9389 (p) REVERT: G 363 MET cc_start: 0.8861 (ptp) cc_final: 0.8345 (ptp) REVERT: G 379 LYS cc_start: 0.9232 (mtpt) cc_final: 0.8860 (ptpt) REVERT: G 392 LYS cc_start: 0.9400 (mtmt) cc_final: 0.9190 (mtmm) REVERT: G 397 TRP cc_start: 0.9135 (m100) cc_final: 0.8699 (m-10) REVERT: D 136 THR cc_start: 0.9247 (m) cc_final: 0.8543 (p) REVERT: D 263 LEU cc_start: 0.9151 (mp) cc_final: 0.8869 (mt) REVERT: D 340 TYR cc_start: 0.8036 (m-80) cc_final: 0.7675 (m-80) REVERT: D 379 LYS cc_start: 0.9242 (mtpt) cc_final: 0.8987 (ptpp) REVERT: D 401 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8007 (mp0) REVERT: I 22 GLU cc_start: 0.8766 (tt0) cc_final: 0.8243 (tm-30) REVERT: I 129 CYS cc_start: 0.8921 (t) cc_final: 0.8633 (t) REVERT: I 135 LEU cc_start: 0.9391 (tt) cc_final: 0.9126 (tp) REVERT: I 263 LEU cc_start: 0.9209 (mp) cc_final: 0.8936 (mt) REVERT: I 297 LYS cc_start: 0.8868 (ptpt) cc_final: 0.8600 (mtmm) REVERT: I 340 TYR cc_start: 0.7964 (m-80) cc_final: 0.7554 (m-80) REVERT: I 380 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.7864 (ptt180) REVERT: I 397 TRP cc_start: 0.9156 (m100) cc_final: 0.8113 (m-10) REVERT: I 401 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7971 (mp0) REVERT: B 6 HIS cc_start: 0.9250 (t70) cc_final: 0.8952 (t-170) REVERT: B 129 CYS cc_start: 0.8467 (t) cc_final: 0.8242 (p) REVERT: B 136 THR cc_start: 0.9377 (m) cc_final: 0.8613 (p) REVERT: B 180 VAL cc_start: 0.9419 (m) cc_final: 0.8914 (t) REVERT: B 340 TYR cc_start: 0.7883 (m-80) cc_final: 0.7546 (m-80) REVERT: B 363 MET cc_start: 0.8933 (ptp) cc_final: 0.8491 (ptp) REVERT: B 401 GLU cc_start: 0.8639 (mp0) cc_final: 0.8261 (mp0) REVERT: H 129 CYS cc_start: 0.8390 (t) cc_final: 0.8160 (p) REVERT: H 136 THR cc_start: 0.9213 (m) cc_final: 0.8546 (p) REVERT: H 276 ARG cc_start: 0.8591 (mmm160) cc_final: 0.8297 (mmm160) REVERT: H 363 MET cc_start: 0.8553 (ptp) cc_final: 0.8315 (ptp) outliers start: 83 outliers final: 41 residues processed: 907 average time/residue: 0.2429 time to fit residues: 363.7370 Evaluate side-chains 711 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 668 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 419 SER Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 351 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain H residue 263 LEU Chi-restraints excluded: chain H residue 415 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 282 optimal weight: 0.0770 chunk 461 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 chunk 321 optimal weight: 10.0000 chunk 280 optimal weight: 9.9990 chunk 474 optimal weight: 30.0000 chunk 414 optimal weight: 10.0000 chunk 236 optimal weight: 0.7980 chunk 402 optimal weight: 5.9990 chunk 447 optimal weight: 20.0000 overall best weight: 3.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 ASN J 85 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 HIS L 301 GLN A 91 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN K 393 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN H 332 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.079818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.068682 restraints weight = 99370.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.071392 restraints weight = 47631.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.073236 restraints weight = 28016.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.074540 restraints weight = 18597.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.075463 restraints weight = 13377.302| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 42204 Z= 0.139 Angle : 0.600 8.447 57414 Z= 0.296 Chirality : 0.045 0.149 6282 Planarity : 0.004 0.036 7452 Dihedral : 11.031 177.513 5796 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.30 % Allowed : 11.63 % Favored : 86.07 % 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: -1.36 (0.11), residues: 5130 helix: -0.32 (0.11), residues: 2238 sheet: -0.03 (0.18), residues: 804 loop : -1.85 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 156 TYR 0.015 0.001 TYR E 24 PHE 0.029 0.001 PHE E 351 TRP 0.013 0.001 TRP D 21 HIS 0.005 0.001 HIS J 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (42204) covalent geometry : angle 0.59977 / 0.30 (57414) hydrogen bonds : bond 0.04235 / 2.81 ( 1620) hydrogen bonds : angle 4.54390 / 3.14 ( 4698) *********************** 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 868 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 767 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 84 ARG cc_start: 0.8805 (ttp-110) cc_final: 0.8580 (mtm110) REVERT: E 127 ASP cc_start: 0.8304 (m-30) cc_final: 0.8081 (m-30) REVERT: E 205 ASP cc_start: 0.8049 (t0) cc_final: 0.7824 (t0) REVERT: E 221 ARG cc_start: 0.9023 (mtt-85) cc_final: 0.8423 (mtt-85) REVERT: E 245 ASP cc_start: 0.8015 (p0) cc_final: 0.7486 (p0) REVERT: E 254 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7478 (mt-10) REVERT: E 313 MET cc_start: 0.8588 (mtm) cc_final: 0.8127 (mtm) REVERT: E 357 TYR cc_start: 0.8121 (m-80) cc_final: 0.7029 (m-80) REVERT: E 377 MET cc_start: 0.8940 (tmm) cc_final: 0.8670 (tmm) REVERT: F 6 HIS cc_start: 0.9215 (t70) cc_final: 0.8868 (t-170) REVERT: F 14 ASN cc_start: 0.9193 (m-40) cc_final: 0.8939 (m-40) REVERT: F 181 GLU cc_start: 0.8246 (pt0) cc_final: 0.7960 (pt0) REVERT: F 203 ASP cc_start: 0.8327 (t70) cc_final: 0.8116 (t70) REVERT: F 291 GLN cc_start: 0.8446 (pt0) cc_final: 0.8113 (pt0) REVERT: F 392 LYS cc_start: 0.9410 (mtmt) cc_final: 0.9175 (mtmm) REVERT: J 2 ARG cc_start: 0.7688 (mtm180) cc_final: 0.6788 (mmt90) REVERT: J 50 ASN cc_start: 0.9160 (t0) cc_final: 0.8551 (t0) REVERT: J 203 MET cc_start: 0.8773 (mmm) cc_final: 0.8491 (mmm) REVERT: J 207 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7987 (tm-30) REVERT: J 210 TYR cc_start: 0.8601 (m-10) cc_final: 0.8400 (m-10) REVERT: J 245 ASP cc_start: 0.8500 (p0) cc_final: 0.8210 (p0) REVERT: J 301 GLN cc_start: 0.8456 (mt0) cc_final: 0.8092 (mm110) REVERT: J 302 MET cc_start: 0.9005 (mpp) cc_final: 0.7524 (mpp) REVERT: J 313 MET cc_start: 0.8799 (mtm) cc_final: 0.6950 (mtm) REVERT: J 357 TYR cc_start: 0.8109 (m-80) cc_final: 0.7703 (m-80) REVERT: J 380 ASN cc_start: 0.8963 (t0) cc_final: 0.8231 (t0) REVERT: J 428 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.7843 (tp) REVERT: C 31 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8112 (mt0) REVERT: C 147 SER cc_start: 0.8981 (p) cc_final: 0.8779 (t) REVERT: C 154 MET cc_start: 0.9436 (mmm) cc_final: 0.8955 (mmm) REVERT: C 170 SER cc_start: 0.9279 (m) cc_final: 0.8972 (t) REVERT: C 187 SER cc_start: 0.9455 (m) cc_final: 0.9224 (p) REVERT: C 218 ASP cc_start: 0.8860 (m-30) cc_final: 0.8634 (t0) REVERT: C 254 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8024 (mt-10) REVERT: C 302 MET cc_start: 0.8683 (mpp) cc_final: 0.8148 (mpp) REVERT: C 322 ASP cc_start: 0.8364 (t0) cc_final: 0.8156 (t0) REVERT: C 345 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8149 (p0) REVERT: C 351 PHE cc_start: 0.9002 (m-80) cc_final: 0.8746 (m-10) REVERT: C 377 MET cc_start: 0.9025 (tmm) cc_final: 0.8749 (tmm) REVERT: C 392 ASP cc_start: 0.9064 (m-30) cc_final: 0.8849 (m-30) REVERT: L 2 ARG cc_start: 0.7986 (mtm180) cc_final: 0.7118 (mpt180) REVERT: L 31 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8105 (mt0) REVERT: L 35 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7959 (mp10) REVERT: L 36 MET cc_start: 0.8652 (ptm) cc_final: 0.8374 (ttp) REVERT: L 170 SER cc_start: 0.9353 (m) cc_final: 0.9017 (t) REVERT: L 279 GLU cc_start: 0.8647 (pt0) cc_final: 0.7960 (pm20) REVERT: L 392 ASP cc_start: 0.9025 (m-30) cc_final: 0.8794 (m-30) REVERT: L 419 SER cc_start: 0.8992 (OUTLIER) cc_final: 0.8657 (p) REVERT: L 431 ASP cc_start: 0.8949 (m-30) cc_final: 0.8705 (m-30) REVERT: A 2 ARG cc_start: 0.8019 (mtm180) cc_final: 0.7537 (ptp90) REVERT: A 50 ASN cc_start: 0.9215 (t0) cc_final: 0.8692 (t0) REVERT: A 54 SER cc_start: 0.8868 (p) cc_final: 0.8665 (p) REVERT: A 77 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8638 (tp30) REVERT: A 90 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8044 (tp30) REVERT: A 170 SER cc_start: 0.9500 (m) cc_final: 0.9070 (t) REVERT: A 279 GLU cc_start: 0.8695 (pt0) cc_final: 0.8422 (pm20) REVERT: A 313 MET cc_start: 0.8691 (mtm) cc_final: 0.7599 (mtm) REVERT: A 351 PHE cc_start: 0.9037 (m-80) cc_final: 0.8678 (m-80) REVERT: A 377 MET cc_start: 0.9015 (tmm) cc_final: 0.8272 (tmm) REVERT: A 417 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 431 ASP cc_start: 0.8846 (m-30) cc_final: 0.8363 (m-30) REVERT: K 2 ARG cc_start: 0.8054 (mtm180) cc_final: 0.6961 (mmt90) REVERT: K 36 MET cc_start: 0.8616 (ptm) cc_final: 0.8394 (ttp) REVERT: K 50 ASN cc_start: 0.9183 (t0) cc_final: 0.8682 (t0) REVERT: K 90 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8027 (tp30) REVERT: K 170 SER cc_start: 0.9439 (m) cc_final: 0.9200 (t) REVERT: K 203 MET cc_start: 0.9026 (mmm) cc_final: 0.8670 (mmm) REVERT: K 214 ARG cc_start: 0.9042 (ttp80) cc_final: 0.8717 (ttp80) REVERT: K 237 SER cc_start: 0.9234 (m) cc_final: 0.8966 (p) REVERT: K 377 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8723 (tmm) REVERT: K 417 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7627 (tm-30) REVERT: K 431 ASP cc_start: 0.8605 (m-30) cc_final: 0.8250 (m-30) REVERT: G 6 HIS cc_start: 0.9177 (t70) cc_final: 0.8871 (t-170) REVERT: G 14 ASN cc_start: 0.9239 (m-40) cc_final: 0.8957 (m-40) REVERT: G 136 THR cc_start: 0.9218 (m) cc_final: 0.8515 (p) REVERT: G 166 THR cc_start: 0.9388 (p) cc_final: 0.9165 (p) REVERT: G 257 MET cc_start: 0.8767 (mmm) cc_final: 0.8328 (mmm) REVERT: G 363 MET cc_start: 0.8809 (ptp) cc_final: 0.8361 (ptp) REVERT: G 379 LYS cc_start: 0.9220 (mtpt) cc_final: 0.9003 (ptpt) REVERT: D 181 GLU cc_start: 0.8982 (pp20) cc_final: 0.8721 (pt0) REVERT: D 205 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: D 263 LEU cc_start: 0.9129 (mp) cc_final: 0.8849 (mt) REVERT: D 280 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: D 325 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: D 340 TYR cc_start: 0.8046 (m-80) cc_final: 0.7711 (m-80) REVERT: D 379 LYS cc_start: 0.9251 (mtpt) cc_final: 0.9032 (ptpp) REVERT: D 401 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8049 (mp0) REVERT: I 22 GLU cc_start: 0.8791 (tt0) cc_final: 0.8283 (tm-30) REVERT: I 129 CYS cc_start: 0.8931 (t) cc_final: 0.8682 (t) REVERT: I 130 LEU cc_start: 0.9233 (tp) cc_final: 0.8819 (tt) REVERT: I 136 THR cc_start: 0.9153 (m) cc_final: 0.8537 (p) REVERT: I 181 GLU cc_start: 0.9024 (pp20) cc_final: 0.8700 (pt0) REVERT: I 225 LEU cc_start: 0.9639 (mt) cc_final: 0.9430 (mt) REVERT: I 257 MET cc_start: 0.8136 (mmm) cc_final: 0.7748 (mmm) REVERT: I 263 LEU cc_start: 0.9186 (mp) cc_final: 0.8920 (mt) REVERT: I 325 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8285 (mp0) REVERT: I 340 TYR cc_start: 0.8016 (m-80) cc_final: 0.7648 (m-80) REVERT: I 368 ILE cc_start: 0.9511 (mt) cc_final: 0.9249 (mt) REVERT: I 379 LYS cc_start: 0.9240 (mtpt) cc_final: 0.8980 (ptpp) REVERT: I 397 TRP cc_start: 0.9249 (m100) cc_final: 0.8129 (m-10) REVERT: I 401 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7966 (mp0) REVERT: I 410 GLU cc_start: 0.8065 (pt0) cc_final: 0.7770 (pt0) REVERT: B 57 ASN cc_start: 0.8196 (t0) cc_final: 0.7942 (t0) REVERT: B 74 ASP cc_start: 0.8561 (m-30) cc_final: 0.8355 (m-30) REVERT: B 136 THR cc_start: 0.9363 (m) cc_final: 0.8608 (p) REVERT: B 180 VAL cc_start: 0.9372 (m) cc_final: 0.9102 (t) REVERT: B 340 TYR cc_start: 0.7934 (m-80) cc_final: 0.7625 (m-80) REVERT: B 347 ASN cc_start: 0.9013 (p0) cc_final: 0.8598 (p0) REVERT: B 363 MET cc_start: 0.8690 (ptp) cc_final: 0.8378 (ptp) REVERT: B 401 GLU cc_start: 0.8674 (mp0) cc_final: 0.8379 (mp0) REVERT: H 103 LYS cc_start: 0.9024 (mttt) cc_final: 0.8707 (mmtp) REVERT: H 129 CYS cc_start: 0.8287 (t) cc_final: 0.7846 (t) REVERT: H 136 THR cc_start: 0.9307 (m) cc_final: 0.8622 (p) REVERT: H 164 MET cc_start: 0.7821 (ttm) cc_final: 0.7592 (ttm) REVERT: H 180 VAL cc_start: 0.9266 (m) cc_final: 0.8756 (t) REVERT: H 347 ASN cc_start: 0.9032 (p0) cc_final: 0.8554 (p0) REVERT: H 363 MET cc_start: 0.8556 (ptp) cc_final: 0.8269 (ptp) REVERT: H 376 GLU cc_start: 0.8491 (pt0) cc_final: 0.8271 (pt0) REVERT: H 379 LYS cc_start: 0.9331 (mtpt) cc_final: 0.9091 (ptpt) outliers start: 101 outliers final: 65 residues processed: 840 average time/residue: 0.2381 time to fit residues: 335.5647 Evaluate side-chains 713 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 641 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 419 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 377 MET Chi-restraints excluded: chain K residue 423 GLU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain I residue 177 ASP Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 419 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 263 LEU Chi-restraints excluded: chain H residue 293 MET Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain H residue 415 MET Chi-restraints excluded: chain H residue 419 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 111 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 258 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 308 optimal weight: 8.9990 chunk 480 optimal weight: 0.9980 chunk 383 optimal weight: 5.9990 chunk 272 optimal weight: 30.0000 chunk 489 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 133 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 301 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN A 85 GLN A 91 GLN A 107 HIS A 186 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN A 393 HIS K 107 HIS ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 99 ASN ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.079256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.068327 restraints weight = 99362.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.070976 restraints weight = 48194.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.072782 restraints weight = 28547.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.074048 restraints weight = 19079.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.074974 restraints weight = 13838.846| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 42204 Z= 0.180 Angle : 0.609 7.720 57414 Z= 0.299 Chirality : 0.045 0.150 6282 Planarity : 0.004 0.037 7452 Dihedral : 10.795 176.364 5796 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.60 % Allowed : 12.73 % Favored : 84.68 % 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: -0.93 (0.12), residues: 5130 helix: 0.16 (0.11), residues: 2244 sheet: 0.09 (0.19), residues: 810 loop : -1.74 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 380 TYR 0.016 0.001 TYR J 399 PHE 0.021 0.001 PHE F 167 TRP 0.014 0.002 TRP D 21 HIS 0.016 0.001 HIS J 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (42204) covalent geometry : angle 0.60884 / 0.30 (57414) hydrogen bonds : bond 0.03985 / 2.64 ( 1620) hydrogen bonds : angle 4.44813 / 3.08 ( 4698) *********************** 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 778 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 664 time to evaluate : 1.459 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: E 254 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7516 (mt-10) REVERT: E 313 MET cc_start: 0.8572 (mtm) cc_final: 0.8136 (mtm) REVERT: E 357 TYR cc_start: 0.8173 (m-80) cc_final: 0.7169 (m-80) REVERT: F 14 ASN cc_start: 0.9141 (m-40) cc_final: 0.8857 (m-40) REVERT: F 181 GLU cc_start: 0.8238 (pt0) cc_final: 0.7995 (pt0) REVERT: F 291 GLN cc_start: 0.8449 (pt0) cc_final: 0.8134 (pt0) REVERT: J 2 ARG cc_start: 0.7953 (mtm180) cc_final: 0.6904 (mmt90) REVERT: J 50 ASN cc_start: 0.9241 (t0) cc_final: 0.8619 (t0) REVERT: J 210 TYR cc_start: 0.8693 (m-10) cc_final: 0.8386 (m-10) REVERT: J 302 MET cc_start: 0.9113 (mpp) cc_final: 0.7562 (mpp) REVERT: J 313 MET cc_start: 0.8722 (mtm) cc_final: 0.6895 (mtm) REVERT: J 357 TYR cc_start: 0.8248 (m-80) cc_final: 0.7845 (m-80) REVERT: J 377 MET cc_start: 0.8294 (ttp) cc_final: 0.7579 (tmm) REVERT: J 380 ASN cc_start: 0.8954 (t0) cc_final: 0.8207 (t0) REVERT: J 428 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.7988 (tp) REVERT: J 433 GLU cc_start: 0.9045 (mp0) cc_final: 0.8763 (mp0) REVERT: C 31 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8286 (mt0) REVERT: C 127 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8184 (p0) REVERT: C 147 SER cc_start: 0.9014 (p) cc_final: 0.8764 (t) REVERT: C 154 MET cc_start: 0.9326 (mmm) cc_final: 0.9075 (mmm) REVERT: C 170 SER cc_start: 0.9317 (m) cc_final: 0.9030 (t) REVERT: C 187 SER cc_start: 0.9454 (m) cc_final: 0.9212 (p) REVERT: C 254 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7934 (mt-10) REVERT: C 302 MET cc_start: 0.8683 (mpp) cc_final: 0.8243 (mpp) REVERT: C 322 ASP cc_start: 0.8333 (t0) cc_final: 0.8113 (t0) REVERT: C 345 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8233 (p0) REVERT: C 351 PHE cc_start: 0.9041 (m-80) cc_final: 0.8764 (m-10) REVERT: C 392 ASP cc_start: 0.8938 (m-30) cc_final: 0.8546 (m-30) REVERT: L 2 ARG cc_start: 0.8012 (mtm180) cc_final: 0.7156 (mpt180) REVERT: L 31 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8212 (mt0) REVERT: L 36 MET cc_start: 0.8610 (ptm) cc_final: 0.8369 (ttp) REVERT: L 170 SER cc_start: 0.9375 (m) cc_final: 0.9057 (t) REVERT: L 279 GLU cc_start: 0.8624 (pt0) cc_final: 0.7970 (pm20) REVERT: L 322 ASP cc_start: 0.8375 (t0) cc_final: 0.8126 (t0) REVERT: A 2 ARG cc_start: 0.8022 (mtm180) cc_final: 0.7647 (ptp90) REVERT: A 77 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8532 (tp30) REVERT: A 170 SER cc_start: 0.9540 (m) cc_final: 0.9184 (t) REVERT: A 322 ASP cc_start: 0.8131 (t0) cc_final: 0.7861 (t0) REVERT: A 377 MET cc_start: 0.9002 (tmm) cc_final: 0.8756 (tmm) REVERT: A 417 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 431 ASP cc_start: 0.8646 (m-30) cc_final: 0.8277 (m-30) REVERT: K 2 ARG cc_start: 0.8091 (mtm180) cc_final: 0.7062 (mmt90) REVERT: K 36 MET cc_start: 0.8522 (ptm) cc_final: 0.8311 (ttp) REVERT: K 50 ASN cc_start: 0.9178 (t0) cc_final: 0.8763 (t0) REVERT: K 203 MET cc_start: 0.8984 (mmm) cc_final: 0.8406 (mmm) REVERT: K 237 SER cc_start: 0.9254 (m) cc_final: 0.8887 (p) REVERT: K 313 MET cc_start: 0.8852 (mtm) cc_final: 0.7806 (mtm) REVERT: K 377 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8781 (tmm) REVERT: K 417 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7633 (tm-30) REVERT: K 431 ASP cc_start: 0.8536 (m-30) cc_final: 0.8211 (m-30) REVERT: G 14 ASN cc_start: 0.9181 (m-40) cc_final: 0.8832 (m-40) REVERT: G 88 ASP cc_start: 0.7826 (p0) cc_final: 0.7456 (t0) REVERT: G 136 THR cc_start: 0.9257 (m) cc_final: 0.8551 (p) REVERT: G 166 THR cc_start: 0.9415 (p) cc_final: 0.9187 (p) REVERT: G 325 GLU cc_start: 0.7922 (mp0) cc_final: 0.7214 (mp0) REVERT: G 363 MET cc_start: 0.8826 (ptp) cc_final: 0.8405 (ptp) REVERT: G 379 LYS cc_start: 0.9258 (mtpt) cc_final: 0.9031 (mtpp) REVERT: D 257 MET cc_start: 0.8481 (mmm) cc_final: 0.7925 (mmm) REVERT: D 263 LEU cc_start: 0.9176 (mp) cc_final: 0.8922 (mt) REVERT: D 280 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8649 (pm20) REVERT: D 312 THR cc_start: 0.9334 (p) cc_final: 0.8372 (p) REVERT: D 325 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: D 340 TYR cc_start: 0.8076 (m-80) cc_final: 0.7740 (m-80) REVERT: D 376 GLU cc_start: 0.8433 (pm20) cc_final: 0.8060 (pm20) REVERT: I 22 GLU cc_start: 0.8731 (tt0) cc_final: 0.8317 (tm-30) REVERT: I 74 ASP cc_start: 0.8740 (m-30) cc_final: 0.8449 (m-30) REVERT: I 129 CYS cc_start: 0.8986 (t) cc_final: 0.8720 (t) REVERT: I 130 LEU cc_start: 0.9261 (tp) cc_final: 0.8883 (tt) REVERT: I 181 GLU cc_start: 0.8995 (pp20) cc_final: 0.8673 (pt0) REVERT: I 253 LEU cc_start: 0.9385 (mt) cc_final: 0.8930 (mp) REVERT: I 257 MET cc_start: 0.8102 (mmm) cc_final: 0.7819 (mmm) REVERT: I 263 LEU cc_start: 0.9230 (mp) cc_final: 0.8955 (mt) REVERT: I 325 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7842 (mp0) REVERT: I 340 TYR cc_start: 0.8109 (m-80) cc_final: 0.7735 (m-80) REVERT: I 376 GLU cc_start: 0.8421 (pm20) cc_final: 0.8062 (pm20) REVERT: I 379 LYS cc_start: 0.9215 (mtpt) cc_final: 0.9015 (mttm) REVERT: I 397 TRP cc_start: 0.9337 (m100) cc_final: 0.8620 (m-10) REVERT: I 410 GLU cc_start: 0.7996 (pt0) cc_final: 0.7735 (pt0) REVERT: B 57 ASN cc_start: 0.8145 (t0) cc_final: 0.7793 (t0) REVERT: B 74 ASP cc_start: 0.8554 (m-30) cc_final: 0.8318 (m-30) REVERT: B 180 VAL cc_start: 0.9387 (m) cc_final: 0.9146 (t) REVERT: B 340 TYR cc_start: 0.8013 (m-80) cc_final: 0.7587 (m-80) REVERT: B 347 ASN cc_start: 0.9007 (p0) cc_final: 0.8552 (p0) REVERT: B 363 MET cc_start: 0.8720 (ptp) cc_final: 0.8434 (ptp) REVERT: B 401 GLU cc_start: 0.8564 (mp0) cc_final: 0.8287 (mp0) REVERT: H 22 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: H 57 ASN cc_start: 0.8115 (t0) cc_final: 0.7696 (t0) REVERT: H 129 CYS cc_start: 0.8247 (t) cc_final: 0.7826 (t) REVERT: H 197 ASP cc_start: 0.8423 (m-30) cc_final: 0.8120 (m-30) REVERT: H 347 ASN cc_start: 0.9032 (p0) cc_final: 0.8510 (p0) REVERT: H 363 MET cc_start: 0.8662 (ptp) cc_final: 0.8386 (ptp) outliers start: 114 outliers final: 90 residues processed: 745 average time/residue: 0.2271 time to fit residues: 285.2570 Evaluate side-chains 708 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 611 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 377 MET Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 351 THR Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain I residue 419 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 263 LEU Chi-restraints excluded: chain H residue 293 MET Chi-restraints excluded: chain H residue 333 VAL Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain H residue 415 MET Chi-restraints excluded: chain H residue 419 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 74 optimal weight: 20.0000 chunk 262 optimal weight: 4.9990 chunk 387 optimal weight: 0.8980 chunk 290 optimal weight: 20.0000 chunk 303 optimal weight: 0.8980 chunk 271 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 320 optimal weight: 8.9990 chunk 311 optimal weight: 0.1980 chunk 82 optimal weight: 6.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.080490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.069734 restraints weight = 98882.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.072386 restraints weight = 47119.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.074197 restraints weight = 27593.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.075492 restraints weight = 18278.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.076403 restraints weight = 13071.000| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 42204 Z= 0.109 Angle : 0.567 9.516 57414 Z= 0.276 Chirality : 0.044 0.154 6282 Planarity : 0.004 0.037 7452 Dihedral : 10.523 179.723 5796 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.14 % Allowed : 13.73 % Favored : 84.13 % 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: -0.63 (0.12), residues: 5130 helix: 0.43 (0.11), residues: 2262 sheet: 0.11 (0.19), residues: 804 loop : -1.56 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 221 TYR 0.012 0.001 TYR E 24 PHE 0.014 0.001 PHE E 351 TRP 0.012 0.001 TRP E 346 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (42204) covalent geometry : angle 0.56729 / 0.28 (57414) hydrogen bonds : bond 0.03524 / 2.34 ( 1620) hydrogen bonds : angle 4.25984 / 2.94 ( 4698) *********************** 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 797 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 703 time to evaluate : 1.668 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 4 CYS cc_start: 0.9068 (t) cc_final: 0.8459 (t) REVERT: E 254 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7611 (mt-10) REVERT: E 259 LEU cc_start: 0.9404 (mt) cc_final: 0.9123 (mt) REVERT: E 339 ARG cc_start: 0.7440 (mmp-170) cc_final: 0.6760 (mmt180) REVERT: E 357 TYR cc_start: 0.8183 (m-80) cc_final: 0.7283 (m-80) REVERT: E 424 ASP cc_start: 0.8644 (t70) cc_final: 0.8358 (t0) REVERT: F 14 ASN cc_start: 0.9083 (m-40) cc_final: 0.8817 (m-40) REVERT: F 181 GLU cc_start: 0.8225 (pt0) cc_final: 0.8002 (pt0) REVERT: F 291 GLN cc_start: 0.8440 (pt0) cc_final: 0.8101 (pt0) REVERT: J 2 ARG cc_start: 0.8017 (mtm180) cc_final: 0.6937 (mmt90) REVERT: J 50 ASN cc_start: 0.9235 (t0) cc_final: 0.8634 (t0) REVERT: J 302 MET cc_start: 0.9153 (mpp) cc_final: 0.7897 (mpp) REVERT: J 313 MET cc_start: 0.8584 (mtm) cc_final: 0.6748 (mtm) REVERT: J 357 TYR cc_start: 0.8242 (m-80) cc_final: 0.7854 (m-80) REVERT: J 380 ASN cc_start: 0.8951 (t0) cc_final: 0.8199 (t0) REVERT: J 428 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.7862 (tp) REVERT: J 433 GLU cc_start: 0.8942 (mp0) cc_final: 0.8703 (mp0) REVERT: C 31 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8213 (mt0) REVERT: C 127 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8126 (p0) REVERT: C 154 MET cc_start: 0.9321 (mmm) cc_final: 0.8962 (mmm) REVERT: C 170 SER cc_start: 0.9350 (m) cc_final: 0.9071 (t) REVERT: C 187 SER cc_start: 0.9444 (m) cc_final: 0.9192 (p) REVERT: C 313 MET cc_start: 0.8722 (mtm) cc_final: 0.8348 (mtm) REVERT: C 322 ASP cc_start: 0.8379 (t0) cc_final: 0.8152 (t0) REVERT: C 345 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8375 (p0) REVERT: C 351 PHE cc_start: 0.8954 (m-80) cc_final: 0.8748 (m-10) REVERT: C 392 ASP cc_start: 0.8923 (m-30) cc_final: 0.8580 (m-30) REVERT: L 2 ARG cc_start: 0.7993 (mtm180) cc_final: 0.6785 (mpt180) REVERT: L 31 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8284 (mt0) REVERT: L 36 MET cc_start: 0.8610 (ptm) cc_final: 0.8360 (ttp) REVERT: L 91 GLN cc_start: 0.8700 (mt0) cc_final: 0.8423 (mt0) REVERT: L 170 SER cc_start: 0.9383 (m) cc_final: 0.9099 (t) REVERT: L 279 GLU cc_start: 0.8592 (pt0) cc_final: 0.7938 (pm20) REVERT: L 322 ASP cc_start: 0.8391 (t0) cc_final: 0.8145 (t0) REVERT: A 2 ARG cc_start: 0.8039 (mtm180) cc_final: 0.7534 (ptp90) REVERT: A 77 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8525 (tp30) REVERT: A 170 SER cc_start: 0.9541 (m) cc_final: 0.9218 (t) REVERT: A 205 ASP cc_start: 0.8259 (t0) cc_final: 0.8041 (t0) REVERT: A 207 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 301 GLN cc_start: 0.8559 (mp10) cc_final: 0.8303 (mp10) REVERT: A 302 MET cc_start: 0.8852 (mpp) cc_final: 0.8624 (mpp) REVERT: A 313 MET cc_start: 0.8644 (mtm) cc_final: 0.7549 (mtm) REVERT: A 322 ASP cc_start: 0.8208 (t0) cc_final: 0.7885 (t0) REVERT: A 377 MET cc_start: 0.8974 (tmm) cc_final: 0.8735 (tmm) REVERT: A 417 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7619 (tm-30) REVERT: A 431 ASP cc_start: 0.8606 (m-30) cc_final: 0.8375 (m-30) REVERT: K 2 ARG cc_start: 0.8106 (mtm180) cc_final: 0.7043 (mmt90) REVERT: K 36 MET cc_start: 0.8429 (ptm) cc_final: 0.8219 (ttp) REVERT: K 50 ASN cc_start: 0.9157 (t0) cc_final: 0.8775 (t0) REVERT: K 127 ASP cc_start: 0.8542 (p0) cc_final: 0.8265 (p0) REVERT: K 203 MET cc_start: 0.8874 (mmm) cc_final: 0.8256 (mmm) REVERT: K 237 SER cc_start: 0.9199 (m) cc_final: 0.8847 (p) REVERT: K 313 MET cc_start: 0.8865 (mtm) cc_final: 0.8587 (mtm) REVERT: K 417 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7586 (tm-30) REVERT: K 431 ASP cc_start: 0.8570 (m-30) cc_final: 0.8326 (m-30) REVERT: G 14 ASN cc_start: 0.9097 (m-40) cc_final: 0.8825 (m110) REVERT: G 136 THR cc_start: 0.9205 (m) cc_final: 0.8486 (p) REVERT: G 255 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8908 (p) REVERT: G 325 GLU cc_start: 0.8010 (mp0) cc_final: 0.7671 (mp0) REVERT: G 379 LYS cc_start: 0.9252 (mtpt) cc_final: 0.9037 (mtpp) REVERT: D 130 LEU cc_start: 0.9087 (tp) cc_final: 0.8738 (tt) REVERT: D 257 MET cc_start: 0.8222 (mmm) cc_final: 0.8000 (mmm) REVERT: D 263 LEU cc_start: 0.9159 (mp) cc_final: 0.8896 (mt) REVERT: D 280 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8666 (pm20) REVERT: D 325 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: D 340 TYR cc_start: 0.8047 (m-80) cc_final: 0.7716 (m-80) REVERT: D 376 GLU cc_start: 0.8369 (pm20) cc_final: 0.8028 (pm20) REVERT: D 401 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8051 (mp0) REVERT: I 57 ASN cc_start: 0.8110 (t0) cc_final: 0.7803 (t0) REVERT: I 129 CYS cc_start: 0.8921 (t) cc_final: 0.8642 (t) REVERT: I 130 LEU cc_start: 0.9211 (tp) cc_final: 0.8819 (tt) REVERT: I 257 MET cc_start: 0.8006 (mmm) cc_final: 0.7754 (mmm) REVERT: I 263 LEU cc_start: 0.9187 (mp) cc_final: 0.8931 (mt) REVERT: I 325 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7770 (mp0) REVERT: I 340 TYR cc_start: 0.8047 (m-80) cc_final: 0.7652 (m-80) REVERT: I 376 GLU cc_start: 0.8332 (pm20) cc_final: 0.8016 (pm20) REVERT: I 379 LYS cc_start: 0.9215 (mtpt) cc_final: 0.8980 (mttm) REVERT: I 397 TRP cc_start: 0.9275 (m100) cc_final: 0.8457 (m-10) REVERT: I 410 GLU cc_start: 0.8045 (pt0) cc_final: 0.7716 (pt0) REVERT: B 57 ASN cc_start: 0.8044 (t0) cc_final: 0.7578 (t0) REVERT: B 88 ASP cc_start: 0.7739 (p0) cc_final: 0.6961 (t0) REVERT: B 340 TYR cc_start: 0.7961 (m-80) cc_final: 0.7604 (m-80) REVERT: B 347 ASN cc_start: 0.9060 (p0) cc_final: 0.8609 (p0) REVERT: B 363 MET cc_start: 0.8659 (ptp) cc_final: 0.8372 (ptp) REVERT: B 379 LYS cc_start: 0.9261 (mtpt) cc_final: 0.9014 (mtpp) REVERT: B 401 GLU cc_start: 0.8548 (mp0) cc_final: 0.8295 (mp0) REVERT: B 410 GLU cc_start: 0.8411 (pt0) cc_final: 0.8171 (pt0) REVERT: H 22 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7378 (tm-30) REVERT: H 57 ASN cc_start: 0.8059 (t0) cc_final: 0.7515 (t0) REVERT: H 129 CYS cc_start: 0.8210 (t) cc_final: 0.7773 (t) REVERT: H 136 THR cc_start: 0.9358 (m) cc_final: 0.8560 (p) REVERT: H 347 ASN cc_start: 0.9086 (p0) cc_final: 0.8814 (p0) REVERT: H 363 MET cc_start: 0.8615 (ptp) cc_final: 0.8341 (ptp) outliers start: 94 outliers final: 71 residues processed: 768 average time/residue: 0.2480 time to fit residues: 321.6598 Evaluate side-chains 720 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 643 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 423 GLU Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 293 MET Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 263 LEU Chi-restraints excluded: chain H residue 293 MET Chi-restraints excluded: chain H residue 333 VAL Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain H residue 415 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 3 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 410 optimal weight: 8.9990 chunk 186 optimal weight: 20.0000 chunk 343 optimal weight: 20.0000 chunk 373 optimal weight: 20.0000 chunk 344 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 298 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN A 91 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 GLN G 291 GLN ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.077888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.067127 restraints weight = 100316.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.069722 restraints weight = 48560.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.071493 restraints weight = 28784.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.072760 restraints weight = 19248.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.073653 restraints weight = 13885.568| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 42204 Z= 0.205 Angle : 0.621 8.571 57414 Z= 0.304 Chirality : 0.046 0.142 6282 Planarity : 0.004 0.043 7452 Dihedral : 10.447 177.429 5796 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.82 % Allowed : 13.75 % Favored : 83.42 % 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: -0.48 (0.12), residues: 5130 helix: 0.61 (0.11), residues: 2262 sheet: 0.10 (0.18), residues: 840 loop : -1.55 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 221 TYR 0.014 0.001 TYR F 200 PHE 0.034 0.001 PHE F 167 TRP 0.013 0.002 TRP D 21 HIS 0.006 0.001 HIS I 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (42204) covalent geometry : angle 0.62075 / 0.30 (57414) hydrogen bonds : bond 0.03701 / 2.45 ( 1620) hydrogen bonds : angle 4.39842 / 3.05 ( 4698) *********************** 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 760 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 636 time to evaluate : 1.735 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 4 CYS cc_start: 0.9065 (t) cc_final: 0.8415 (t) REVERT: E 313 MET cc_start: 0.8424 (mtm) cc_final: 0.7576 (mtm) REVERT: E 339 ARG cc_start: 0.7579 (mmp-170) cc_final: 0.6885 (mmt180) REVERT: E 357 TYR cc_start: 0.8294 (m-80) cc_final: 0.7891 (m-80) REVERT: F 14 ASN cc_start: 0.9106 (m-40) cc_final: 0.8802 (m110) REVERT: F 291 GLN cc_start: 0.8442 (pt0) cc_final: 0.8099 (pt0) REVERT: F 313 VAL cc_start: 0.9472 (t) cc_final: 0.9232 (p) REVERT: F 321 MET cc_start: 0.8635 (ptp) cc_final: 0.8413 (ptp) REVERT: J 2 ARG cc_start: 0.8181 (mtm180) cc_final: 0.6997 (mmt90) REVERT: J 302 MET cc_start: 0.9129 (mpp) cc_final: 0.7845 (mpp) REVERT: J 313 MET cc_start: 0.8796 (mtm) cc_final: 0.6835 (mtm) REVERT: J 357 TYR cc_start: 0.8275 (m-80) cc_final: 0.7893 (m-80) REVERT: J 380 ASN cc_start: 0.8996 (t0) cc_final: 0.8226 (t0) REVERT: J 433 GLU cc_start: 0.8867 (mp0) cc_final: 0.8660 (mp0) REVERT: C 31 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8271 (mt0) REVERT: C 127 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8139 (p0) REVERT: C 154 MET cc_start: 0.9392 (mmm) cc_final: 0.9155 (mmm) REVERT: C 170 SER cc_start: 0.9354 (m) cc_final: 0.9062 (t) REVERT: C 187 SER cc_start: 0.9473 (m) cc_final: 0.9223 (p) REVERT: C 254 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7638 (mt-10) REVERT: C 301 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8250 (mp10) REVERT: C 322 ASP cc_start: 0.8422 (t0) cc_final: 0.8207 (t0) REVERT: C 345 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8411 (p0) REVERT: C 351 PHE cc_start: 0.9062 (m-80) cc_final: 0.8810 (m-10) REVERT: C 392 ASP cc_start: 0.8847 (m-30) cc_final: 0.8499 (m-30) REVERT: L 2 ARG cc_start: 0.8106 (mtm180) cc_final: 0.7146 (mpt180) REVERT: L 31 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8336 (mt0) REVERT: L 36 MET cc_start: 0.8646 (ptm) cc_final: 0.8403 (ttp) REVERT: L 170 SER cc_start: 0.9439 (m) cc_final: 0.9124 (t) REVERT: L 279 GLU cc_start: 0.8636 (pt0) cc_final: 0.7962 (pm20) REVERT: L 302 MET cc_start: 0.8566 (mpp) cc_final: 0.7916 (mpp) REVERT: L 322 ASP cc_start: 0.8415 (t0) cc_final: 0.8165 (t0) REVERT: A 170 SER cc_start: 0.9560 (m) cc_final: 0.9218 (t) REVERT: A 205 ASP cc_start: 0.8420 (t0) cc_final: 0.8150 (t0) REVERT: A 207 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 284 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8397 (pt0) REVERT: A 301 GLN cc_start: 0.8574 (mp10) cc_final: 0.8276 (mp10) REVERT: A 313 MET cc_start: 0.8690 (mtm) cc_final: 0.7695 (mtm) REVERT: A 322 ASP cc_start: 0.8197 (t0) cc_final: 0.7858 (t0) REVERT: A 377 MET cc_start: 0.9046 (tmm) cc_final: 0.8775 (tmm) REVERT: A 417 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7652 (tm-30) REVERT: A 431 ASP cc_start: 0.8641 (m-30) cc_final: 0.8399 (m-30) REVERT: K 2 ARG cc_start: 0.8235 (mtm180) cc_final: 0.7076 (mmt90) REVERT: K 127 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8344 (p0) REVERT: K 203 MET cc_start: 0.8868 (mmm) cc_final: 0.8258 (mmm) REVERT: K 237 SER cc_start: 0.9257 (m) cc_final: 0.8880 (p) REVERT: K 313 MET cc_start: 0.8686 (mtm) cc_final: 0.7723 (mtm) REVERT: K 417 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7705 (tm-30) REVERT: K 431 ASP cc_start: 0.8625 (m-30) cc_final: 0.8340 (m-30) REVERT: G 88 ASP cc_start: 0.7852 (p0) cc_final: 0.7531 (t0) REVERT: G 136 THR cc_start: 0.9255 (m) cc_final: 0.8543 (p) REVERT: G 257 MET cc_start: 0.8580 (mmm) cc_final: 0.7889 (mmm) REVERT: G 325 GLU cc_start: 0.7969 (mp0) cc_final: 0.7542 (mp0) REVERT: G 327 ASP cc_start: 0.8374 (t70) cc_final: 0.8093 (t0) REVERT: D 181 GLU cc_start: 0.9062 (pp20) cc_final: 0.8799 (pt0) REVERT: D 257 MET cc_start: 0.8236 (mmm) cc_final: 0.7993 (mmm) REVERT: D 263 LEU cc_start: 0.9217 (mp) cc_final: 0.8966 (mt) REVERT: D 280 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8726 (pm20) REVERT: D 325 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: D 340 TYR cc_start: 0.8146 (m-80) cc_final: 0.7794 (m-80) REVERT: D 376 GLU cc_start: 0.8337 (pm20) cc_final: 0.7938 (pm20) REVERT: I 22 GLU cc_start: 0.8709 (tt0) cc_final: 0.8305 (tm-30) REVERT: I 57 ASN cc_start: 0.8199 (t0) cc_final: 0.7874 (t0) REVERT: I 74 ASP cc_start: 0.8823 (m-30) cc_final: 0.8569 (m-30) REVERT: I 129 CYS cc_start: 0.8926 (t) cc_final: 0.8636 (t) REVERT: I 130 LEU cc_start: 0.9264 (tp) cc_final: 0.8851 (tt) REVERT: I 263 LEU cc_start: 0.9262 (mp) cc_final: 0.9002 (mt) REVERT: I 325 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7820 (mp0) REVERT: I 340 TYR cc_start: 0.8120 (m-80) cc_final: 0.7728 (m-80) REVERT: I 379 LYS cc_start: 0.9228 (mtpt) cc_final: 0.9020 (mttm) REVERT: I 410 GLU cc_start: 0.8056 (pt0) cc_final: 0.7806 (pt0) REVERT: B 57 ASN cc_start: 0.8109 (t0) cc_final: 0.7632 (t0) REVERT: B 88 ASP cc_start: 0.7757 (p0) cc_final: 0.7042 (t0) REVERT: B 347 ASN cc_start: 0.9036 (p0) cc_final: 0.8518 (p0) REVERT: B 363 MET cc_start: 0.8762 (ptp) cc_final: 0.8456 (ptp) REVERT: B 379 LYS cc_start: 0.9291 (mtpt) cc_final: 0.9055 (mtpp) REVERT: B 410 GLU cc_start: 0.8534 (pt0) cc_final: 0.8070 (pt0) REVERT: H 22 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: H 57 ASN cc_start: 0.7988 (t0) cc_final: 0.7440 (t0) REVERT: H 88 ASP cc_start: 0.7833 (p0) cc_final: 0.6952 (t0) REVERT: H 129 CYS cc_start: 0.8188 (t) cc_final: 0.7747 (t) REVERT: H 197 ASP cc_start: 0.8436 (m-30) cc_final: 0.8147 (m-30) REVERT: H 363 MET cc_start: 0.8752 (ptp) cc_final: 0.8441 (ptp) outliers start: 124 outliers final: 97 residues processed: 723 average time/residue: 0.2407 time to fit residues: 292.9194 Evaluate side-chains 708 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 603 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain J residue 425 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 301 GLN Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 423 GLU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 293 MET Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 351 THR Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 263 LEU Chi-restraints excluded: chain H residue 293 MET Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain H residue 415 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 315 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 387 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 246 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 370 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 GLN K 15 GLN ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN G 291 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.078324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.067681 restraints weight = 99810.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.070299 restraints weight = 47715.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.072072 restraints weight = 28025.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.073327 restraints weight = 18607.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.074220 restraints weight = 13404.756| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 42204 Z= 0.152 Angle : 0.595 8.771 57414 Z= 0.289 Chirality : 0.045 0.138 6282 Planarity : 0.004 0.047 7452 Dihedral : 10.307 176.115 5796 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.80 % Allowed : 14.03 % Favored : 83.17 % 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: -0.35 (0.12), residues: 5130 helix: 0.75 (0.11), residues: 2268 sheet: 0.14 (0.18), residues: 810 loop : -1.50 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 221 TYR 0.021 0.001 TYR F 200 PHE 0.018 0.001 PHE F 167 TRP 0.012 0.001 TRP F 344 HIS 0.005 0.001 HIS I 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (42204) covalent geometry : angle 0.59499 / 0.29 (57414) hydrogen bonds : bond 0.03547 / 2.34 ( 1620) hydrogen bonds : angle 4.30410 / 2.98 ( 4698) *********************** 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 763 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 640 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 254 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7533 (mt-10) REVERT: E 313 MET cc_start: 0.8388 (mtm) cc_final: 0.7608 (mtm) REVERT: E 339 ARG cc_start: 0.7599 (mmp-170) cc_final: 0.6968 (mmt180) REVERT: E 357 TYR cc_start: 0.8264 (m-80) cc_final: 0.7841 (m-80) REVERT: F 14 ASN cc_start: 0.9092 (m-40) cc_final: 0.8752 (m110) REVERT: F 136 THR cc_start: 0.9256 (m) cc_final: 0.8464 (p) REVERT: F 291 GLN cc_start: 0.8434 (pt0) cc_final: 0.8111 (pt0) REVERT: F 313 VAL cc_start: 0.9518 (t) cc_final: 0.9269 (p) REVERT: J 2 ARG cc_start: 0.8189 (mtm180) cc_final: 0.7252 (mmt90) REVERT: J 4 CYS cc_start: 0.9060 (t) cc_final: 0.8382 (t) REVERT: J 302 MET cc_start: 0.9148 (mpp) cc_final: 0.7963 (mpp) REVERT: J 313 MET cc_start: 0.8829 (mtm) cc_final: 0.7713 (mtm) REVERT: J 357 TYR cc_start: 0.8262 (m-80) cc_final: 0.7879 (m-80) REVERT: C 31 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8271 (mt0) REVERT: C 127 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8095 (p0) REVERT: C 154 MET cc_start: 0.9390 (mmm) cc_final: 0.9162 (mmm) REVERT: C 170 SER cc_start: 0.9378 (m) cc_final: 0.9080 (t) REVERT: C 187 SER cc_start: 0.9472 (m) cc_final: 0.9220 (p) REVERT: C 254 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7738 (mt-10) REVERT: C 304 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8193 (mmtp) REVERT: C 322 ASP cc_start: 0.8436 (t0) cc_final: 0.8164 (t0) REVERT: C 345 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8440 (p0) REVERT: C 351 PHE cc_start: 0.9021 (m-80) cc_final: 0.8798 (m-10) REVERT: C 392 ASP cc_start: 0.8860 (m-30) cc_final: 0.8489 (m-30) REVERT: L 2 ARG cc_start: 0.8150 (mtm180) cc_final: 0.6801 (mpt180) REVERT: L 31 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8375 (mt0) REVERT: L 36 MET cc_start: 0.8628 (ptm) cc_final: 0.8364 (ttp) REVERT: L 91 GLN cc_start: 0.8711 (mt0) cc_final: 0.8432 (mt0) REVERT: L 170 SER cc_start: 0.9438 (m) cc_final: 0.9179 (t) REVERT: L 279 GLU cc_start: 0.8620 (pt0) cc_final: 0.7940 (pm20) REVERT: L 302 MET cc_start: 0.8635 (mpp) cc_final: 0.8140 (mpp) REVERT: L 322 ASP cc_start: 0.8414 (t0) cc_final: 0.8161 (t0) REVERT: A 170 SER cc_start: 0.9568 (m) cc_final: 0.9239 (t) REVERT: A 205 ASP cc_start: 0.8435 (t0) cc_final: 0.8113 (t0) REVERT: A 207 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 377 MET cc_start: 0.9010 (tmm) cc_final: 0.8724 (tmm) REVERT: A 417 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 431 ASP cc_start: 0.8629 (m-30) cc_final: 0.8369 (m-30) REVERT: K 2 ARG cc_start: 0.8085 (mtm180) cc_final: 0.6919 (mmt90) REVERT: K 124 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9089 (tttt) REVERT: K 155 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8551 (mt-10) REVERT: K 203 MET cc_start: 0.8826 (mmm) cc_final: 0.8222 (mmm) REVERT: K 301 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8490 (mp10) REVERT: K 313 MET cc_start: 0.8736 (mtm) cc_final: 0.7713 (mtm) REVERT: K 417 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7664 (tm-30) REVERT: K 431 ASP cc_start: 0.8601 (m-30) cc_final: 0.8309 (m-30) REVERT: G 136 THR cc_start: 0.9240 (m) cc_final: 0.8480 (p) REVERT: G 257 MET cc_start: 0.8567 (mmm) cc_final: 0.7904 (mmm) REVERT: G 327 ASP cc_start: 0.8521 (t70) cc_final: 0.8262 (t0) REVERT: D 67 ASP cc_start: 0.7918 (t0) cc_final: 0.7503 (t0) REVERT: D 73 MET cc_start: 0.9051 (mmt) cc_final: 0.8648 (mmm) REVERT: D 181 GLU cc_start: 0.8978 (pp20) cc_final: 0.8755 (pt0) REVERT: D 257 MET cc_start: 0.8155 (mmm) cc_final: 0.7922 (mmm) REVERT: D 263 LEU cc_start: 0.9210 (mp) cc_final: 0.8952 (mt) REVERT: D 280 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8755 (pm20) REVERT: D 325 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8179 (mp0) REVERT: D 327 ASP cc_start: 0.8410 (t70) cc_final: 0.8145 (t70) REVERT: D 340 TYR cc_start: 0.8153 (m-80) cc_final: 0.7806 (m-80) REVERT: I 22 GLU cc_start: 0.8708 (tt0) cc_final: 0.8271 (tm-30) REVERT: I 57 ASN cc_start: 0.8252 (t0) cc_final: 0.7893 (t0) REVERT: I 129 CYS cc_start: 0.8921 (t) cc_final: 0.8628 (t) REVERT: I 130 LEU cc_start: 0.9243 (tp) cc_final: 0.8823 (tt) REVERT: I 257 MET cc_start: 0.8614 (mmm) cc_final: 0.8276 (mmm) REVERT: I 263 LEU cc_start: 0.9248 (mp) cc_final: 0.8993 (mt) REVERT: I 325 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7793 (mp0) REVERT: I 340 TYR cc_start: 0.8142 (m-80) cc_final: 0.7761 (m-80) REVERT: I 379 LYS cc_start: 0.9231 (mtpt) cc_final: 0.8996 (mttm) REVERT: I 410 GLU cc_start: 0.8035 (pt0) cc_final: 0.7786 (pt0) REVERT: B 57 ASN cc_start: 0.8016 (t0) cc_final: 0.7514 (t0) REVERT: B 88 ASP cc_start: 0.7829 (p0) cc_final: 0.7150 (t0) REVERT: B 291 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8683 (mm-40) REVERT: B 300 MET cc_start: 0.9299 (mtt) cc_final: 0.9096 (mmt) REVERT: B 347 ASN cc_start: 0.8998 (p0) cc_final: 0.8522 (p0) REVERT: B 363 MET cc_start: 0.8768 (ptp) cc_final: 0.8455 (ptp) REVERT: B 379 LYS cc_start: 0.9294 (mtpt) cc_final: 0.9018 (mtpp) REVERT: B 410 GLU cc_start: 0.8517 (pt0) cc_final: 0.8069 (pt0) REVERT: H 22 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: H 57 ASN cc_start: 0.7987 (t0) cc_final: 0.7417 (t0) REVERT: H 88 ASP cc_start: 0.7831 (p0) cc_final: 0.6965 (t0) REVERT: H 129 CYS cc_start: 0.8210 (t) cc_final: 0.7749 (t) REVERT: H 156 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7802 (tpt-90) REVERT: H 197 ASP cc_start: 0.8448 (m-30) cc_final: 0.8159 (m-30) REVERT: H 291 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8642 (mm-40) REVERT: H 350 LYS cc_start: 0.9167 (tptp) cc_final: 0.8896 (tptp) REVERT: H 363 MET cc_start: 0.8757 (ptp) cc_final: 0.8431 (ptp) REVERT: H 403 MET cc_start: 0.8594 (mtm) cc_final: 0.8371 (mtp) outliers start: 123 outliers final: 94 residues processed: 724 average time/residue: 0.2394 time to fit residues: 292.7058 Evaluate side-chains 709 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 607 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain J residue 425 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 423 GLU Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 293 MET Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 156 ARG Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 263 LEU Chi-restraints excluded: chain H residue 293 MET Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain H residue 415 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 471 optimal weight: 5.9990 chunk 163 optimal weight: 20.0000 chunk 466 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 329 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 chunk 508 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 139 HIS G 291 GLN B 14 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.078665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.067487 restraints weight = 99727.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.070170 restraints weight = 47791.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.072010 restraints weight = 28247.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.073301 restraints weight = 18892.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.074243 restraints weight = 13718.328| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 42204 Z= 0.139 Angle : 0.591 9.306 57414 Z= 0.284 Chirality : 0.044 0.146 6282 Planarity : 0.003 0.043 7452 Dihedral : 10.151 179.593 5796 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.89 % Allowed : 14.21 % Favored : 82.90 % 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: -0.20 (0.12), residues: 5130 helix: 0.88 (0.11), residues: 2268 sheet: 0.20 (0.19), residues: 810 loop : -1.41 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 221 TYR 0.011 0.001 TYR F 425 PHE 0.011 0.001 PHE E 351 TRP 0.015 0.001 TRP F 344 HIS 0.004 0.001 HIS J 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (42204) covalent geometry : angle 0.59066 / 0.28 (57414) hydrogen bonds : bond 0.03432 / 2.27 ( 1620) hydrogen bonds : angle 4.24991 / 2.95 ( 4698) *********************** 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 770 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 643 time to evaluate : 1.680 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: E 69 ASP cc_start: 0.9060 (t0) cc_final: 0.8789 (t70) REVERT: E 254 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7528 (mt-10) REVERT: E 339 ARG cc_start: 0.7656 (mmp-170) cc_final: 0.7049 (mmt180) REVERT: E 357 TYR cc_start: 0.8321 (m-80) cc_final: 0.7857 (m-80) REVERT: E 424 ASP cc_start: 0.8787 (t70) cc_final: 0.8438 (t0) REVERT: F 14 ASN cc_start: 0.9067 (m-40) cc_final: 0.8768 (m110) REVERT: F 136 THR cc_start: 0.9253 (m) cc_final: 0.8474 (p) REVERT: F 291 GLN cc_start: 0.8480 (pt0) cc_final: 0.8114 (pt0) REVERT: F 313 VAL cc_start: 0.9508 (t) cc_final: 0.9266 (p) REVERT: F 323 MET cc_start: 0.7793 (mmm) cc_final: 0.7578 (mmm) REVERT: F 330 MET cc_start: 0.9018 (mmp) cc_final: 0.8785 (tpp) REVERT: F 351 THR cc_start: 0.9504 (m) cc_final: 0.9175 (p) REVERT: J 2 ARG cc_start: 0.8209 (mtm180) cc_final: 0.7244 (mmt90) REVERT: J 4 CYS cc_start: 0.9030 (t) cc_final: 0.8322 (t) REVERT: J 302 MET cc_start: 0.9079 (mpp) cc_final: 0.7874 (mpp) REVERT: J 313 MET cc_start: 0.8831 (mtm) cc_final: 0.7666 (mtm) REVERT: J 357 TYR cc_start: 0.8271 (m-80) cc_final: 0.7890 (m-80) REVERT: C 31 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8252 (mt0) REVERT: C 125 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9177 (mm) REVERT: C 127 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8122 (p0) REVERT: C 154 MET cc_start: 0.9412 (mmm) cc_final: 0.9174 (mmm) REVERT: C 170 SER cc_start: 0.9430 (m) cc_final: 0.9136 (t) REVERT: C 187 SER cc_start: 0.9467 (m) cc_final: 0.9206 (p) REVERT: C 254 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7779 (mt-10) REVERT: C 297 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8577 (mm-30) REVERT: C 301 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8141 (mp10) REVERT: C 302 MET cc_start: 0.8553 (mmm) cc_final: 0.8031 (mmm) REVERT: C 313 MET cc_start: 0.8750 (mtm) cc_final: 0.8401 (mtm) REVERT: C 322 ASP cc_start: 0.8475 (t0) cc_final: 0.8201 (t0) REVERT: C 345 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8317 (p0) REVERT: C 351 PHE cc_start: 0.9062 (m-80) cc_final: 0.8853 (m-10) REVERT: C 392 ASP cc_start: 0.8898 (m-30) cc_final: 0.8545 (m-30) REVERT: L 2 ARG cc_start: 0.8192 (mtm180) cc_final: 0.6779 (mpt180) REVERT: L 31 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8309 (mt0) REVERT: L 36 MET cc_start: 0.8667 (ptm) cc_final: 0.8385 (ttp) REVERT: L 91 GLN cc_start: 0.8718 (mt0) cc_final: 0.8398 (mt0) REVERT: L 170 SER cc_start: 0.9448 (m) cc_final: 0.9163 (t) REVERT: L 279 GLU cc_start: 0.8647 (pt0) cc_final: 0.7900 (pm20) REVERT: L 302 MET cc_start: 0.8589 (mpp) cc_final: 0.8031 (mpp) REVERT: L 313 MET cc_start: 0.8850 (mtm) cc_final: 0.8505 (mtm) REVERT: L 322 ASP cc_start: 0.8450 (t0) cc_final: 0.8187 (t0) REVERT: A 147 SER cc_start: 0.9258 (p) cc_final: 0.8888 (t) REVERT: A 170 SER cc_start: 0.9574 (m) cc_final: 0.9223 (t) REVERT: A 207 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 284 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8327 (pt0) REVERT: A 301 GLN cc_start: 0.8690 (mp10) cc_final: 0.8427 (mp10) REVERT: A 313 MET cc_start: 0.8672 (mtm) cc_final: 0.7741 (mtm) REVERT: A 322 ASP cc_start: 0.8277 (t0) cc_final: 0.7920 (t0) REVERT: A 377 MET cc_start: 0.9015 (tmm) cc_final: 0.8711 (tmm) REVERT: A 417 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7700 (tm-30) REVERT: A 431 ASP cc_start: 0.8645 (m-30) cc_final: 0.8354 (m-30) REVERT: K 2 ARG cc_start: 0.8009 (mtm180) cc_final: 0.6715 (mmt90) REVERT: K 33 ASP cc_start: 0.8832 (m-30) cc_final: 0.8618 (t0) REVERT: K 155 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8543 (mt-10) REVERT: K 203 MET cc_start: 0.8799 (mmm) cc_final: 0.8186 (mmm) REVERT: K 302 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8126 (mpp) REVERT: K 417 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7674 (tm-30) REVERT: K 431 ASP cc_start: 0.8650 (m-30) cc_final: 0.8330 (m-30) REVERT: G 37 HIS cc_start: 0.8450 (m90) cc_final: 0.8245 (m-70) REVERT: G 136 THR cc_start: 0.9245 (m) cc_final: 0.8498 (p) REVERT: G 257 MET cc_start: 0.8527 (mmm) cc_final: 0.7975 (mmm) REVERT: G 327 ASP cc_start: 0.8583 (t70) cc_final: 0.8282 (t0) REVERT: D 67 ASP cc_start: 0.7917 (t0) cc_final: 0.7539 (t0) REVERT: D 73 MET cc_start: 0.9141 (mmt) cc_final: 0.8695 (mmm) REVERT: D 181 GLU cc_start: 0.8972 (pp20) cc_final: 0.8764 (pt0) REVERT: D 257 MET cc_start: 0.8089 (mmm) cc_final: 0.7792 (mmm) REVERT: D 263 LEU cc_start: 0.9197 (mp) cc_final: 0.8935 (mt) REVERT: D 280 GLN cc_start: 0.9264 (OUTLIER) cc_final: 0.8885 (pm20) REVERT: D 325 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8198 (mp0) REVERT: D 327 ASP cc_start: 0.8478 (t70) cc_final: 0.8218 (t70) REVERT: D 340 TYR cc_start: 0.8188 (m-80) cc_final: 0.7788 (m-80) REVERT: I 57 ASN cc_start: 0.8267 (t0) cc_final: 0.7865 (t0) REVERT: I 129 CYS cc_start: 0.8931 (t) cc_final: 0.8489 (t) REVERT: I 257 MET cc_start: 0.8473 (mmm) cc_final: 0.8157 (mmm) REVERT: I 263 LEU cc_start: 0.9237 (mp) cc_final: 0.8973 (mt) REVERT: I 325 GLU cc_start: 0.8647 (mm-30) cc_final: 0.7764 (mp0) REVERT: I 340 TYR cc_start: 0.8172 (m-80) cc_final: 0.7787 (m-80) REVERT: I 379 LYS cc_start: 0.9275 (mtpt) cc_final: 0.9024 (mttm) REVERT: I 410 GLU cc_start: 0.8085 (pt0) cc_final: 0.7823 (pt0) REVERT: B 57 ASN cc_start: 0.8019 (t0) cc_final: 0.7498 (t0) REVERT: B 88 ASP cc_start: 0.7850 (p0) cc_final: 0.7220 (t0) REVERT: B 291 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8520 (mm-40) REVERT: B 347 ASN cc_start: 0.8972 (p0) cc_final: 0.8486 (p0) REVERT: B 363 MET cc_start: 0.8774 (ptp) cc_final: 0.8443 (ptp) REVERT: B 379 LYS cc_start: 0.9340 (mtpt) cc_final: 0.9093 (mtpp) REVERT: B 410 GLU cc_start: 0.8549 (pt0) cc_final: 0.8097 (pt0) REVERT: H 22 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: H 57 ASN cc_start: 0.7962 (t0) cc_final: 0.7364 (t0) REVERT: H 88 ASP cc_start: 0.7864 (p0) cc_final: 0.7016 (t0) REVERT: H 129 CYS cc_start: 0.8298 (t) cc_final: 0.7816 (t) REVERT: H 156 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7896 (tpt-90) REVERT: H 197 ASP cc_start: 0.8507 (m-30) cc_final: 0.8187 (m-30) REVERT: H 291 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8658 (mm-40) REVERT: H 350 LYS cc_start: 0.9193 (tptp) cc_final: 0.8909 (tptp) REVERT: H 363 MET cc_start: 0.8772 (ptp) cc_final: 0.8425 (ptp) REVERT: H 403 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8394 (mtp) outliers start: 127 outliers final: 102 residues processed: 731 average time/residue: 0.2424 time to fit residues: 299.2450 Evaluate side-chains 719 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 606 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain J residue 425 MET Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 301 GLN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 302 MET Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 423 GLU Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 293 MET Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 351 THR Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 156 ARG Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 263 LEU Chi-restraints excluded: chain H residue 293 MET Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 403 MET Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain H residue 415 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 170 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 171 optimal weight: 20.0000 chunk 369 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 256 optimal weight: 8.9990 chunk 222 optimal weight: 20.0000 chunk 396 optimal weight: 20.0000 chunk 141 optimal weight: 0.0470 chunk 131 optimal weight: 20.0000 chunk 418 optimal weight: 10.0000 overall best weight: 2.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN B 14 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.079439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.068744 restraints weight = 99555.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.071381 restraints weight = 47806.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.073181 restraints weight = 28088.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.074430 restraints weight = 18666.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.075334 restraints weight = 13465.797| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 42204 Z= 0.112 Angle : 0.592 13.035 57414 Z= 0.282 Chirality : 0.044 0.219 6282 Planarity : 0.003 0.047 7452 Dihedral : 10.012 176.889 5796 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.48 % Allowed : 14.75 % Favored : 82.76 % 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: -0.07 (0.12), residues: 5130 helix: 0.93 (0.11), residues: 2280 sheet: 0.27 (0.19), residues: 810 loop : -1.28 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 320 TYR 0.017 0.001 TYR F 200 PHE 0.024 0.001 PHE F 167 TRP 0.018 0.001 TRP F 344 HIS 0.004 0.001 HIS I 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (42204) covalent geometry : angle 0.59204 / 0.28 (57414) hydrogen bonds : bond 0.03232 / 2.14 ( 1620) hydrogen bonds : angle 4.21510 / 2.93 ( 4698) *********************** 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 765 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 656 time to evaluate : 1.606 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 69 ASP cc_start: 0.9105 (t0) cc_final: 0.8882 (t70) REVERT: E 254 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7468 (mt-10) REVERT: E 313 MET cc_start: 0.8366 (mtm) cc_final: 0.7875 (mtm) REVERT: E 339 ARG cc_start: 0.7648 (mmp-170) cc_final: 0.7046 (mmt180) REVERT: E 357 TYR cc_start: 0.8332 (m-80) cc_final: 0.7912 (m-80) REVERT: E 424 ASP cc_start: 0.8709 (t70) cc_final: 0.8406 (t0) REVERT: F 14 ASN cc_start: 0.9109 (m-40) cc_final: 0.8724 (m110) REVERT: F 136 THR cc_start: 0.9252 (m) cc_final: 0.8585 (p) REVERT: F 291 GLN cc_start: 0.8458 (pt0) cc_final: 0.8112 (pt0) REVERT: F 313 VAL cc_start: 0.9546 (t) cc_final: 0.9344 (p) REVERT: F 330 MET cc_start: 0.8969 (mmp) cc_final: 0.8720 (tpp) REVERT: F 351 THR cc_start: 0.9487 (m) cc_final: 0.9192 (p) REVERT: J 2 ARG cc_start: 0.8183 (mtm180) cc_final: 0.7249 (mmt90) REVERT: J 4 CYS cc_start: 0.8872 (t) cc_final: 0.7964 (t) REVERT: J 69 ASP cc_start: 0.9212 (t0) cc_final: 0.8543 (t0) REVERT: J 302 MET cc_start: 0.9023 (mpp) cc_final: 0.7971 (mpp) REVERT: J 313 MET cc_start: 0.8759 (mtm) cc_final: 0.8435 (mtm) REVERT: J 357 TYR cc_start: 0.8261 (m-80) cc_final: 0.7891 (m-80) REVERT: J 380 ASN cc_start: 0.9025 (t0) cc_final: 0.8703 (t0) REVERT: J 431 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7996 (m-30) REVERT: J 433 GLU cc_start: 0.8717 (mp0) cc_final: 0.8388 (mp0) REVERT: C 31 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8305 (mt0) REVERT: C 125 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9183 (mm) REVERT: C 170 SER cc_start: 0.9455 (m) cc_final: 0.9227 (t) REVERT: C 187 SER cc_start: 0.9425 (m) cc_final: 0.9177 (p) REVERT: C 210 TYR cc_start: 0.8863 (m-10) cc_final: 0.8244 (m-80) REVERT: C 254 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7741 (mt-10) REVERT: C 297 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8570 (mm-30) REVERT: C 304 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8375 (mmtp) REVERT: C 313 MET cc_start: 0.8691 (mtm) cc_final: 0.8342 (mtm) REVERT: C 345 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8323 (p0) REVERT: C 351 PHE cc_start: 0.8992 (m-80) cc_final: 0.8761 (m-10) REVERT: C 357 TYR cc_start: 0.8431 (m-80) cc_final: 0.7979 (m-80) REVERT: C 392 ASP cc_start: 0.8876 (m-30) cc_final: 0.8557 (m-30) REVERT: L 2 ARG cc_start: 0.8108 (mtm180) cc_final: 0.6753 (mpt180) REVERT: L 36 MET cc_start: 0.8604 (ptm) cc_final: 0.8376 (ttp) REVERT: L 91 GLN cc_start: 0.8609 (mt0) cc_final: 0.8335 (mt0) REVERT: L 170 SER cc_start: 0.9427 (m) cc_final: 0.9178 (t) REVERT: L 302 MET cc_start: 0.8717 (mpp) cc_final: 0.8133 (mpp) REVERT: L 313 MET cc_start: 0.8785 (mtm) cc_final: 0.8547 (mtm) REVERT: L 322 ASP cc_start: 0.8400 (t0) cc_final: 0.8153 (t0) REVERT: L 380 ASN cc_start: 0.9400 (t0) cc_final: 0.9007 (t0) REVERT: A 147 SER cc_start: 0.9159 (p) cc_final: 0.8808 (t) REVERT: A 170 SER cc_start: 0.9554 (m) cc_final: 0.9274 (t) REVERT: A 207 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7945 (tm-30) REVERT: A 284 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8262 (pt0) REVERT: A 301 GLN cc_start: 0.8629 (mp10) cc_final: 0.8379 (mp10) REVERT: A 313 MET cc_start: 0.8572 (mtm) cc_final: 0.7722 (mtm) REVERT: A 322 ASP cc_start: 0.8298 (t0) cc_final: 0.7946 (t0) REVERT: A 377 MET cc_start: 0.8991 (tmm) cc_final: 0.8701 (tmm) REVERT: A 417 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7640 (tm-30) REVERT: A 431 ASP cc_start: 0.8499 (m-30) cc_final: 0.8213 (m-30) REVERT: K 2 ARG cc_start: 0.7957 (mtm180) cc_final: 0.6795 (mmt90) REVERT: K 127 ASP cc_start: 0.8440 (p0) cc_final: 0.8238 (p0) REVERT: K 155 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8487 (mt-10) REVERT: K 172 TYR cc_start: 0.8589 (t80) cc_final: 0.8319 (t80) REVERT: K 203 MET cc_start: 0.8807 (mmm) cc_final: 0.8209 (mmm) REVERT: K 301 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8518 (mp10) REVERT: K 302 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8038 (mpp) REVERT: K 313 MET cc_start: 0.8781 (mtm) cc_final: 0.7878 (mtm) REVERT: K 417 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7626 (tm-30) REVERT: K 431 ASP cc_start: 0.8495 (m-30) cc_final: 0.8198 (m-30) REVERT: G 136 THR cc_start: 0.9208 (m) cc_final: 0.8475 (p) REVERT: G 257 MET cc_start: 0.8496 (mmm) cc_final: 0.7866 (mmm) REVERT: G 327 ASP cc_start: 0.8406 (t70) cc_final: 0.8128 (t0) REVERT: D 67 ASP cc_start: 0.7638 (t0) cc_final: 0.7290 (t0) REVERT: D 73 MET cc_start: 0.9020 (mmt) cc_final: 0.8654 (mmm) REVERT: D 257 MET cc_start: 0.8047 (mmm) cc_final: 0.7787 (mmm) REVERT: D 263 LEU cc_start: 0.9159 (mp) cc_final: 0.8921 (mt) REVERT: D 280 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8903 (pm20) REVERT: D 325 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: D 327 ASP cc_start: 0.8395 (t70) cc_final: 0.8137 (t70) REVERT: D 340 TYR cc_start: 0.8157 (m-80) cc_final: 0.7807 (m-80) REVERT: I 57 ASN cc_start: 0.8143 (t0) cc_final: 0.7713 (t0) REVERT: I 129 CYS cc_start: 0.8845 (t) cc_final: 0.8427 (t) REVERT: I 257 MET cc_start: 0.8401 (mmm) cc_final: 0.8140 (mmm) REVERT: I 263 LEU cc_start: 0.9202 (mp) cc_final: 0.8928 (mt) REVERT: I 325 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8238 (mp0) REVERT: I 340 TYR cc_start: 0.8141 (m-80) cc_final: 0.7749 (m-80) REVERT: I 379 LYS cc_start: 0.9237 (mtpt) cc_final: 0.9012 (mttm) REVERT: I 407 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8155 (mm-30) REVERT: I 410 GLU cc_start: 0.8048 (pt0) cc_final: 0.7475 (pt0) REVERT: B 57 ASN cc_start: 0.7955 (t0) cc_final: 0.7432 (t0) REVERT: B 88 ASP cc_start: 0.7859 (p0) cc_final: 0.7137 (t0) REVERT: B 103 LYS cc_start: 0.9124 (mttt) cc_final: 0.8921 (mmtp) REVERT: B 291 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8484 (mm-40) REVERT: B 347 ASN cc_start: 0.8900 (p0) cc_final: 0.8433 (p0) REVERT: B 363 MET cc_start: 0.8727 (ptp) cc_final: 0.8411 (ptp) REVERT: B 379 LYS cc_start: 0.9325 (mtpt) cc_final: 0.9051 (mtpp) REVERT: B 410 GLU cc_start: 0.8377 (pt0) cc_final: 0.7969 (pt0) REVERT: H 22 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7504 (tm-30) REVERT: H 57 ASN cc_start: 0.7885 (t0) cc_final: 0.7293 (t0) REVERT: H 88 ASP cc_start: 0.7771 (p0) cc_final: 0.6942 (t0) REVERT: H 118 ASP cc_start: 0.8527 (p0) cc_final: 0.8134 (p0) REVERT: H 129 CYS cc_start: 0.8181 (t) cc_final: 0.7705 (t) REVERT: H 156 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7950 (tpt-90) REVERT: H 197 ASP cc_start: 0.8427 (m-30) cc_final: 0.8137 (m-30) REVERT: H 350 LYS cc_start: 0.9179 (tptp) cc_final: 0.8951 (tptp) REVERT: H 363 MET cc_start: 0.8714 (ptp) cc_final: 0.8389 (ptp) REVERT: H 403 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8423 (mtp) outliers start: 109 outliers final: 84 residues processed: 730 average time/residue: 0.2394 time to fit residues: 296.7424 Evaluate side-chains 712 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 618 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 239 CYS Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain J residue 431 ASP Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 302 MET Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 423 GLU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 293 MET Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain H residue 156 ARG Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 263 LEU Chi-restraints excluded: chain H residue 293 MET Chi-restraints excluded: chain H residue 403 MET Chi-restraints excluded: chain H residue 406 MET Chi-restraints excluded: chain H residue 415 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 186 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 276 optimal weight: 20.0000 chunk 260 optimal weight: 20.0000 chunk 412 optimal weight: 6.9990 chunk 341 optimal weight: 10.0000 chunk 213 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 91 GLN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS K 11 GLN K 15 GLN G 291 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.076565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.066053 restraints weight = 101223.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.068603 restraints weight = 48706.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.070324 restraints weight = 28697.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.071545 restraints weight = 19180.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.072413 restraints weight = 13893.919| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 42204 Z= 0.249 Angle : 0.674 11.664 57414 Z= 0.327 Chirality : 0.047 0.160 6282 Planarity : 0.004 0.046 7452 Dihedral : 10.114 177.395 5796 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.57 % Allowed : 14.94 % Favored : 82.49 % 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: -0.17 (0.12), residues: 5130 helix: 0.87 (0.11), residues: 2280 sheet: 0.27 (0.19), residues: 768 loop : -1.37 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 221 TYR 0.024 0.002 TYR F 200 PHE 0.031 0.001 PHE F 167 TRP 0.013 0.002 TRP D 21 HIS 0.009 0.001 HIS F 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.25 (42204) covalent geometry : angle 0.67357 / 0.33 (57414) hydrogen bonds : bond 0.03758 / 2.49 ( 1620) hydrogen bonds : angle 4.44915 / 3.09 ( 4698) ********************** 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 716 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 603 time to evaluate : 1.372 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 69 ASP cc_start: 0.9094 (t0) cc_final: 0.8860 (t70) REVERT: E 313 MET cc_start: 0.8357 (mtm) cc_final: 0.7897 (mtm) REVERT: E 424 ASP cc_start: 0.8785 (t70) cc_final: 0.8501 (t0) REVERT: F 14 ASN cc_start: 0.9054 (m-40) cc_final: 0.8740 (m110) REVERT: F 291 GLN cc_start: 0.8468 (pt0) cc_final: 0.8138 (pt0) REVERT: F 313 VAL cc_start: 0.9660 (t) cc_final: 0.9442 (p) REVERT: F 330 MET cc_start: 0.9007 (mmp) cc_final: 0.8762 (tpp) REVERT: J 2 ARG cc_start: 0.8265 (mtm180) cc_final: 0.7200 (mmt90) REVERT: J 4 CYS cc_start: 0.8974 (t) cc_final: 0.8326 (t) REVERT: J 302 MET cc_start: 0.9088 (mpp) cc_final: 0.7999 (mpp) REVERT: J 313 MET cc_start: 0.8787 (mtm) cc_final: 0.7676 (mtm) REVERT: J 357 TYR cc_start: 0.8325 (m-80) cc_final: 0.7916 (m-80) REVERT: J 431 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7969 (m-30) REVERT: C 31 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8342 (mt0) REVERT: C 170 SER cc_start: 0.9557 (m) cc_final: 0.9316 (t) REVERT: C 187 SER cc_start: 0.9509 (m) cc_final: 0.9264 (p) REVERT: C 254 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7922 (mt-10) REVERT: C 304 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8318 (mmtp) REVERT: C 313 MET cc_start: 0.8799 (mtm) cc_final: 0.8465 (mtm) REVERT: C 345 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8497 (p0) REVERT: C 392 ASP cc_start: 0.8849 (m-30) cc_final: 0.8492 (m-30) REVERT: L 2 ARG cc_start: 0.8255 (mtm180) cc_final: 0.7184 (mpt180) REVERT: L 36 MET cc_start: 0.8581 (ptm) cc_final: 0.8379 (ttp) REVERT: L 91 GLN cc_start: 0.8675 (mt0) cc_final: 0.8386 (mt0) REVERT: L 170 SER cc_start: 0.9508 (m) cc_final: 0.9305 (t) REVERT: L 279 GLU cc_start: 0.8622 (pt0) cc_final: 0.7988 (pm20) REVERT: L 302 MET cc_start: 0.8797 (mpp) cc_final: 0.8265 (mpp) REVERT: L 322 ASP cc_start: 0.8447 (t0) cc_final: 0.8211 (t0) REVERT: A 147 SER cc_start: 0.9286 (p) cc_final: 0.8868 (t) REVERT: A 170 SER cc_start: 0.9562 (m) cc_final: 0.9163 (t) REVERT: A 205 ASP cc_start: 0.8459 (t0) cc_final: 0.8159 (t0) REVERT: A 207 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7950 (tm-30) REVERT: A 284 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8338 (pt0) REVERT: A 301 GLN cc_start: 0.8677 (mp10) cc_final: 0.8432 (mp10) REVERT: A 313 MET cc_start: 0.8677 (mtm) cc_final: 0.7818 (mtm) REVERT: A 322 ASP cc_start: 0.8272 (t0) cc_final: 0.7947 (t0) REVERT: A 377 MET cc_start: 0.8991 (tmm) cc_final: 0.8666 (tmm) REVERT: A 417 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7693 (tm-30) REVERT: A 431 ASP cc_start: 0.8620 (m-30) cc_final: 0.8312 (m-30) REVERT: K 2 ARG cc_start: 0.8041 (mtm180) cc_final: 0.6817 (mmt90) REVERT: K 203 MET cc_start: 0.8870 (mmm) cc_final: 0.8264 (mmm) REVERT: K 302 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8115 (mpp) REVERT: K 313 MET cc_start: 0.8758 (mtm) cc_final: 0.7779 (mtm) REVERT: K 417 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7686 (tm-30) REVERT: K 431 ASP cc_start: 0.8622 (m-30) cc_final: 0.8334 (m-30) REVERT: G 88 ASP cc_start: 0.7811 (p0) cc_final: 0.7509 (t0) REVERT: G 257 MET cc_start: 0.8626 (mmm) cc_final: 0.8041 (mmm) REVERT: G 327 ASP cc_start: 0.8492 (t70) cc_final: 0.8183 (t70) REVERT: D 22 GLU cc_start: 0.8690 (tt0) cc_final: 0.8280 (tm-30) REVERT: D 67 ASP cc_start: 0.7904 (t0) cc_final: 0.7540 (t0) REVERT: D 73 MET cc_start: 0.9056 (mmt) cc_final: 0.8577 (mmm) REVERT: D 257 MET cc_start: 0.8107 (mmm) cc_final: 0.7806 (mmm) REVERT: D 263 LEU cc_start: 0.9259 (mp) cc_final: 0.8997 (mt) REVERT: D 280 GLN cc_start: 0.9284 (OUTLIER) cc_final: 0.8941 (pm20) REVERT: D 325 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: D 327 ASP cc_start: 0.8378 (t70) cc_final: 0.8149 (t70) REVERT: D 340 TYR cc_start: 0.8225 (m-80) cc_final: 0.7836 (m-80) REVERT: I 22 GLU cc_start: 0.8719 (tt0) cc_final: 0.8339 (tm-30) REVERT: I 57 ASN cc_start: 0.8215 (t0) cc_final: 0.7809 (t0) REVERT: I 129 CYS cc_start: 0.8826 (t) cc_final: 0.8387 (t) REVERT: I 257 MET cc_start: 0.8315 (mmm) cc_final: 0.8006 (mmm) REVERT: I 325 GLU cc_start: 0.8745 (mm-30) cc_final: 0.7816 (mp0) REVERT: I 340 TYR cc_start: 0.8222 (m-80) cc_final: 0.7824 (m-80) REVERT: I 379 LYS cc_start: 0.9281 (mtpt) cc_final: 0.9037 (mttm) REVERT: I 410 GLU cc_start: 0.7999 (pt0) cc_final: 0.7788 (pt0) REVERT: B 57 ASN cc_start: 0.8170 (t0) cc_final: 0.7629 (t0) REVERT: B 67 ASP cc_start: 0.8472 (t0) cc_final: 0.8218 (t0) REVERT: B 88 ASP cc_start: 0.7901 (p0) cc_final: 0.7243 (t0) REVERT: B 103 LYS cc_start: 0.9205 (mttt) cc_final: 0.8859 (mmtp) REVERT: B 291 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8443 (mm-40) REVERT: B 363 MET cc_start: 0.8852 (ptp) cc_final: 0.8425 (ptp) REVERT: B 379 LYS cc_start: 0.9338 (mtpt) cc_final: 0.9105 (mtpp) REVERT: B 410 GLU cc_start: 0.8494 (pt0) cc_final: 0.8068 (pt0) REVERT: H 22 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7623 (tm-30) REVERT: H 57 ASN cc_start: 0.7995 (t0) cc_final: 0.7428 (t0) REVERT: H 67 ASP cc_start: 0.8419 (t0) cc_final: 0.8147 (t0) REVERT: H 88 ASP cc_start: 0.7881 (p0) cc_final: 0.7029 (t0) REVERT: H 129 CYS cc_start: 0.8278 (t) cc_final: 0.7857 (t) REVERT: H 156 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7932 (tpt-90) REVERT: H 197 ASP cc_start: 0.8541 (m-30) cc_final: 0.8219 (m-30) REVERT: H 300 MET cc_start: 0.9242 (mtt) cc_final: 0.9027 (mtt) REVERT: H 350 LYS cc_start: 0.9188 (tptp) cc_final: 0.8939 (tptp) REVERT: H 363 MET cc_start: 0.8784 (ptp) cc_final: 0.8437 (ptp) REVERT: H 403 MET cc_start: 0.8631 (mtm) cc_final: 0.8416 (mtp) outliers start: 113 outliers final: 95 residues processed: 683 average time/residue: 0.2377 time to fit residues: 275.8531 Evaluate side-chains 686 residues out of total 4410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 583 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 239 CYS Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 431 ASP Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 302 MET Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 423 GLU Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 293 MET Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 255 VAL Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 351 THR Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain H residue 147 MET Chi-restraints excluded: chain H residue 156 ARG Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 263 LEU Chi-restraints excluded: chain H residue 293 MET Chi-restraints excluded: chain H residue 415 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 205 optimal weight: 10.0000 chunk 324 optimal weight: 0.9980 chunk 337 optimal weight: 10.0000 chunk 493 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 402 optimal weight: 7.9990 chunk 223 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 246 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.078177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.067592 restraints weight = 100407.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.070199 restraints weight = 48093.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.071958 restraints weight = 28245.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.073213 restraints weight = 18790.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.074105 restraints weight = 13494.225| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 42204 Z= 0.134 Angle : 0.624 11.574 57414 Z= 0.298 Chirality : 0.045 0.163 6282 Planarity : 0.004 0.046 7452 Dihedral : 10.034 178.957 5796 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.41 % Allowed : 15.41 % Favored : 82.17 % 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: -0.08 (0.12), residues: 5130 helix: 0.92 (0.11), residues: 2286 sheet: 0.24 (0.19), residues: 810 loop : -1.28 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 320 TYR 0.021 0.001 TYR F 200 PHE 0.027 0.001 PHE F 167 TRP 0.017 0.001 TRP F 344 HIS 0.005 0.001 HIS I 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (42204) covalent geometry : angle 0.62358 / 0.30 (57414) hydrogen bonds : bond 0.03455 / 2.28 ( 1620) hydrogen bonds : angle 4.28554 / 2.98 ( 4698) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7347.32 seconds wall clock time: 128 minutes 0.55 seconds (7680.55 seconds total)